Iron in PDB 5jt1: The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
Enzymatic activity of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
All present enzymatic activity of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution:
1.12.7.2;
Protein crystallography data
The structure of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution, PDB code: 5jt1
was solved by
M.C.Marques,
I.A.C.Pereira,
P.M.Matias,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.63 /
1.35
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.778,
63.183,
110.664,
90.00,
105.27,
90.00
|
|
R / Rfree (%)
|
11.6 /
14.5
|
Other elements in 5jt1:
The structure of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Iron atom in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
(pdb code 5jt1). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the
The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution, PDB code: 5jt1:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 1 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:11.5
occ:1.00
|
FE1
|
A:SF4301
|
0.0
|
11.5
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
11.4
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
11.9
|
1.0
|
|
SG
|
A:CYS238
|
2.3
|
10.8
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
12.4
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
11.9
|
1.0
|
|
FE2
|
A:SF4301
|
2.8
|
12.3
|
1.0
|
|
FE3
|
A:SF4301
|
2.8
|
12.3
|
1.0
|
|
HB3
|
A:CYS238
|
3.0
|
13.9
|
1.0
|
|
CB
|
A:CYS238
|
3.2
|
11.6
|
1.0
|
|
HB2
|
A:CYS238
|
3.6
|
13.9
|
1.0
|
|
HD3
|
A:PRO241
|
3.6
|
14.4
|
1.0
|
|
HA3
|
A:GLY240
|
3.8
|
12.9
|
1.0
|
|
HB2
|
A:ARG233
|
3.8
|
13.2
|
1.0
|
|
H
|
A:GLY240
|
3.8
|
12.4
|
1.0
|
|
HG13
|
A:VAL260
|
3.9
|
15.6
|
1.0
|
|
S1
|
A:SF4301
|
3.9
|
12.4
|
1.0
|
|
HG11
|
A:VAL260
|
4.1
|
15.6
|
1.0
|
|
H
|
A:ARG233
|
4.2
|
13.1
|
1.0
|
|
HG22
|
A:VAL260
|
4.2
|
14.3
|
1.0
|
|
HG21
|
A:VAL260
|
4.4
|
14.3
|
1.0
|
|
CG1
|
A:VAL260
|
4.5
|
13.0
|
1.0
|
|
N
|
A:GLY240
|
4.5
|
10.3
|
1.0
|
|
CA
|
A:GLY240
|
4.6
|
10.8
|
1.0
|
|
CA
|
A:CYS238
|
4.6
|
10.8
|
1.0
|
|
CD
|
A:PRO241
|
4.6
|
12.0
|
1.0
|
|
HA
|
A:TYR234
|
4.7
|
15.8
|
1.0
|
|
CG2
|
A:VAL260
|
4.7
|
11.9
|
1.0
|
|
ND1
|
A:HIS208
|
4.7
|
12.3
|
1.0
|
|
CB
|
A:ARG233
|
4.7
|
11.0
|
1.0
|
|
SG
|
A:CYS232
|
4.7
|
13.1
|
1.0
|
|
SG
|
A:CYS211
|
4.8
|
12.0
|
1.0
|
|
H
|
A:TYR234
|
4.8
|
15.6
|
1.0
|
|
C
|
A:CYS238
|
4.8
|
11.6
|
1.0
|
|
N
|
A:TYR234
|
4.8
|
13.0
|
1.0
|
|
HB2
|
A:TYR234
|
4.9
|
15.5
|
1.0
|
|
O
|
A:CYS238
|
4.9
|
11.8
|
1.0
|
|
HA
|
A:HIS208
|
4.9
|
12.9
|
1.0
|
|
N
|
A:ARG233
|
4.9
|
10.9
|
1.0
|
|
HB2
|
A:HIS208
|
4.9
|
13.6
|
1.0
|
|
HD2
|
A:PRO241
|
4.9
|
14.4
|
1.0
|
|
HD3
|
A:ARG233
|
5.0
|
14.9
|
1.0
|
|
C
|
A:ARG233
|
5.0
|
12.1
|
1.0
|
|
HA
|
A:CYS238
|
5.0
|
13.0
|
1.0
|
|
Iron binding site 2 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 2 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:12.3
occ:1.00
|
FE2
|
A:SF4301
|
0.0
|
12.3
|
1.0
|
|
ND1
|
A:HIS208
|
2.1
|
12.3
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
11.4
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
11.9
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
12.4
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
11.9
|
1.0
|
|
FE3
|
A:SF4301
|
2.7
|
12.3
|
1.0
|
|
FE1
|
A:SF4301
|
2.8
|
11.5
|
1.0
|
|
CE1
|
A:HIS208
|
2.9
|
14.7
|
1.0
|
|
HE1
|
A:HIS208
|
3.0
|
17.6
|
1.0
|
|
CG
|
A:HIS208
|
3.2
|
11.9
|
1.0
|
|
HA
|
A:HIS208
|
3.3
|
12.9
|
1.0
|
|
HB2
|
A:HIS208
|
3.3
|
13.6
|
1.0
|
|
HD3
|
A:PRO241
|
3.4
|
14.4
|
1.0
|
|
CB
|
A:HIS208
|
3.6
|
11.4
|
1.0
|
|
HG3
|
A:PRO241
|
3.6
|
15.7
|
1.0
|
|
S2
|
A:SF4301
|
3.9
|
12.4
|
1.0
|
|
CA
|
A:HIS208
|
3.9
|
10.7
|
1.0
|
|
NE2
|
A:HIS208
|
4.1
|
15.1
|
1.0
|
|
HB3
|
A:CYS211
|
4.1
|
13.7
|
1.0
|
|
CD
|
A:PRO241
|
4.2
|
12.0
|
1.0
|
|
HA3
|
A:GLY240
|
4.2
|
12.9
|
1.0
|
|
CD2
|
A:HIS208
|
4.2
|
13.7
|
1.0
|
|
HB2
|
A:CYS211
|
4.3
|
13.7
|
1.0
|
|
CG
|
A:PRO241
|
4.3
|
13.1
|
1.0
|
|
HB2
|
A:TYR217
|
4.3
|
19.0
|
1.0
|
|
HD1
|
A:TYR217
|
4.5
|
19.8
|
1.0
|
|
CB
|
A:CYS211
|
4.5
|
11.4
|
1.0
|
|
HD13
|
A:LEU214
|
4.5
|
18.3
|
1.0
|
|
HB3
|
A:HIS208
|
4.5
|
13.6
|
1.0
|
|
O
|
A:HIS208
|
4.6
|
11.5
|
1.0
|
|
SG
|
A:CYS211
|
4.7
|
12.0
|
1.0
|
|
SG
|
A:CYS232
|
4.7
|
13.1
|
1.0
|
|
CD1
|
A:TYR217
|
4.7
|
16.5
|
1.0
|
|
C
|
A:HIS208
|
4.7
|
11.8
|
1.0
|
|
N
|
A:PRO241
|
4.8
|
11.6
|
1.0
|
|
HA
|
A:LEU214
|
4.8
|
17.3
|
1.0
|
|
HG2
|
A:PRO241
|
4.8
|
15.7
|
1.0
|
|
SG
|
A:CYS238
|
4.8
|
10.8
|
1.0
|
|
HD12
|
A:LEU214
|
4.8
|
18.3
|
1.0
|
|
HE2
|
A:HIS208
|
4.9
|
18.1
|
1.0
|
|
HD2
|
A:PRO241
|
4.9
|
14.4
|
1.0
|
|
HB2
|
A:TYR234
|
5.0
|
15.5
|
1.0
|
|
CA
|
A:GLY240
|
5.0
|
10.8
|
1.0
|
|
CG
|
A:TYR217
|
5.0
|
15.3
|
1.0
|
|
Iron binding site 3 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 3 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:12.3
occ:1.00
|
FE3
|
A:SF4301
|
0.0
|
12.3
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
12.4
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
12.4
|
1.0
|
|
SG
|
A:CYS232
|
2.3
|
13.1
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
11.9
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
12.3
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
11.9
|
1.0
|
|
FE1
|
A:SF4301
|
2.8
|
11.5
|
1.0
|
|
H
|
A:ARG233
|
3.2
|
13.1
|
1.0
|
|
HB2
|
A:TYR217
|
3.3
|
19.0
|
1.0
|
|
CB
|
A:CYS232
|
3.5
|
14.3
|
1.0
|
|
HB2
|
A:CYS232
|
3.5
|
17.2
|
1.0
|
|
H
|
A:TYR234
|
3.7
|
15.6
|
1.0
|
|
HA
|
A:CYS232
|
3.7
|
15.7
|
1.0
|
|
HD1
|
A:TYR217
|
3.7
|
19.8
|
1.0
|
|
HB2
|
A:TYR234
|
3.8
|
15.5
|
1.0
|
|
HB2
|
A:TYR213
|
3.8
|
16.4
|
1.0
|
|
N
|
A:ARG233
|
3.8
|
10.9
|
1.0
|
|
S3
|
A:SF4301
|
3.9
|
11.4
|
1.0
|
|
CA
|
A:CYS232
|
4.0
|
13.1
|
1.0
|
|
N
|
A:TYR234
|
4.2
|
13.0
|
1.0
|
|
HE1
|
A:HIS208
|
4.2
|
17.6
|
1.0
|
|
CB
|
A:TYR217
|
4.3
|
15.8
|
1.0
|
|
HB3
|
A:CYS232
|
4.3
|
17.2
|
1.0
|
|
C
|
A:CYS232
|
4.4
|
12.0
|
1.0
|
|
HB2
|
A:ARG233
|
4.4
|
13.2
|
1.0
|
|
CD1
|
A:TYR217
|
4.4
|
16.5
|
1.0
|
|
ND1
|
A:HIS208
|
4.4
|
12.3
|
1.0
|
|
HB3
|
A:CYS238
|
4.5
|
13.9
|
1.0
|
|
CB
|
A:TYR234
|
4.6
|
12.9
|
1.0
|
|
CB
|
A:TYR213
|
4.6
|
13.7
|
1.0
|
|
HB3
|
A:TYR213
|
4.7
|
16.4
|
1.0
|
|
O
|
A:TYR213
|
4.7
|
15.5
|
1.0
|
|
HB3
|
A:TYR217
|
4.7
|
19.0
|
1.0
|
|
CE1
|
A:HIS208
|
4.7
|
14.7
|
1.0
|
|
CG
|
A:TYR217
|
4.8
|
15.3
|
1.0
|
|
CA
|
A:ARG233
|
4.8
|
10.8
|
1.0
|
|
HD3
|
A:ARG233
|
4.8
|
14.9
|
1.0
|
|
HA
|
A:LEU214
|
4.8
|
17.3
|
1.0
|
|
HA
|
A:TYR234
|
4.8
|
15.8
|
1.0
|
|
C
|
A:ARG233
|
4.8
|
12.1
|
1.0
|
|
CA
|
A:TYR234
|
4.8
|
13.2
|
1.0
|
|
SG
|
A:CYS211
|
4.9
|
12.0
|
1.0
|
|
H
|
A:TYR217
|
4.9
|
18.9
|
1.0
|
|
SG
|
A:CYS238
|
4.9
|
10.8
|
1.0
|
|
HB3
|
A:TYR234
|
5.0
|
15.5
|
1.0
|
|
C
|
A:TYR213
|
5.0
|
14.1
|
1.0
|
|
Iron binding site 4 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 4 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:11.9
occ:1.00
|
FE4
|
A:SF4301
|
0.0
|
11.9
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
12.4
|
1.0
|
|
SG
|
A:CYS211
|
2.3
|
12.0
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
12.4
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
11.4
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
12.3
|
1.0
|
|
FE1
|
A:SF4301
|
2.7
|
11.5
|
1.0
|
|
FE3
|
A:SF4301
|
2.7
|
12.3
|
1.0
|
|
HB3
|
A:CYS211
|
3.1
|
13.7
|
1.0
|
|
CB
|
A:CYS211
|
3.1
|
11.4
|
1.0
|
|
HB2
|
A:CYS211
|
3.2
|
13.7
|
1.0
|
|
HB2
|
A:TYR213
|
3.2
|
16.4
|
1.0
|
|
HG11
|
A:VAL260
|
3.4
|
15.6
|
1.0
|
|
HD2
|
A:TYR213
|
3.6
|
18.7
|
1.0
|
|
S4
|
A:SF4301
|
3.9
|
11.9
|
1.0
|
|
H
|
A:TYR213
|
3.9
|
16.4
|
1.0
|
|
HA
|
A:HIS208
|
4.0
|
12.9
|
1.0
|
|
HG13
|
A:VAL260
|
4.1
|
15.6
|
1.0
|
|
CG1
|
A:VAL260
|
4.2
|
13.0
|
1.0
|
|
CB
|
A:TYR213
|
4.2
|
13.7
|
1.0
|
|
CD2
|
A:TYR213
|
4.5
|
15.6
|
1.0
|
|
ND1
|
A:HIS208
|
4.5
|
12.3
|
1.0
|
|
CA
|
A:CYS211
|
4.6
|
11.4
|
1.0
|
|
HG21
|
A:VAL260
|
4.6
|
14.3
|
1.0
|
|
HG12
|
A:VAL260
|
4.6
|
15.6
|
1.0
|
|
N
|
A:TYR213
|
4.6
|
13.7
|
1.0
|
|
C
|
A:TYR213
|
4.7
|
14.1
|
1.0
|
|
CA
|
A:TYR213
|
4.7
|
13.2
|
1.0
|
|
HA
|
A:LEU214
|
4.7
|
17.3
|
1.0
|
|
H
|
A:ARG233
|
4.7
|
13.1
|
1.0
|
|
HB3
|
A:TYR213
|
4.8
|
16.4
|
1.0
|
|
N
|
A:LEU214
|
4.8
|
13.8
|
1.0
|
|
SG
|
A:CYS238
|
4.8
|
10.8
|
1.0
|
|
HG22
|
A:ILE207
|
4.9
|
16.0
|
0.5
|
|
CG
|
A:TYR213
|
4.9
|
15.4
|
1.0
|
|
HG22
|
A:ILE207
|
4.9
|
14.3
|
0.5
|
|
H
|
A:LEU214
|
4.9
|
16.5
|
1.0
|
|
HA
|
A:CYS211
|
4.9
|
13.7
|
1.0
|
|
CA
|
A:HIS208
|
4.9
|
10.7
|
1.0
|
|
SG
|
A:CYS232
|
5.0
|
13.1
|
1.0
|
|
HD3
|
A:ARG233
|
5.0
|
14.9
|
1.0
|
|
Iron binding site 5 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 5 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:9.7
occ:1.00
|
FE1
|
A:SF4302
|
0.0
|
9.7
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
10.1
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
9.5
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
10.1
|
1.0
|
|
SG
|
A:CYS268
|
2.3
|
9.8
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
10.1
|
1.0
|
|
FE2
|
A:SF4302
|
2.8
|
10.0
|
1.0
|
|
FE4
|
A:SF4302
|
2.8
|
10.1
|
1.0
|
|
H
|
A:CYS268
|
3.0
|
11.5
|
1.0
|
|
HB3
|
A:CYS268
|
3.4
|
11.3
|
1.0
|
|
CB
|
A:CYS268
|
3.4
|
9.4
|
1.0
|
|
N
|
A:CYS268
|
3.7
|
9.6
|
1.0
|
|
HH12
|
B:ARG182
|
3.8
|
13.2
|
1.0
|
|
HG13
|
A:VAL269
|
3.8
|
12.3
|
1.0
|
|
HH22
|
B:ARG182
|
3.9
|
14.1
|
1.0
|
|
S1
|
A:SF4302
|
3.9
|
10.6
|
1.0
|
|
NH1
|
B:ARG182
|
4.0
|
11.0
|
1.0
|
|
CA
|
A:CYS268
|
4.1
|
9.2
|
1.0
|
|
NH2
|
B:ARG182
|
4.1
|
11.7
|
1.0
|
|
H
|
A:VAL269
|
4.2
|
11.6
|
1.0
|
|
HB2
|
A:CYS268
|
4.2
|
11.3
|
1.0
|
|
CZ
|
B:ARG182
|
4.3
|
11.3
|
1.0
|
|
HH11
|
B:ARG182
|
4.5
|
13.2
|
1.0
|
|
H
|
A:GLY267
|
4.5
|
11.5
|
1.0
|
|
N
|
A:VAL269
|
4.6
|
9.7
|
1.0
|
|
HH2
|
A:TRP165
|
4.6
|
11.2
|
1.0
|
|
HH21
|
B:ARG182
|
4.6
|
14.1
|
1.0
|
|
C
|
A:CYS268
|
4.6
|
9.7
|
1.0
|
|
H
|
A:ILE266
|
4.7
|
11.5
|
1.0
|
|
CG1
|
A:VAL269
|
4.7
|
10.2
|
1.0
|
|
HG12
|
A:ILE266
|
4.7
|
12.2
|
1.0
|
|
HG22
|
A:VAL269
|
4.7
|
11.3
|
1.0
|
|
H
|
A:CYS159
|
4.7
|
10.7
|
1.0
|
|
HZ2
|
A:TRP252
|
4.8
|
11.4
|
1.0
|
|
HG21
|
A:THR243
|
4.8
|
13.3
|
1.0
|
|
SG
|
A:CYS247
|
4.8
|
10.5
|
1.0
|
|
SG
|
A:CYS259
|
4.8
|
10.2
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
10.4
|
1.0
|
|
C
|
A:GLY267
|
4.8
|
9.6
|
1.0
|
|
N
|
A:GLY267
|
4.9
|
9.6
|
1.0
|
|
HA
|
A:CYS268
|
4.9
|
11.1
|
1.0
|
|
HA2
|
A:GLY158
|
5.0
|
9.9
|
1.0
|
|
HG13
|
A:ILE266
|
5.0
|
12.2
|
1.0
|
|
HE21
|
B:GLN187
|
5.0
|
14.0
|
1.0
|
|
Iron binding site 6 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 6 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:10.0
occ:1.00
|
FE2
|
A:SF4302
|
0.0
|
10.0
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
10.1
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
10.6
|
1.0
|
|
SG
|
A:CYS265
|
2.3
|
10.4
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
10.1
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
10.1
|
1.0
|
|
FE4
|
A:SF4302
|
2.8
|
10.1
|
1.0
|
|
FE1
|
A:SF4302
|
2.8
|
9.7
|
1.0
|
|
H
|
A:GLY267
|
3.3
|
11.5
|
1.0
|
|
CB
|
A:CYS265
|
3.4
|
10.9
|
1.0
|
|
HA
|
A:CYS265
|
3.4
|
12.4
|
1.0
|
|
HB2
|
A:CYS265
|
3.4
|
13.1
|
1.0
|
|
HG21
|
A:THR243
|
3.4
|
13.3
|
1.0
|
|
HD12
|
A:ILE207
|
3.5
|
13.6
|
0.5
|
|
H
|
A:ILE266
|
3.6
|
11.5
|
1.0
|
|
HD11
|
A:ILE207
|
3.6
|
13.6
|
0.5
|
|
HD13
|
A:ILE207
|
3.7
|
13.6
|
0.5
|
|
H
|
A:CYS268
|
3.7
|
11.5
|
1.0
|
|
CD1
|
A:ILE207
|
3.8
|
11.3
|
0.5
|
|
CA
|
A:CYS265
|
3.8
|
10.3
|
1.0
|
|
S2
|
A:SF4302
|
3.9
|
9.5
|
1.0
|
|
HB2
|
A:CYS259
|
4.1
|
11.9
|
1.0
|
|
N
|
A:GLY267
|
4.1
|
9.6
|
1.0
|
|
N
|
A:ILE266
|
4.1
|
9.6
|
1.0
|
|
HB3
|
A:CYS265
|
4.2
|
13.1
|
1.0
|
|
HA2
|
A:GLY267
|
4.3
|
12.0
|
1.0
|
|
HG13
|
A:ILE207
|
4.4
|
15.2
|
0.5
|
|
CG2
|
A:THR243
|
4.4
|
11.1
|
1.0
|
|
C
|
A:CYS265
|
4.4
|
9.8
|
1.0
|
|
N
|
A:CYS268
|
4.5
|
9.6
|
1.0
|
|
CA
|
A:GLY267
|
4.6
|
10.0
|
1.0
|
|
HG22
|
A:THR243
|
4.7
|
13.3
|
1.0
|
|
HD12
|
A:ILE207
|
4.7
|
16.6
|
0.5
|
|
SG
|
A:CYS259
|
4.7
|
10.2
|
1.0
|
|
CB
|
A:CYS259
|
4.8
|
9.9
|
1.0
|
|
HG23
|
A:THR243
|
4.8
|
13.3
|
1.0
|
|
HD11
|
A:ILE207
|
4.8
|
16.6
|
0.5
|
|
SG
|
A:CYS268
|
4.9
|
9.8
|
1.0
|
|
SG
|
A:CYS247
|
4.9
|
10.5
|
1.0
|
|
HB3
|
A:CYS259
|
4.9
|
11.9
|
1.0
|
|
HG23
|
A:VAL260
|
5.0
|
14.3
|
1.0
|
|
HB2
|
A:CYS247
|
5.0
|
11.9
|
1.0
|
|
HG12
|
A:ILE266
|
5.0
|
12.2
|
1.0
|
|
Iron binding site 7 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 7 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:10.1
occ:1.00
|
FE3
|
A:SF4302
|
0.0
|
10.1
|
1.0
|
|
S2
|
A:SF4302
|
2.2
|
9.5
|
1.0
|
|
SG
|
A:CYS259
|
2.3
|
10.2
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
10.1
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
10.6
|
1.0
|
|
FE4
|
A:SF4302
|
2.7
|
10.1
|
1.0
|
|
FE1
|
A:SF4302
|
2.7
|
9.7
|
1.0
|
|
FE2
|
A:SF4302
|
2.7
|
10.0
|
1.0
|
|
HB2
|
A:CYS259
|
2.9
|
11.9
|
1.0
|
|
CB
|
A:CYS259
|
3.1
|
9.9
|
1.0
|
|
HE21
|
B:GLN187
|
3.5
|
14.0
|
1.0
|
|
HB3
|
A:CYS259
|
3.5
|
11.9
|
1.0
|
|
S3
|
A:SF4302
|
3.8
|
10.1
|
1.0
|
|
H
|
A:CYS259
|
3.9
|
13.3
|
1.0
|
|
HA
|
A:CYS265
|
4.0
|
12.4
|
1.0
|
|
HD3
|
B:ARG182
|
4.2
|
13.1
|
1.0
|
|
CZ
|
B:ARG182
|
4.2
|
11.3
|
1.0
|
|
NE2
|
B:GLN187
|
4.2
|
11.7
|
1.0
|
|
HE1
|
A:TRP252
|
4.3
|
13.2
|
1.0
|
|
NE
|
B:ARG182
|
4.4
|
11.2
|
1.0
|
|
HE22
|
B:GLN187
|
4.4
|
14.0
|
1.0
|
|
NH2
|
B:ARG182
|
4.4
|
11.7
|
1.0
|
|
H
|
A:ILE266
|
4.4
|
11.5
|
1.0
|
|
CA
|
A:CYS259
|
4.4
|
10.5
|
1.0
|
|
NH1
|
B:ARG182
|
4.5
|
11.0
|
1.0
|
|
N
|
A:CYS259
|
4.6
|
11.1
|
1.0
|
|
HE
|
B:ARG182
|
4.6
|
13.4
|
1.0
|
|
HH21
|
B:ARG182
|
4.6
|
14.1
|
1.0
|
|
SG
|
A:CYS247
|
4.6
|
10.5
|
1.0
|
|
HH11
|
B:ARG182
|
4.6
|
13.2
|
1.0
|
|
NE1
|
A:TRP252
|
4.7
|
11.0
|
1.0
|
|
HH22
|
B:ARG182
|
4.7
|
14.1
|
1.0
|
|
HH12
|
B:ARG182
|
4.7
|
13.2
|
1.0
|
|
SG
|
A:CYS268
|
4.7
|
9.8
|
1.0
|
|
HB3
|
A:CYS247
|
4.8
|
11.9
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
10.4
|
1.0
|
|
CD
|
B:ARG182
|
4.8
|
10.9
|
1.0
|
|
HB2
|
A:CYS265
|
4.8
|
13.1
|
1.0
|
|
HG3
|
B:GLN187
|
4.8
|
12.6
|
1.0
|
|
CA
|
A:CYS265
|
4.9
|
10.3
|
1.0
|
|
HG12
|
A:ILE266
|
4.9
|
12.2
|
1.0
|
|
HA
|
A:CYS259
|
4.9
|
12.6
|
1.0
|
|
Iron binding site 8 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 8 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:10.1
occ:1.00
|
FE4
|
A:SF4302
|
0.0
|
10.1
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
10.6
|
1.0
|
|
SG
|
A:CYS247
|
2.3
|
10.5
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
10.1
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
9.5
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
10.1
|
1.0
|
|
FE2
|
A:SF4302
|
2.8
|
10.0
|
1.0
|
|
FE1
|
A:SF4302
|
2.8
|
9.7
|
1.0
|
|
HB2
|
A:CYS247
|
3.2
|
11.9
|
1.0
|
|
CB
|
A:CYS247
|
3.3
|
9.9
|
1.0
|
|
HD11
|
A:ILE207
|
3.4
|
13.6
|
0.5
|
|
HB3
|
A:CYS247
|
3.4
|
11.9
|
1.0
|
|
HE1
|
A:TRP252
|
3.5
|
13.2
|
1.0
|
|
HH2
|
A:TRP165
|
3.8
|
11.2
|
1.0
|
|
HD11
|
A:ILE207
|
3.9
|
16.6
|
0.5
|
|
S4
|
A:SF4302
|
3.9
|
10.1
|
1.0
|
|
HB3
|
A:ALA245
|
3.9
|
13.2
|
1.0
|
|
HD13
|
A:ILE207
|
3.9
|
13.6
|
0.5
|
|
CD1
|
A:ILE207
|
4.1
|
11.3
|
0.5
|
|
HB1
|
A:ALA245
|
4.2
|
13.2
|
1.0
|
|
NE1
|
A:TRP252
|
4.2
|
11.0
|
1.0
|
|
HD12
|
A:ILE207
|
4.3
|
16.6
|
0.5
|
|
HD12
|
A:ILE207
|
4.4
|
13.6
|
0.5
|
|
CB
|
A:ALA245
|
4.5
|
11.0
|
1.0
|
|
HZ2
|
A:TRP252
|
4.5
|
11.4
|
1.0
|
|
H
|
A:CYS247
|
4.5
|
12.9
|
1.0
|
|
CD1
|
A:ILE207
|
4.6
|
13.8
|
0.5
|
|
CH2
|
A:TRP165
|
4.7
|
9.3
|
1.0
|
|
CA
|
A:CYS247
|
4.7
|
10.0
|
1.0
|
|
SG
|
A:CYS259
|
4.7
|
10.2
|
1.0
|
|
HG13
|
A:VAL269
|
4.7
|
12.3
|
1.0
|
|
HE3
|
A:TRP258
|
4.7
|
12.1
|
1.0
|
|
HB2
|
A:ALA245
|
4.7
|
13.2
|
1.0
|
|
HG21
|
A:THR243
|
4.7
|
13.3
|
1.0
|
|
HB2
|
A:CYS259
|
4.8
|
11.9
|
1.0
|
|
HZ2
|
A:TRP165
|
4.8
|
11.8
|
1.0
|
|
SG
|
A:CYS268
|
4.8
|
9.8
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
10.4
|
1.0
|
|
HG13
|
A:ILE207
|
4.9
|
15.2
|
0.5
|
|
HA
|
A:CYS247
|
5.0
|
12.0
|
1.0
|
|
Iron binding site 9 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 9 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:9.7
occ:0.69
|
FE1
|
A:SF4303
|
0.0
|
9.7
|
0.7
|
|
FE1
|
A:6ML304
|
0.5
|
10.3
|
0.3
|
|
O12
|
A:6ML304
|
1.6
|
11.3
|
0.3
|
|
S3
|
A:6ML304
|
2.1
|
10.4
|
0.3
|
|
S2
|
A:SF4303
|
2.3
|
10.1
|
0.7
|
|
S4
|
A:SF4303
|
2.3
|
9.2
|
0.7
|
|
SG
|
A:CYS18
|
2.3
|
11.5
|
1.0
|
|
S3
|
A:SF4303
|
2.3
|
11.6
|
0.7
|
|
S2
|
A:6ML304
|
2.5
|
9.6
|
0.3
|
|
FE3
|
A:6ML304
|
2.7
|
10.3
|
0.3
|
|
FE4
|
A:SF4303
|
2.7
|
11.2
|
0.7
|
|
FE3
|
A:SF4303
|
2.8
|
9.6
|
0.7
|
|
FE2
|
A:SF4303
|
2.8
|
9.6
|
0.7
|
|
H
|
A:CYS18
|
2.9
|
12.4
|
1.0
|
|
FE2
|
A:6ML304
|
3.0
|
11.7
|
0.3
|
|
HB3
|
A:CYS18
|
3.2
|
12.2
|
1.0
|
|
FE4
|
A:6ML304
|
3.2
|
11.2
|
0.3
|
|
O24
|
A:6ML304
|
3.3
|
12.8
|
0.3
|
|
CB
|
A:CYS18
|
3.3
|
10.2
|
1.0
|
|
H
|
A:GLY20
|
3.4
|
12.5
|
1.0
|
|
HE2
|
B:HIS185
|
3.4
|
11.3
|
1.0
|
|
N
|
A:CYS18
|
3.6
|
10.3
|
1.0
|
|
HA3
|
A:GLY20
|
3.8
|
12.8
|
1.0
|
|
S1
|
A:SF4303
|
3.8
|
10.2
|
0.7
|
|
CA
|
A:CYS18
|
3.9
|
10.3
|
1.0
|
|
S1
|
A:6ML304
|
3.9
|
12.6
|
0.3
|
|
S4
|
A:6ML304
|
4.0
|
11.3
|
0.3
|
|
OE2
|
A:GLU77
|
4.0
|
16.3
|
0.3
|
|
N
|
A:GLY20
|
4.1
|
10.4
|
1.0
|
|
HB2
|
A:CYS18
|
4.1
|
12.2
|
1.0
|
|
H
|
A:CYS21
|
4.2
|
14.0
|
0.3
|
|
HG3
|
B:ARG73
|
4.2
|
11.8
|
1.0
|
|
NE2
|
B:HIS185
|
4.3
|
9.4
|
1.0
|
|
H
|
A:CYS21
|
4.3
|
14.6
|
0.7
|
|
HA2
|
A:GLY17
|
4.4
|
14.4
|
1.0
|
|
CA
|
A:GLY20
|
4.4
|
10.6
|
1.0
|
|
H
|
A:THR19
|
4.5
|
12.3
|
1.0
|
|
C
|
A:CYS18
|
4.5
|
10.0
|
1.0
|
|
O
|
A:HOH562
|
4.5
|
12.6
|
1.0
|
|
HB3
|
B:ARG73
|
4.6
|
11.4
|
1.0
|
|
HA
|
B:ARG73
|
4.6
|
10.4
|
1.0
|
|
N
|
A:THR19
|
4.6
|
10.2
|
1.0
|
|
C
|
A:GLY17
|
4.7
|
11.8
|
1.0
|
|
SG
|
A:CYS21
|
4.8
|
11.3
|
0.7
|
|
N
|
A:CYS21
|
4.8
|
11.7
|
0.3
|
|
N
|
A:CYS21
|
4.8
|
12.2
|
0.7
|
|
HA
|
A:CYS18
|
4.8
|
12.3
|
1.0
|
|
SG
|
A:CYS159
|
4.8
|
9.2
|
1.0
|
|
O
|
B:ARG73
|
4.8
|
10.4
|
1.0
|
|
SG
|
A:CYS121
|
4.9
|
11.8
|
1.0
|
|
CA
|
A:GLY17
|
5.0
|
12.0
|
1.0
|
|
CG
|
B:ARG73
|
5.0
|
9.8
|
1.0
|
|
HG2
|
B:ARG73
|
5.0
|
11.8
|
1.0
|
|
Iron binding site 10 out
of 18 in 5jt1
Go back to
Iron Binding Sites List in 5jt1
Iron binding site 10 out
of 18 in the The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of The 3D Structure of Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.35 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:9.6
occ:0.69
|
FE2
|
A:SF4303
|
0.0
|
9.6
|
0.7
|
|
FE4
|
A:6ML304
|
0.5
|
11.2
|
0.3
|
|
O24
|
A:6ML304
|
1.6
|
12.8
|
0.3
|
|
S3
|
A:6ML304
|
2.0
|
10.4
|
0.3
|
|
S1
|
A:SF4303
|
2.3
|
10.2
|
0.7
|
|
S3
|
A:SF4303
|
2.3
|
11.6
|
0.7
|
|
S4
|
A:SF4303
|
2.3
|
9.2
|
0.7
|
|
SG
|
A:CYS121
|
2.4
|
11.8
|
1.0
|
|
S4
|
A:6ML304
|
2.5
|
11.3
|
0.3
|
|
FE3
|
A:6ML304
|
2.6
|
10.3
|
0.3
|
|
FE3
|
A:SF4303
|
2.7
|
9.6
|
0.7
|
|
FE1
|
A:SF4303
|
2.8
|
9.7
|
0.7
|
|
FE4
|
A:SF4303
|
2.8
|
11.2
|
0.7
|
|
FE2
|
A:6ML304
|
3.0
|
11.7
|
0.3
|
|
HB2
|
A:CYS121
|
3.1
|
14.6
|
1.0
|
|
FE1
|
A:6ML304
|
3.1
|
10.3
|
0.3
|
|
O12
|
A:6ML304
|
3.2
|
11.3
|
0.3
|
|
CB
|
A:CYS121
|
3.4
|
12.2
|
1.0
|
|
H
|
A:CYS121
|
3.4
|
10.9
|
1.0
|
|
O
|
A:HOH422
|
3.8
|
11.2
|
1.0
|
|
HA2
|
A:GLY17
|
3.9
|
14.4
|
1.0
|
|
S2
|
A:SF4303
|
3.9
|
10.1
|
0.7
|
|
O
|
A:HOH562
|
3.9
|
12.6
|
1.0
|
|
S2
|
A:6ML304
|
4.0
|
9.6
|
0.3
|
|
HB3
|
A:CYS121
|
4.0
|
14.6
|
1.0
|
|
H
|
A:CYS18
|
4.1
|
12.4
|
1.0
|
|
S1
|
A:6ML304
|
4.1
|
12.6
|
0.3
|
|
N
|
A:CYS121
|
4.1
|
9.1
|
1.0
|
|
O
|
A:HOH598
|
4.1
|
12.3
|
1.0
|
|
HA2
|
A:GLY78
|
4.2
|
12.7
|
0.7
|
|
HA2
|
A:GLY78
|
4.2
|
13.9
|
0.3
|
|
CA
|
A:CYS121
|
4.4
|
9.5
|
1.0
|
|
H
|
A:GLY78
|
4.4
|
14.7
|
0.3
|
|
HG2
|
A:GLU77
|
4.5
|
20.7
|
0.3
|
|
SG
|
A:CYS159
|
4.6
|
9.2
|
1.0
|
|
HA3
|
A:GLY119
|
4.6
|
10.4
|
1.0
|
|
SG
|
A:CYS21
|
4.7
|
11.3
|
0.7
|
|
CA
|
A:GLY17
|
4.8
|
12.0
|
1.0
|
|
N
|
A:CYS18
|
4.8
|
10.3
|
1.0
|
|
H
|
A:GLY78
|
4.8
|
12.6
|
0.7
|
|
HA
|
A:CYS121
|
4.8
|
11.4
|
1.0
|
|
HB3
|
A:CYS18
|
4.9
|
12.2
|
1.0
|
|
O
|
A:GLN16
|
4.9
|
13.8
|
1.0
|
|
OE2
|
A:GLU77
|
4.9
|
16.3
|
0.3
|
|
HA3
|
A:GLY17
|
5.0
|
14.4
|
1.0
|
|
H
|
A:THR120
|
5.0
|
10.9
|
1.0
|
|
HA
|
A:CYS159
|
5.0
|
10.2
|
1.0
|
|
SG
|
A:CYS18
|
5.0
|
11.5
|
1.0
|
|
Reference:
M.C.Marques,
C.Tapia,
O.Gutierrez-Sanz,
A.R.Ramos,
K.L.Keller,
J.D.Wall,
A.L.De Lacey,
P.M.Matias,
I.A.C.Pereira.
The Direct Role of Selenocysteine in [Nifese] Hydrogenase Maturation and Catalysis. Nat. Chem. Biol. V. 13 544 2017.
ISSN: ESSN 1552-4469
PubMed: 28319099
DOI: 10.1038/NCHEMBIO.2335
Page generated: Tue Aug 6 02:54:41 2024
|
