Iron in PDB 6rtp: The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution
Enzymatic activity of The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution
All present enzymatic activity of The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution:
1.12.7.2;
Protein crystallography data
The structure of The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution, PDB code: 6rtp
was solved by
P.M.Matias,
S.Zacarias,
I.Pereita,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.38 /
1.10
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.138,
62.712,
110.240,
90.00,
105.11,
90.00
|
|
R / Rfree (%)
|
13.9 /
15.8
|
Other elements in 6rtp:
The structure of The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution
(pdb code 6rtp). 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution, PDB code: 6rtp:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 1 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:10.7
occ:1.00
|
FE1
|
A:SF4301
|
0.0
|
10.7
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
11.2
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
10.6
|
1.0
|
|
SG
|
A:CYS238
|
2.3
|
10.2
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
10.9
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
10.9
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
11.2
|
1.0
|
|
FE3
|
A:SF4301
|
2.8
|
11.6
|
1.0
|
|
HB3
|
A:CYS238
|
3.0
|
13.3
|
1.0
|
|
CB
|
A:CYS238
|
3.2
|
11.1
|
1.0
|
|
HB2
|
A:CYS238
|
3.5
|
13.3
|
1.0
|
|
HD3
|
A:PRO241
|
3.6
|
14.5
|
1.0
|
|
HA3
|
A:GLY240
|
3.8
|
12.7
|
1.0
|
|
HB2
|
A:ARG233
|
3.8
|
14.1
|
1.0
|
|
H
|
A:GLY240
|
3.8
|
12.0
|
1.0
|
|
HG11
|
A:VAL260
|
3.9
|
14.8
|
1.0
|
|
S1
|
A:SF4301
|
3.9
|
12.0
|
1.0
|
|
HG13
|
A:VAL260
|
4.1
|
14.8
|
1.0
|
|
H
|
A:ARG233
|
4.1
|
14.1
|
1.0
|
|
HG22
|
A:VAL260
|
4.2
|
14.3
|
1.0
|
|
HG21
|
A:VAL260
|
4.4
|
14.3
|
1.0
|
|
N
|
A:GLY240
|
4.5
|
10.0
|
1.0
|
|
CG1
|
A:VAL260
|
4.5
|
12.3
|
1.0
|
|
CA
|
A:GLY240
|
4.5
|
10.6
|
1.0
|
|
CD
|
A:PRO241
|
4.5
|
12.1
|
1.0
|
|
CA
|
A:CYS238
|
4.6
|
10.6
|
1.0
|
|
HA
|
A:TYR234
|
4.7
|
14.5
|
1.0
|
|
ND1
|
A:HIS208
|
4.7
|
11.8
|
1.0
|
|
CB
|
A:ARG233
|
4.7
|
11.8
|
1.0
|
|
SG
|
A:CYS232
|
4.7
|
11.9
|
1.0
|
|
CG2
|
A:VAL260
|
4.7
|
11.9
|
1.0
|
|
C
|
A:CYS238
|
4.8
|
10.1
|
1.0
|
|
SG
|
A:CYS211
|
4.8
|
11.3
|
1.0
|
|
H
|
A:TYR234
|
4.8
|
13.7
|
1.0
|
|
N
|
A:TYR234
|
4.8
|
11.4
|
1.0
|
|
HB2
|
A:TYR234
|
4.8
|
15.7
|
1.0
|
|
N
|
A:ARG233
|
4.9
|
11.8
|
1.0
|
|
HB2
|
A:HIS208
|
4.9
|
13.2
|
1.0
|
|
O
|
A:CYS238
|
4.9
|
11.1
|
1.0
|
|
HD2
|
A:PRO241
|
4.9
|
14.5
|
1.0
|
|
HA
|
A:HIS208
|
4.9
|
12.1
|
1.0
|
|
HD3
|
A:ARG233
|
4.9
|
14.5
|
1.0
|
|
C
|
A:ARG233
|
5.0
|
10.8
|
1.0
|
|
HA
|
A:CYS238
|
5.0
|
12.7
|
1.0
|
|
Iron binding site 2 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 2 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:11.2
occ:1.00
|
FE2
|
A:SF4301
|
0.0
|
11.2
|
1.0
|
|
ND1
|
A:HIS208
|
2.1
|
11.8
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
10.6
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
11.2
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
12.0
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
10.9
|
1.0
|
|
FE3
|
A:SF4301
|
2.7
|
11.6
|
1.0
|
|
FE1
|
A:SF4301
|
2.7
|
10.7
|
1.0
|
|
CE1
|
A:HIS208
|
2.9
|
13.4
|
1.0
|
|
HE1
|
A:HIS208
|
3.1
|
16.1
|
1.0
|
|
CG
|
A:HIS208
|
3.1
|
11.7
|
1.0
|
|
HB2
|
A:HIS208
|
3.3
|
13.2
|
1.0
|
|
HA
|
A:HIS208
|
3.3
|
12.1
|
1.0
|
|
HD3
|
A:PRO241
|
3.4
|
14.5
|
1.0
|
|
HG3
|
A:PRO241
|
3.5
|
16.2
|
1.0
|
|
CB
|
A:HIS208
|
3.6
|
11.0
|
1.0
|
|
S2
|
A:SF4301
|
3.9
|
10.9
|
1.0
|
|
CA
|
A:HIS208
|
3.9
|
10.1
|
1.0
|
|
NE2
|
A:HIS208
|
4.1
|
14.0
|
1.0
|
|
HB3
|
A:CYS211
|
4.1
|
13.1
|
1.0
|
|
CD
|
A:PRO241
|
4.1
|
12.1
|
1.0
|
|
CD2
|
A:HIS208
|
4.2
|
11.8
|
1.0
|
|
HA3
|
A:GLY240
|
4.2
|
12.7
|
1.0
|
|
CG
|
A:PRO241
|
4.2
|
13.5
|
1.0
|
|
HB2
|
A:CYS211
|
4.3
|
13.1
|
1.0
|
|
HB2
|
A:TYR217
|
4.3
|
17.7
|
1.0
|
|
HD1
|
A:TYR217
|
4.5
|
18.9
|
1.0
|
|
HB3
|
A:HIS208
|
4.5
|
13.2
|
1.0
|
|
HD13
|
A:LEU214
|
4.5
|
17.2
|
1.0
|
|
CB
|
A:CYS211
|
4.5
|
10.9
|
1.0
|
|
O
|
A:HIS208
|
4.6
|
10.2
|
1.0
|
|
SG
|
A:CYS232
|
4.6
|
11.9
|
1.0
|
|
HG2
|
A:PRO241
|
4.6
|
16.2
|
1.0
|
|
SG
|
A:CYS211
|
4.7
|
11.3
|
1.0
|
|
CD1
|
A:TYR217
|
4.7
|
15.7
|
1.0
|
|
C
|
A:HIS208
|
4.7
|
9.9
|
1.0
|
|
N
|
A:PRO241
|
4.7
|
10.4
|
1.0
|
|
HA
|
A:LEU214
|
4.7
|
16.0
|
1.0
|
|
SG
|
A:CYS238
|
4.8
|
10.2
|
1.0
|
|
HE2
|
A:HIS208
|
4.8
|
16.8
|
1.0
|
|
HD2
|
A:PRO241
|
4.9
|
14.5
|
1.0
|
|
HB2
|
A:TYR234
|
4.9
|
15.7
|
1.0
|
|
CG
|
A:TYR217
|
5.0
|
14.7
|
1.0
|
|
HD12
|
A:LEU214
|
5.0
|
17.2
|
1.0
|
|
CA
|
A:GLY240
|
5.0
|
10.6
|
1.0
|
|
CB
|
A:TYR217
|
5.0
|
14.7
|
1.0
|
|
N
|
A:HIS208
|
5.0
|
10.4
|
1.0
|
|
Iron binding site 3 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 3 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:11.6
occ:1.00
|
FE3
|
A:SF4301
|
0.0
|
11.6
|
1.0
|
|
SG
|
A:CYS232
|
2.3
|
11.9
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
10.9
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
12.0
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
11.2
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
11.2
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
10.9
|
1.0
|
|
FE1
|
A:SF4301
|
2.8
|
10.7
|
1.0
|
|
H
|
A:ARG233
|
3.1
|
14.1
|
1.0
|
|
HB2
|
A:TYR217
|
3.3
|
17.7
|
1.0
|
|
CB
|
A:CYS232
|
3.5
|
12.3
|
1.0
|
|
HB2
|
A:CYS232
|
3.5
|
14.7
|
1.0
|
|
HA
|
A:CYS232
|
3.7
|
14.5
|
1.0
|
|
H
|
A:TYR234
|
3.7
|
13.7
|
1.0
|
|
HB2
|
A:TYR234
|
3.7
|
15.7
|
1.0
|
|
HD1
|
A:TYR217
|
3.7
|
18.9
|
1.0
|
|
N
|
A:ARG233
|
3.8
|
11.8
|
1.0
|
|
HB2
|
A:TYR213
|
3.8
|
15.8
|
1.0
|
|
S3
|
A:SF4301
|
3.9
|
10.6
|
1.0
|
|
CA
|
A:CYS232
|
4.0
|
12.1
|
1.0
|
|
N
|
A:TYR234
|
4.2
|
11.4
|
1.0
|
|
HE1
|
A:HIS208
|
4.2
|
16.1
|
1.0
|
|
CB
|
A:TYR217
|
4.3
|
14.7
|
1.0
|
|
HB3
|
A:CYS232
|
4.3
|
14.7
|
1.0
|
|
C
|
A:CYS232
|
4.3
|
11.9
|
1.0
|
|
HB2
|
A:ARG233
|
4.3
|
14.1
|
1.0
|
|
CD1
|
A:TYR217
|
4.4
|
15.7
|
1.0
|
|
ND1
|
A:HIS208
|
4.4
|
11.8
|
1.0
|
|
HB3
|
A:CYS238
|
4.5
|
13.3
|
1.0
|
|
CB
|
A:TYR234
|
4.6
|
13.1
|
1.0
|
|
O
|
A:TYR213
|
4.6
|
12.9
|
1.0
|
|
CB
|
A:TYR213
|
4.7
|
13.2
|
1.0
|
|
HB3
|
A:TYR217
|
4.7
|
17.7
|
1.0
|
|
CE1
|
A:HIS208
|
4.7
|
13.4
|
1.0
|
|
HB3
|
A:TYR213
|
4.7
|
15.8
|
1.0
|
|
CG
|
A:TYR217
|
4.7
|
14.7
|
1.0
|
|
CA
|
A:ARG233
|
4.7
|
11.0
|
1.0
|
|
HD3
|
A:ARG233
|
4.7
|
14.5
|
1.0
|
|
HA
|
A:TYR234
|
4.8
|
14.5
|
1.0
|
|
C
|
A:ARG233
|
4.8
|
10.8
|
1.0
|
|
CA
|
A:TYR234
|
4.8
|
12.1
|
1.0
|
|
HA
|
A:LEU214
|
4.8
|
16.0
|
1.0
|
|
SG
|
A:CYS211
|
4.9
|
11.3
|
1.0
|
|
H
|
A:TYR217
|
4.9
|
16.8
|
1.0
|
|
SG
|
A:CYS238
|
4.9
|
10.2
|
1.0
|
|
HB3
|
A:TYR234
|
4.9
|
15.7
|
1.0
|
|
C
|
A:TYR213
|
5.0
|
12.3
|
1.0
|
|
Iron binding site 4 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 4 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:10.9
occ:1.00
|
FE4
|
A:SF4301
|
0.0
|
10.9
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
12.0
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
10.9
|
1.0
|
|
SG
|
A:CYS211
|
2.3
|
11.3
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
10.6
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
11.2
|
1.0
|
|
FE1
|
A:SF4301
|
2.7
|
10.7
|
1.0
|
|
FE3
|
A:SF4301
|
2.7
|
11.6
|
1.0
|
|
HB3
|
A:CYS211
|
3.0
|
13.1
|
1.0
|
|
CB
|
A:CYS211
|
3.1
|
10.9
|
1.0
|
|
HB2
|
A:CYS211
|
3.2
|
13.1
|
1.0
|
|
HB2
|
A:TYR213
|
3.3
|
15.8
|
1.0
|
|
HG11
|
A:VAL260
|
3.3
|
14.8
|
1.0
|
|
HD2
|
A:TYR213
|
3.6
|
19.4
|
1.0
|
|
S4
|
A:SF4301
|
3.9
|
11.2
|
1.0
|
|
HA
|
A:HIS208
|
3.9
|
12.1
|
1.0
|
|
H
|
A:TYR213
|
4.0
|
14.6
|
1.0
|
|
CG1
|
A:VAL260
|
4.2
|
12.3
|
1.0
|
|
CB
|
A:TYR213
|
4.2
|
13.2
|
1.0
|
|
HG13
|
A:VAL260
|
4.3
|
14.8
|
1.0
|
|
CD2
|
A:TYR213
|
4.4
|
16.2
|
1.0
|
|
ND1
|
A:HIS208
|
4.4
|
11.8
|
1.0
|
|
CA
|
A:CYS211
|
4.5
|
10.6
|
1.0
|
|
HG12
|
A:VAL260
|
4.6
|
14.8
|
1.0
|
|
C
|
A:TYR213
|
4.6
|
12.3
|
1.0
|
|
HG21
|
A:VAL260
|
4.6
|
14.3
|
1.0
|
|
N
|
A:TYR213
|
4.7
|
12.1
|
1.0
|
|
H
|
A:ARG233
|
4.7
|
14.1
|
1.0
|
|
HA
|
A:LEU214
|
4.7
|
16.0
|
1.0
|
|
CA
|
A:TYR213
|
4.7
|
12.2
|
1.0
|
|
N
|
A:LEU214
|
4.7
|
13.3
|
1.0
|
|
SG
|
A:CYS238
|
4.8
|
10.2
|
1.0
|
|
HB3
|
A:TYR213
|
4.8
|
15.8
|
1.0
|
|
HG21
|
A:ILE207
|
4.8
|
13.7
|
0.5
|
|
HG21
|
A:ILE207
|
4.8
|
15.0
|
0.5
|
|
CG
|
A:TYR213
|
4.9
|
15.2
|
1.0
|
|
H
|
A:LEU214
|
4.9
|
16.0
|
1.0
|
|
CA
|
A:HIS208
|
4.9
|
10.1
|
1.0
|
|
HA
|
A:CYS211
|
4.9
|
12.7
|
1.0
|
|
SG
|
A:CYS232
|
4.9
|
11.9
|
1.0
|
|
HD3
|
A:ARG233
|
5.0
|
14.5
|
1.0
|
|
Iron binding site 5 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 5 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:9.3
occ:1.00
|
FE1
|
A:SF4302
|
0.0
|
9.3
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
9.4
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
9.4
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
9.4
|
1.0
|
|
SG
|
A:CYS268
|
2.3
|
9.3
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
9.6
|
1.0
|
|
FE2
|
A:SF4302
|
2.8
|
9.4
|
1.0
|
|
FE4
|
A:SF4302
|
2.8
|
9.6
|
1.0
|
|
H
|
A:CYS268
|
2.9
|
10.6
|
1.0
|
|
HB3
|
A:CYS268
|
3.3
|
11.6
|
1.0
|
|
CB
|
A:CYS268
|
3.4
|
9.6
|
1.0
|
|
N
|
A:CYS268
|
3.7
|
8.8
|
1.0
|
|
HG13
|
A:VAL269
|
3.7
|
11.1
|
1.0
|
|
HH12
|
B:ARG182
|
3.7
|
13.6
|
1.0
|
|
HH22
|
B:ARG182
|
3.8
|
14.5
|
1.0
|
|
S1
|
A:SF4302
|
3.9
|
10.1
|
1.0
|
|
CA
|
A:CYS268
|
4.0
|
8.6
|
1.0
|
|
NH1
|
B:ARG182
|
4.0
|
11.3
|
1.0
|
|
NH2
|
B:ARG182
|
4.1
|
12.1
|
1.0
|
|
H
|
A:VAL269
|
4.1
|
9.9
|
1.0
|
|
HB2
|
A:CYS268
|
4.2
|
11.6
|
1.0
|
|
CZ
|
B:ARG182
|
4.3
|
11.0
|
1.0
|
|
HH11
|
B:ARG182
|
4.5
|
13.6
|
1.0
|
|
H
|
A:GLY267
|
4.5
|
10.8
|
1.0
|
|
N
|
A:VAL269
|
4.5
|
8.2
|
1.0
|
|
HH2
|
A:TRP165
|
4.6
|
10.9
|
1.0
|
|
HH21
|
B:ARG182
|
4.6
|
14.5
|
1.0
|
|
C
|
A:CYS268
|
4.6
|
8.4
|
1.0
|
|
H
|
A:ILE266
|
4.6
|
10.8
|
1.0
|
|
HG22
|
A:VAL269
|
4.6
|
11.9
|
1.0
|
|
CG1
|
A:VAL269
|
4.7
|
9.2
|
1.0
|
|
HG12
|
A:ILE266
|
4.7
|
11.1
|
1.0
|
|
H
|
A:CYS159
|
4.7
|
10.2
|
1.0
|
|
HG21
|
A:THR243
|
4.7
|
12.8
|
1.0
|
|
HZ2
|
A:TRP252
|
4.8
|
11.1
|
1.0
|
|
C
|
A:GLY267
|
4.8
|
9.2
|
1.0
|
|
SG
|
A:CYS259
|
4.8
|
9.5
|
1.0
|
|
SG
|
A:CYS247
|
4.8
|
10.1
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
9.8
|
1.0
|
|
HA
|
A:CYS268
|
4.9
|
10.3
|
1.0
|
|
HA2
|
A:GLY158
|
4.9
|
10.1
|
1.0
|
|
N
|
A:GLY267
|
4.9
|
9.0
|
1.0
|
|
HG13
|
A:ILE266
|
5.0
|
11.1
|
1.0
|
|
HE21
|
B:GLN187
|
5.0
|
13.1
|
1.0
|
|
Iron binding site 6 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 6 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:9.4
occ:1.00
|
FE2
|
A:SF4302
|
0.0
|
9.4
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
9.4
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
10.1
|
1.0
|
|
SG
|
A:CYS265
|
2.3
|
9.8
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
9.4
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
9.6
|
1.0
|
|
FE4
|
A:SF4302
|
2.7
|
9.6
|
1.0
|
|
FE1
|
A:SF4302
|
2.8
|
9.3
|
1.0
|
|
H
|
A:GLY267
|
3.3
|
10.8
|
1.0
|
|
HA
|
A:CYS265
|
3.3
|
11.6
|
1.0
|
|
HB2
|
A:CYS265
|
3.3
|
12.0
|
1.0
|
|
CB
|
A:CYS265
|
3.3
|
10.0
|
1.0
|
|
HG21
|
A:THR243
|
3.4
|
12.8
|
1.0
|
|
HD11
|
A:ILE207
|
3.6
|
11.2
|
0.5
|
|
HD12
|
A:ILE207
|
3.6
|
11.2
|
0.5
|
|
H
|
A:ILE266
|
3.6
|
10.8
|
1.0
|
|
HD13
|
A:ILE207
|
3.6
|
11.2
|
0.5
|
|
H
|
A:CYS268
|
3.7
|
10.6
|
1.0
|
|
CD1
|
A:ILE207
|
3.8
|
9.3
|
0.5
|
|
CA
|
A:CYS265
|
3.8
|
9.7
|
1.0
|
|
S2
|
A:SF4302
|
3.9
|
9.4
|
1.0
|
|
N
|
A:GLY267
|
4.1
|
9.0
|
1.0
|
|
HB2
|
A:CYS259
|
4.1
|
11.4
|
1.0
|
|
N
|
A:ILE266
|
4.1
|
9.0
|
1.0
|
|
HB3
|
A:CYS265
|
4.2
|
12.0
|
1.0
|
|
HA2
|
A:GLY267
|
4.2
|
11.5
|
1.0
|
|
CG2
|
A:THR243
|
4.3
|
10.7
|
1.0
|
|
HG13
|
A:ILE207
|
4.3
|
14.0
|
0.5
|
|
C
|
A:CYS265
|
4.4
|
9.4
|
1.0
|
|
N
|
A:CYS268
|
4.5
|
8.8
|
1.0
|
|
HG22
|
A:THR243
|
4.6
|
12.8
|
1.0
|
|
CA
|
A:GLY267
|
4.6
|
9.6
|
1.0
|
|
HD11
|
A:ILE207
|
4.7
|
15.3
|
0.5
|
|
SG
|
A:CYS259
|
4.7
|
9.5
|
1.0
|
|
CB
|
A:CYS259
|
4.8
|
9.5
|
1.0
|
|
HG23
|
A:THR243
|
4.8
|
12.8
|
1.0
|
|
HD12
|
A:ILE207
|
4.9
|
15.3
|
0.5
|
|
SG
|
A:CYS268
|
4.9
|
9.3
|
1.0
|
|
SG
|
A:CYS247
|
4.9
|
10.1
|
1.0
|
|
HB3
|
A:CYS259
|
4.9
|
11.4
|
1.0
|
|
HG23
|
A:VAL260
|
5.0
|
14.3
|
1.0
|
|
HG12
|
A:ILE266
|
5.0
|
11.1
|
1.0
|
|
HG22
|
A:ILE207
|
5.0
|
15.0
|
0.5
|
|
Iron binding site 7 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 7 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:9.6
occ:1.00
|
FE3
|
A:SF4302
|
0.0
|
9.6
|
1.0
|
|
S2
|
A:SF4302
|
2.2
|
9.4
|
1.0
|
|
SG
|
A:CYS259
|
2.3
|
9.5
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
9.4
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
10.1
|
1.0
|
|
FE4
|
A:SF4302
|
2.7
|
9.6
|
1.0
|
|
FE1
|
A:SF4302
|
2.7
|
9.3
|
1.0
|
|
FE2
|
A:SF4302
|
2.7
|
9.4
|
1.0
|
|
HB2
|
A:CYS259
|
2.9
|
11.4
|
1.0
|
|
CB
|
A:CYS259
|
3.1
|
9.5
|
1.0
|
|
HE21
|
B:GLN187
|
3.5
|
13.1
|
1.0
|
|
HB3
|
A:CYS259
|
3.5
|
11.4
|
1.0
|
|
S3
|
A:SF4302
|
3.8
|
9.4
|
1.0
|
|
HA
|
A:CYS265
|
3.9
|
11.6
|
1.0
|
|
H
|
A:CYS259
|
3.9
|
11.2
|
1.0
|
|
HD3
|
B:ARG182
|
4.1
|
13.5
|
1.0
|
|
NE2
|
B:GLN187
|
4.2
|
10.9
|
1.0
|
|
CZ
|
B:ARG182
|
4.2
|
11.0
|
1.0
|
|
HE1
|
A:TRP252
|
4.3
|
11.7
|
1.0
|
|
NE
|
B:ARG182
|
4.4
|
10.8
|
1.0
|
|
HE22
|
B:GLN187
|
4.4
|
13.1
|
1.0
|
|
NH2
|
B:ARG182
|
4.4
|
12.1
|
1.0
|
|
H
|
A:ILE266
|
4.4
|
10.8
|
1.0
|
|
NH1
|
B:ARG182
|
4.4
|
11.3
|
1.0
|
|
CA
|
A:CYS259
|
4.5
|
9.3
|
1.0
|
|
HH21
|
B:ARG182
|
4.6
|
14.5
|
1.0
|
|
N
|
A:CYS259
|
4.6
|
9.3
|
1.0
|
|
HE
|
B:ARG182
|
4.6
|
13.0
|
1.0
|
|
SG
|
A:CYS247
|
4.6
|
10.1
|
1.0
|
|
HH22
|
B:ARG182
|
4.6
|
14.5
|
1.0
|
|
NE1
|
A:TRP252
|
4.6
|
9.7
|
1.0
|
|
HH11
|
B:ARG182
|
4.7
|
13.6
|
1.0
|
|
HH12
|
B:ARG182
|
4.7
|
13.6
|
1.0
|
|
SG
|
A:CYS268
|
4.7
|
9.3
|
1.0
|
|
HB2
|
A:CYS265
|
4.7
|
12.0
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
9.8
|
1.0
|
|
CD
|
B:ARG182
|
4.8
|
11.3
|
1.0
|
|
HB3
|
A:CYS247
|
4.8
|
12.3
|
1.0
|
|
HG3
|
B:GLN187
|
4.8
|
12.7
|
1.0
|
|
CA
|
A:CYS265
|
4.8
|
9.7
|
1.0
|
|
HG12
|
A:ILE266
|
4.9
|
11.1
|
1.0
|
|
HA
|
A:CYS259
|
5.0
|
11.1
|
1.0
|
|
Iron binding site 8 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 8 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:9.6
occ:1.00
|
FE4
|
A:SF4302
|
0.0
|
9.6
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
10.1
|
1.0
|
|
SG
|
A:CYS247
|
2.3
|
10.1
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
9.4
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
9.4
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
9.6
|
1.0
|
|
FE2
|
A:SF4302
|
2.7
|
9.4
|
1.0
|
|
FE1
|
A:SF4302
|
2.8
|
9.3
|
1.0
|
|
HB2
|
A:CYS247
|
3.2
|
12.3
|
1.0
|
|
CB
|
A:CYS247
|
3.3
|
10.2
|
1.0
|
|
HD12
|
A:ILE207
|
3.4
|
11.2
|
0.5
|
|
HB3
|
A:CYS247
|
3.4
|
12.3
|
1.0
|
|
HE1
|
A:TRP252
|
3.5
|
11.7
|
1.0
|
|
HH2
|
A:TRP165
|
3.7
|
10.9
|
1.0
|
|
HD13
|
A:ILE207
|
3.8
|
11.2
|
0.5
|
|
HB3
|
A:ALA245
|
3.9
|
12.8
|
1.0
|
|
S4
|
A:SF4302
|
3.9
|
9.4
|
1.0
|
|
HD12
|
A:ILE207
|
3.9
|
15.3
|
0.5
|
|
CD1
|
A:ILE207
|
4.0
|
9.3
|
0.5
|
|
HD11
|
A:ILE207
|
4.2
|
15.3
|
0.5
|
|
HB1
|
A:ALA245
|
4.3
|
12.8
|
1.0
|
|
NE1
|
A:TRP252
|
4.3
|
9.7
|
1.0
|
|
HD11
|
A:ILE207
|
4.4
|
11.2
|
0.5
|
|
CB
|
A:ALA245
|
4.5
|
10.7
|
1.0
|
|
H
|
A:CYS247
|
4.5
|
12.5
|
1.0
|
|
HZ2
|
A:TRP252
|
4.5
|
11.1
|
1.0
|
|
CD1
|
A:ILE207
|
4.5
|
12.7
|
0.5
|
|
CH2
|
A:TRP165
|
4.6
|
9.1
|
1.0
|
|
HG13
|
A:VAL269
|
4.6
|
11.1
|
1.0
|
|
HE3
|
A:TRP258
|
4.7
|
12.7
|
1.0
|
|
CA
|
A:CYS247
|
4.7
|
10.2
|
1.0
|
|
SG
|
A:CYS259
|
4.7
|
9.5
|
1.0
|
|
HB2
|
A:ALA245
|
4.7
|
12.8
|
1.0
|
|
HB2
|
A:CYS259
|
4.7
|
11.4
|
1.0
|
|
HG21
|
A:THR243
|
4.7
|
12.8
|
1.0
|
|
HZ2
|
A:TRP165
|
4.8
|
10.6
|
1.0
|
|
HG13
|
A:ILE207
|
4.8
|
14.0
|
0.5
|
|
SG
|
A:CYS268
|
4.8
|
9.3
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
9.8
|
1.0
|
|
Iron binding site 9 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 9 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:7.1
occ:0.61
|
FE1
|
A:SF4303
|
0.0
|
7.1
|
0.6
|
|
FE1
|
A:6ML304
|
0.6
|
8.7
|
0.4
|
|
O12
|
A:6ML304
|
1.5
|
9.2
|
0.4
|
|
S3
|
A:6ML304
|
2.0
|
9.5
|
0.4
|
|
S4
|
A:SF4303
|
2.3
|
7.1
|
0.6
|
|
S2
|
A:SF4303
|
2.3
|
9.7
|
0.6
|
|
S3
|
A:SF4303
|
2.3
|
9.8
|
0.6
|
|
SG
|
A:CYS18
|
2.4
|
10.5
|
1.0
|
|
S2
|
A:6ML304
|
2.5
|
8.0
|
0.4
|
|
FE4
|
A:SF4303
|
2.7
|
9.2
|
0.6
|
|
FE2
|
A:SF4303
|
2.7
|
7.7
|
0.6
|
|
FE3
|
A:SF4303
|
2.7
|
7.5
|
0.6
|
|
FE3
|
A:6ML304
|
2.7
|
9.8
|
0.4
|
|
H
|
A:CYS18
|
2.9
|
11.4
|
1.0
|
|
FE2
|
A:6ML304
|
2.9
|
9.4
|
0.4
|
|
FE4
|
A:6ML304
|
3.2
|
8.8
|
0.4
|
|
HB3
|
A:CYS18
|
3.2
|
10.5
|
1.0
|
|
O24
|
A:6ML304
|
3.2
|
9.9
|
0.4
|
|
CB
|
A:CYS18
|
3.3
|
8.8
|
1.0
|
|
H
|
A:GLY20
|
3.4
|
12.1
|
1.0
|
|
HE2
|
B:HIS185
|
3.4
|
10.9
|
1.0
|
|
N
|
A:CYS18
|
3.6
|
9.5
|
1.0
|
|
HA3
|
A:GLY20
|
3.8
|
12.0
|
1.0
|
|
S1
|
A:SF4303
|
3.8
|
10.3
|
0.6
|
|
S4
|
A:6ML304
|
3.9
|
8.6
|
0.4
|
|
CA
|
A:CYS18
|
3.9
|
8.9
|
1.0
|
|
S1
|
A:6ML304
|
4.0
|
8.8
|
0.4
|
|
N
|
A:GLY20
|
4.1
|
10.1
|
1.0
|
|
HB2
|
A:CYS18
|
4.2
|
10.5
|
1.0
|
|
HG3
|
B:ARG73
|
4.2
|
10.5
|
1.0
|
|
H
|
A:CYS21
|
4.2
|
11.9
|
0.4
|
|
NE2
|
B:HIS185
|
4.3
|
9.1
|
1.0
|
|
H
|
A:CYS21
|
4.3
|
12.4
|
0.6
|
|
HA2
|
A:GLY17
|
4.4
|
14.9
|
1.0
|
|
CA
|
A:GLY20
|
4.4
|
10.0
|
1.0
|
|
C
|
A:CYS18
|
4.4
|
8.8
|
1.0
|
|
H
|
A:THR19
|
4.5
|
10.6
|
1.0
|
|
OE2
|
A:GLU77
|
4.5
|
16.9
|
0.4
|
|
O
|
B:HOH846
|
4.5
|
12.3
|
1.0
|
|
HB3
|
B:ARG73
|
4.6
|
10.6
|
1.0
|
|
HA
|
B:ARG73
|
4.6
|
10.1
|
1.0
|
|
N
|
A:THR19
|
4.6
|
8.8
|
1.0
|
|
C
|
A:GLY17
|
4.7
|
10.4
|
1.0
|
|
N
|
A:CYS21
|
4.8
|
9.9
|
0.4
|
|
SG
|
A:CYS159
|
4.8
|
8.7
|
1.0
|
|
SG
|
A:CYS21
|
4.8
|
9.3
|
0.6
|
|
N
|
A:CYS21
|
4.8
|
10.3
|
0.6
|
|
HA
|
A:CYS18
|
4.8
|
10.7
|
1.0
|
|
SG
|
A:CYS121
|
4.8
|
10.0
|
1.0
|
|
CG
|
B:ARG73
|
4.9
|
8.8
|
1.0
|
|
HG2
|
B:ARG73
|
4.9
|
10.5
|
1.0
|
|
O
|
B:ARG73
|
4.9
|
9.3
|
1.0
|
|
CA
|
A:GLY17
|
4.9
|
12.4
|
1.0
|
|
C
|
A:GLY20
|
5.0
|
9.7
|
1.0
|
|
Iron binding site 10 out
of 18 in 6rtp
Go back to
Iron Binding Sites List in 6rtp
Iron binding site 10 out
of 18 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 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 [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:7.7
occ:0.61
|
FE2
|
A:SF4303
|
0.0
|
7.7
|
0.6
|
|
FE4
|
A:6ML304
|
0.5
|
8.8
|
0.4
|
|
O24
|
A:6ML304
|
1.8
|
9.9
|
0.4
|
|
S3
|
A:6ML304
|
1.9
|
9.5
|
0.4
|
|
S1
|
A:SF4303
|
2.3
|
10.3
|
0.6
|
|
S3
|
A:SF4303
|
2.3
|
9.8
|
0.6
|
|
S4
|
A:SF4303
|
2.3
|
7.1
|
0.6
|
|
S4
|
A:6ML304
|
2.4
|
8.6
|
0.4
|
|
SG
|
A:CYS121
|
2.4
|
10.0
|
1.0
|
|
FE3
|
A:SF4303
|
2.6
|
7.5
|
0.6
|
|
FE3
|
A:6ML304
|
2.6
|
9.8
|
0.4
|
|
FE1
|
A:SF4303
|
2.7
|
7.1
|
0.6
|
|
FE4
|
A:SF4303
|
2.8
|
9.2
|
0.6
|
|
FE2
|
A:6ML304
|
3.0
|
9.4
|
0.4
|
|
HB2
|
A:CYS121
|
3.1
|
11.4
|
1.0
|
|
FE1
|
A:6ML304
|
3.2
|
8.7
|
0.4
|
|
O12
|
A:6ML304
|
3.2
|
9.2
|
0.4
|
|
H
|
A:CYS121
|
3.4
|
10.2
|
1.0
|
|
CB
|
A:CYS121
|
3.4
|
9.5
|
1.0
|
|
O
|
A:HOH425
|
3.8
|
9.9
|
1.0
|
|
HA2
|
A:GLY17
|
3.8
|
14.9
|
1.0
|
|
S2
|
A:SF4303
|
3.9
|
9.7
|
0.6
|
|
S2
|
A:6ML304
|
4.0
|
8.0
|
0.4
|
|
O
|
B:HOH846
|
4.0
|
12.3
|
1.0
|
|
H
|
A:CYS18
|
4.0
|
11.4
|
1.0
|
|
HB3
|
A:CYS121
|
4.1
|
11.4
|
1.0
|
|
N
|
A:CYS121
|
4.1
|
8.5
|
1.0
|
|
O
|
A:HOH604
|
4.1
|
11.9
|
1.0
|
|
S1
|
A:6ML304
|
4.1
|
8.8
|
0.4
|
|
HA2
|
A:GLY78
|
4.2
|
12.7
|
1.0
|
|
CA
|
A:CYS121
|
4.4
|
8.6
|
1.0
|
|
SG
|
A:CYS159
|
4.5
|
8.7
|
1.0
|
|
HA3
|
A:GLY119
|
4.6
|
10.1
|
1.0
|
|
CA
|
A:GLY17
|
4.7
|
12.4
|
1.0
|
|
N
|
A:CYS18
|
4.7
|
9.5
|
1.0
|
|
SG
|
A:CYS21
|
4.7
|
9.3
|
0.6
|
|
H
|
A:GLY78
|
4.8
|
12.5
|
1.0
|
|
HB3
|
A:CYS18
|
4.8
|
10.5
|
1.0
|
|
HA
|
A:CYS121
|
4.8
|
10.4
|
1.0
|
|
HA3
|
A:GLY17
|
4.9
|
14.9
|
1.0
|
|
HG3
|
A:GLU77
|
4.9
|
19.2
|
0.4
|
|
HA
|
A:CYS159
|
4.9
|
10.3
|
1.0
|
|
H
|
A:THR120
|
4.9
|
9.8
|
1.0
|
|
O
|
A:GLN16
|
4.9
|
12.6
|
1.0
|
|
SG
|
A:CYS18
|
4.9
|
10.5
|
1.0
|
|
H
|
A:ALA122
|
5.0
|
10.3
|
1.0
|
|
Reference:
S.Zacarias,
A.Temporao,
M.Del Barrio,
V.Fourmond,
C.Leger,
P.M.Matias,
I.A.C.Pereira.
A Hydrophilic Channel Is Involved in Oxidative Inactivation of A [Nifese] Hydrogenase Acs Catalysis 2019.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.9B02347
Page generated: Wed Aug 7 09:22:42 2024
|
