Iron in PDB 6z8j: Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
Enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
All present enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2:
1.12.7.2;
Protein crystallography data
The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2, PDB code: 6z8j
was solved by
S.Zacarias,
A.Temporao,
P.Carpentier,
P.Van Der Linden,
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)
|
42.41 /
1.09
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.864,
93.988,
98.612,
90.00,
93.16,
90.00
|
|
R / Rfree (%)
|
14 /
16.4
|
Other elements in 6z8j:
The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Page 4, Binding sites: 31 -
36;
Binding sites:
The binding sites of Iron atom in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
(pdb code 6z8j). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the
Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2, PDB code: 6z8j:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 1 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:13.7
occ:1.00
|
FE1
|
A:SF4301
|
0.0
|
13.7
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
14.6
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
14.2
|
1.0
|
|
SG
|
A:CYS238
|
2.3
|
13.0
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
14.0
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
14.7
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
15.3
|
1.0
|
|
FE3
|
A:SF4301
|
2.8
|
14.5
|
1.0
|
|
HB3
|
A:CYS238
|
3.0
|
15.7
|
1.0
|
|
CB
|
A:CYS238
|
3.2
|
13.0
|
1.0
|
|
HD3
|
A:PRO241
|
3.5
|
18.4
|
1.0
|
|
HB2
|
A:CYS238
|
3.5
|
15.7
|
1.0
|
|
HA3
|
A:GLY240
|
3.7
|
16.7
|
1.0
|
|
HB2
|
A:ARG233
|
3.8
|
14.9
|
1.0
|
|
H
|
A:GLY240
|
3.8
|
16.4
|
1.0
|
|
S1
|
A:SF4301
|
3.9
|
15.2
|
1.0
|
|
HG12
|
A:VAL260
|
4.0
|
16.4
|
1.0
|
|
HG13
|
A:VAL260
|
4.0
|
16.4
|
1.0
|
|
H
|
A:ARG233
|
4.1
|
15.7
|
1.0
|
|
HG21
|
A:VAL260
|
4.2
|
16.5
|
1.0
|
|
HG22
|
A:VAL260
|
4.4
|
16.5
|
1.0
|
|
CG1
|
A:VAL260
|
4.5
|
13.7
|
1.0
|
|
N
|
A:GLY240
|
4.5
|
13.7
|
1.0
|
|
CD
|
A:PRO241
|
4.5
|
15.3
|
1.0
|
|
CA
|
A:GLY240
|
4.5
|
13.9
|
1.0
|
|
CA
|
A:CYS238
|
4.6
|
12.8
|
1.0
|
|
HA
|
A:TYR234
|
4.6
|
17.5
|
1.0
|
|
CB
|
A:ARG233
|
4.7
|
12.4
|
1.0
|
|
SG
|
A:CYS232
|
4.7
|
14.5
|
1.0
|
|
ND1
|
A:HIS208
|
4.7
|
16.3
|
1.0
|
|
SG
|
A:CYS211
|
4.7
|
15.7
|
1.0
|
|
CG2
|
A:VAL260
|
4.7
|
13.7
|
1.0
|
|
C
|
A:CYS238
|
4.8
|
12.9
|
1.0
|
|
N
|
A:TYR234
|
4.8
|
14.4
|
1.0
|
|
H
|
A:TYR234
|
4.8
|
17.3
|
1.0
|
|
HB2
|
A:TYR234
|
4.8
|
18.8
|
1.0
|
|
N
|
A:ARG233
|
4.8
|
13.1
|
1.0
|
|
HD2
|
A:PRO241
|
4.8
|
18.4
|
1.0
|
|
O
|
A:CYS238
|
4.9
|
13.4
|
1.0
|
|
HA
|
A:HIS208
|
4.9
|
19.5
|
1.0
|
|
C
|
A:ARG233
|
4.9
|
13.4
|
1.0
|
|
HB2
|
A:HIS208
|
4.9
|
20.0
|
1.0
|
|
HD3
|
A:ARG233
|
4.9
|
17.0
|
1.0
|
|
HG21
|
A:ILE207
|
5.0
|
19.4
|
0.5
|
|
HA
|
A:CYS238
|
5.0
|
15.3
|
1.0
|
|
HG3
|
A:PRO241
|
5.0
|
20.0
|
1.0
|
|
Iron binding site 2 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 2 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:15.3
occ:1.00
|
FE2
|
A:SF4301
|
0.0
|
15.3
|
1.0
|
|
ND1
|
A:HIS208
|
2.1
|
16.3
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
14.6
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
14.2
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
15.2
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
14.7
|
1.0
|
|
FE3
|
A:SF4301
|
2.7
|
14.5
|
1.0
|
|
FE1
|
A:SF4301
|
2.7
|
13.7
|
1.0
|
|
CE1
|
A:HIS208
|
2.9
|
17.2
|
1.0
|
|
HE1
|
A:HIS208
|
3.0
|
20.7
|
1.0
|
|
CG
|
A:HIS208
|
3.2
|
16.9
|
1.0
|
|
HA
|
A:HIS208
|
3.3
|
19.5
|
1.0
|
|
HB2
|
A:HIS208
|
3.3
|
20.0
|
1.0
|
|
HD3
|
A:PRO241
|
3.4
|
18.4
|
1.0
|
|
HG3
|
A:PRO241
|
3.5
|
20.0
|
1.0
|
|
CB
|
A:HIS208
|
3.6
|
16.6
|
1.0
|
|
S2
|
A:SF4301
|
3.9
|
14.0
|
1.0
|
|
CA
|
A:HIS208
|
3.9
|
16.3
|
1.0
|
|
HB3
|
A:CYS211
|
4.1
|
19.8
|
1.0
|
|
NE2
|
A:HIS208
|
4.1
|
17.9
|
1.0
|
|
CD
|
A:PRO241
|
4.1
|
15.3
|
1.0
|
|
HA3
|
A:GLY240
|
4.2
|
16.7
|
1.0
|
|
CG
|
A:PRO241
|
4.2
|
16.7
|
1.0
|
|
CD2
|
A:HIS208
|
4.3
|
17.7
|
1.0
|
|
HB2
|
A:CYS211
|
4.3
|
19.8
|
1.0
|
|
HB2
|
A:TYR217
|
4.3
|
22.2
|
1.0
|
|
HD1
|
A:TYR217
|
4.4
|
23.2
|
1.0
|
|
HD13
|
A:LEU214
|
4.5
|
25.4
|
1.0
|
|
CB
|
A:CYS211
|
4.5
|
16.5
|
1.0
|
|
HB3
|
A:HIS208
|
4.6
|
20.0
|
1.0
|
|
SG
|
A:CYS211
|
4.6
|
15.7
|
1.0
|
|
SG
|
A:CYS232
|
4.6
|
14.5
|
1.0
|
|
HG2
|
A:PRO241
|
4.7
|
20.0
|
1.0
|
|
O
|
A:HIS208
|
4.7
|
16.4
|
1.0
|
|
CD1
|
A:TYR217
|
4.7
|
19.4
|
1.0
|
|
N
|
A:PRO241
|
4.7
|
15.0
|
1.0
|
|
HA
|
A:LEU214
|
4.7
|
23.4
|
1.0
|
|
C
|
A:HIS208
|
4.8
|
17.1
|
1.0
|
|
SG
|
A:CYS238
|
4.8
|
13.0
|
1.0
|
|
HD11
|
A:LEU214
|
4.8
|
25.4
|
1.0
|
|
HE2
|
A:HIS208
|
4.9
|
21.6
|
1.0
|
|
HB2
|
A:TYR234
|
4.9
|
18.8
|
1.0
|
|
HD2
|
A:PRO241
|
4.9
|
18.4
|
1.0
|
|
CG
|
A:TYR217
|
5.0
|
18.7
|
1.0
|
|
CA
|
A:GLY240
|
5.0
|
13.9
|
1.0
|
|
N
|
A:HIS208
|
5.0
|
15.5
|
1.0
|
|
C
|
A:GLY240
|
5.0
|
14.4
|
1.0
|
|
Iron binding site 3 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 3 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:14.5
occ:1.00
|
FE3
|
A:SF4301
|
0.0
|
14.5
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
14.0
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
15.2
|
1.0
|
|
SG
|
A:CYS232
|
2.3
|
14.5
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
14.2
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
15.3
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
14.7
|
1.0
|
|
FE1
|
A:SF4301
|
2.8
|
13.7
|
1.0
|
|
H
|
A:ARG233
|
3.1
|
15.7
|
1.0
|
|
HB2
|
A:TYR217
|
3.3
|
22.2
|
1.0
|
|
CB
|
A:CYS232
|
3.5
|
14.3
|
1.0
|
|
HB2
|
A:CYS232
|
3.5
|
17.2
|
1.0
|
|
HA
|
A:CYS232
|
3.6
|
16.9
|
1.0
|
|
H
|
A:TYR234
|
3.7
|
17.3
|
1.0
|
|
HD1
|
A:TYR217
|
3.7
|
23.2
|
1.0
|
|
HB2
|
A:TYR213
|
3.8
|
23.0
|
1.0
|
|
HB2
|
A:TYR234
|
3.8
|
18.8
|
1.0
|
|
N
|
A:ARG233
|
3.8
|
13.1
|
1.0
|
|
S3
|
A:SF4301
|
3.9
|
14.6
|
1.0
|
|
CA
|
A:CYS232
|
4.0
|
14.1
|
1.0
|
|
N
|
A:TYR234
|
4.2
|
14.4
|
1.0
|
|
HE1
|
A:HIS208
|
4.2
|
20.7
|
1.0
|
|
CB
|
A:TYR217
|
4.3
|
18.5
|
1.0
|
|
HB3
|
A:CYS232
|
4.3
|
17.2
|
1.0
|
|
C
|
A:CYS232
|
4.3
|
13.9
|
1.0
|
|
HB2
|
A:ARG233
|
4.4
|
14.9
|
1.0
|
|
CD1
|
A:TYR217
|
4.4
|
19.4
|
1.0
|
|
ND1
|
A:HIS208
|
4.4
|
16.3
|
1.0
|
|
HB3
|
A:CYS238
|
4.5
|
15.7
|
1.0
|
|
HB3
|
A:TYR213
|
4.6
|
23.0
|
1.0
|
|
CB
|
A:TYR213
|
4.6
|
19.2
|
1.0
|
|
CB
|
A:TYR234
|
4.6
|
15.6
|
1.0
|
|
O
|
A:TYR213
|
4.6
|
18.2
|
1.0
|
|
HB3
|
A:TYR217
|
4.7
|
22.2
|
1.0
|
|
CE1
|
A:HIS208
|
4.7
|
17.2
|
1.0
|
|
CA
|
A:ARG233
|
4.7
|
12.7
|
1.0
|
|
CG
|
A:TYR217
|
4.7
|
18.7
|
1.0
|
|
HD3
|
A:ARG233
|
4.7
|
17.0
|
1.0
|
|
HA
|
A:TYR234
|
4.8
|
17.5
|
1.0
|
|
HA
|
A:LEU214
|
4.8
|
23.4
|
1.0
|
|
C
|
A:ARG233
|
4.8
|
13.4
|
1.0
|
|
CA
|
A:TYR234
|
4.8
|
14.6
|
1.0
|
|
SG
|
A:CYS211
|
4.8
|
15.7
|
1.0
|
|
H
|
A:TYR217
|
4.9
|
22.7
|
1.0
|
|
SG
|
A:CYS238
|
4.9
|
13.0
|
1.0
|
|
HB3
|
A:TYR234
|
4.9
|
18.8
|
1.0
|
|
C
|
A:TYR213
|
5.0
|
18.3
|
1.0
|
|
HD2
|
A:TYR213
|
5.0
|
25.1
|
1.0
|
|
Iron binding site 4 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 4 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:14.7
occ:1.00
|
FE4
|
A:SF4301
|
0.0
|
14.7
|
1.0
|
|
SG
|
A:CYS211
|
2.3
|
15.7
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
15.2
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
14.0
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
14.6
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
15.3
|
1.0
|
|
FE1
|
A:SF4301
|
2.7
|
13.7
|
1.0
|
|
FE3
|
A:SF4301
|
2.7
|
14.5
|
1.0
|
|
HB3
|
A:CYS211
|
3.0
|
19.8
|
1.0
|
|
CB
|
A:CYS211
|
3.1
|
16.5
|
1.0
|
|
HB2
|
A:CYS211
|
3.2
|
19.8
|
1.0
|
|
HB2
|
A:TYR213
|
3.2
|
23.0
|
1.0
|
|
HG12
|
A:VAL260
|
3.3
|
16.4
|
1.0
|
|
HD2
|
A:TYR213
|
3.6
|
25.1
|
1.0
|
|
S4
|
A:SF4301
|
3.9
|
14.2
|
1.0
|
|
H
|
A:TYR213
|
3.9
|
21.0
|
1.0
|
|
HA
|
A:HIS208
|
4.0
|
19.5
|
1.0
|
|
CB
|
A:TYR213
|
4.1
|
19.2
|
1.0
|
|
CG1
|
A:VAL260
|
4.2
|
13.7
|
1.0
|
|
HG13
|
A:VAL260
|
4.2
|
16.4
|
1.0
|
|
CD2
|
A:TYR213
|
4.4
|
20.9
|
1.0
|
|
ND1
|
A:HIS208
|
4.5
|
16.3
|
1.0
|
|
CA
|
A:CYS211
|
4.5
|
17.0
|
1.0
|
|
HG11
|
A:VAL260
|
4.6
|
16.4
|
1.0
|
|
C
|
A:TYR213
|
4.6
|
18.3
|
1.0
|
|
HG22
|
A:VAL260
|
4.6
|
16.5
|
1.0
|
|
N
|
A:TYR213
|
4.6
|
17.5
|
1.0
|
|
H
|
A:ARG233
|
4.7
|
15.7
|
1.0
|
|
CA
|
A:TYR213
|
4.7
|
18.4
|
1.0
|
|
HA
|
A:LEU214
|
4.7
|
23.4
|
1.0
|
|
HB3
|
A:TYR213
|
4.7
|
23.0
|
1.0
|
|
N
|
A:LEU214
|
4.7
|
18.2
|
1.0
|
|
HG21
|
A:ILE207
|
4.7
|
19.4
|
0.5
|
|
HG21
|
A:ILE207
|
4.8
|
20.3
|
0.5
|
|
SG
|
A:CYS238
|
4.8
|
13.0
|
1.0
|
|
CG
|
A:TYR213
|
4.8
|
20.3
|
1.0
|
|
H
|
A:LEU214
|
4.8
|
21.8
|
1.0
|
|
HA
|
A:CYS211
|
4.9
|
20.4
|
1.0
|
|
CA
|
A:HIS208
|
4.9
|
16.3
|
1.0
|
|
SG
|
A:CYS232
|
4.9
|
14.5
|
1.0
|
|
HD3
|
A:ARG233
|
5.0
|
17.0
|
1.0
|
|
HH2
|
A:TRP258
|
5.0
|
15.3
|
1.0
|
|
Iron binding site 5 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 5 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:10.6
occ:1.00
|
FE1
|
A:SF4302
|
0.0
|
10.6
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
11.2
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
10.8
|
1.0
|
|
SG
|
A:CYS268
|
2.3
|
10.7
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
11.5
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
11.0
|
1.0
|
|
FE2
|
A:SF4302
|
2.8
|
11.0
|
1.0
|
|
FE4
|
A:SF4302
|
2.8
|
11.3
|
1.0
|
|
H
|
A:CYS268
|
3.0
|
12.6
|
1.0
|
|
HB3
|
A:CYS268
|
3.3
|
13.1
|
1.0
|
|
CB
|
A:CYS268
|
3.4
|
10.9
|
1.0
|
|
HG13
|
A:VAL269
|
3.7
|
11.5
|
1.0
|
|
N
|
A:CYS268
|
3.7
|
10.5
|
1.0
|
|
HH12
|
B:ARG182
|
3.7
|
13.1
|
1.0
|
|
HH22
|
B:ARG182
|
3.8
|
15.3
|
1.0
|
|
S1
|
A:SF4302
|
3.9
|
11.6
|
1.0
|
|
NH1
|
B:ARG182
|
4.0
|
10.9
|
1.0
|
|
NH2
|
B:ARG182
|
4.0
|
12.8
|
1.0
|
|
CA
|
A:CYS268
|
4.1
|
10.8
|
1.0
|
|
H
|
A:VAL269
|
4.1
|
12.0
|
1.0
|
|
CZ
|
B:ARG182
|
4.2
|
11.8
|
1.0
|
|
HB2
|
A:CYS268
|
4.2
|
13.1
|
1.0
|
|
HH11
|
B:ARG182
|
4.5
|
13.1
|
1.0
|
|
HH21
|
B:ARG182
|
4.5
|
15.3
|
1.0
|
|
N
|
A:VAL269
|
4.5
|
10.0
|
1.0
|
|
H
|
A:GLY267
|
4.5
|
13.1
|
1.0
|
|
HH2
|
A:TRP165
|
4.6
|
14.6
|
1.0
|
|
C
|
A:CYS268
|
4.6
|
10.6
|
1.0
|
|
H
|
A:ILE266
|
4.6
|
13.0
|
1.0
|
|
CG1
|
A:VAL269
|
4.7
|
9.6
|
1.0
|
|
HG21
|
A:VAL269
|
4.7
|
11.6
|
1.0
|
|
HG12
|
A:ILE266
|
4.7
|
13.2
|
1.0
|
|
H
|
A:CYS159
|
4.7
|
10.8
|
1.0
|
|
HZ2
|
A:TRP252
|
4.7
|
12.8
|
1.0
|
|
HG22
|
A:THR243
|
4.7
|
15.3
|
1.0
|
|
SG
|
A:CYS259
|
4.8
|
11.1
|
1.0
|
|
SG
|
A:CYS247
|
4.8
|
11.7
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
11.3
|
1.0
|
|
C
|
A:GLY267
|
4.8
|
10.8
|
1.0
|
|
HA2
|
A:GLY158
|
4.9
|
10.8
|
1.0
|
|
N
|
A:GLY267
|
4.9
|
10.9
|
1.0
|
|
HG13
|
A:ILE266
|
4.9
|
13.2
|
1.0
|
|
HA
|
A:CYS268
|
4.9
|
12.9
|
1.0
|
|
HG12
|
A:VAL269
|
4.9
|
11.5
|
1.0
|
|
HE22
|
B:GLN187
|
5.0
|
14.3
|
1.0
|
|
Iron binding site 6 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 6 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:11.0
occ:1.00
|
FE2
|
A:SF4302
|
0.0
|
11.0
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
11.5
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
11.6
|
1.0
|
|
SG
|
A:CYS265
|
2.3
|
11.3
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
10.8
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
11.0
|
1.0
|
|
FE4
|
A:SF4302
|
2.7
|
11.3
|
1.0
|
|
FE1
|
A:SF4302
|
2.8
|
10.6
|
1.0
|
|
H
|
A:GLY267
|
3.3
|
13.1
|
1.0
|
|
HA
|
A:CYS265
|
3.3
|
13.2
|
1.0
|
|
CB
|
A:CYS265
|
3.3
|
11.2
|
1.0
|
|
HB2
|
A:CYS265
|
3.4
|
13.5
|
1.0
|
|
HG22
|
A:THR243
|
3.4
|
15.3
|
1.0
|
|
HD13
|
A:ILE207
|
3.5
|
16.6
|
0.5
|
|
HD12
|
A:ILE207
|
3.5
|
16.6
|
0.5
|
|
H
|
A:ILE266
|
3.6
|
13.0
|
1.0
|
|
HD11
|
A:ILE207
|
3.7
|
16.6
|
0.5
|
|
H
|
A:CYS268
|
3.7
|
12.6
|
1.0
|
|
CD1
|
A:ILE207
|
3.8
|
13.9
|
0.5
|
|
CA
|
A:CYS265
|
3.8
|
11.0
|
1.0
|
|
S2
|
A:SF4302
|
3.9
|
11.2
|
1.0
|
|
HB2
|
A:CYS259
|
4.0
|
13.5
|
1.0
|
|
N
|
A:GLY267
|
4.1
|
10.9
|
1.0
|
|
N
|
A:ILE266
|
4.1
|
10.8
|
1.0
|
|
HB3
|
A:CYS265
|
4.2
|
13.5
|
1.0
|
|
HA2
|
A:GLY267
|
4.3
|
13.6
|
1.0
|
|
HD11
|
A:ILE207
|
4.3
|
19.3
|
0.5
|
|
C
|
A:CYS265
|
4.4
|
10.7
|
1.0
|
|
CG2
|
A:THR243
|
4.4
|
12.7
|
1.0
|
|
HG13
|
A:ILE207
|
4.4
|
20.0
|
0.5
|
|
N
|
A:CYS268
|
4.5
|
10.5
|
1.0
|
|
HG21
|
A:THR243
|
4.6
|
15.3
|
1.0
|
|
CA
|
A:GLY267
|
4.6
|
11.3
|
1.0
|
|
HD12
|
A:ILE207
|
4.7
|
19.3
|
0.5
|
|
CB
|
A:CYS259
|
4.7
|
11.2
|
1.0
|
|
SG
|
A:CYS259
|
4.7
|
11.1
|
1.0
|
|
HG1
|
A:THR243
|
4.7
|
15.8
|
1.0
|
|
HG23
|
A:THR243
|
4.9
|
15.3
|
1.0
|
|
HB3
|
A:CYS259
|
4.9
|
13.5
|
1.0
|
|
CD1
|
A:ILE207
|
4.9
|
16.1
|
0.5
|
|
SG
|
A:CYS268
|
4.9
|
10.7
|
1.0
|
|
SG
|
A:CYS247
|
4.9
|
11.7
|
1.0
|
|
HG23
|
A:VAL260
|
4.9
|
16.5
|
1.0
|
|
HG12
|
A:ILE266
|
5.0
|
13.2
|
1.0
|
|
HB2
|
A:CYS247
|
5.0
|
14.1
|
1.0
|
|
Iron binding site 7 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 7 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:11.0
occ:1.00
|
FE3
|
A:SF4302
|
0.0
|
11.0
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
11.2
|
1.0
|
|
SG
|
A:CYS259
|
2.3
|
11.1
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
10.8
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
11.6
|
1.0
|
|
FE4
|
A:SF4302
|
2.7
|
11.3
|
1.0
|
|
FE2
|
A:SF4302
|
2.7
|
11.0
|
1.0
|
|
FE1
|
A:SF4302
|
2.7
|
10.6
|
1.0
|
|
HB2
|
A:CYS259
|
2.8
|
13.5
|
1.0
|
|
CB
|
A:CYS259
|
3.1
|
11.2
|
1.0
|
|
HE22
|
B:GLN187
|
3.4
|
14.3
|
1.0
|
|
HB3
|
A:CYS259
|
3.5
|
13.5
|
1.0
|
|
S3
|
A:SF4302
|
3.8
|
11.5
|
1.0
|
|
H
|
A:CYS259
|
3.9
|
13.1
|
1.0
|
|
HA
|
A:CYS265
|
3.9
|
13.2
|
1.0
|
|
HD3
|
B:ARG182
|
4.2
|
13.8
|
1.0
|
|
NE2
|
B:GLN187
|
4.2
|
11.9
|
1.0
|
|
CZ
|
B:ARG182
|
4.2
|
11.8
|
1.0
|
|
HE1
|
A:TRP252
|
4.3
|
12.2
|
1.0
|
|
NE
|
B:ARG182
|
4.3
|
11.9
|
1.0
|
|
HE21
|
B:GLN187
|
4.4
|
14.3
|
1.0
|
|
NH2
|
B:ARG182
|
4.4
|
12.8
|
1.0
|
|
CA
|
A:CYS259
|
4.4
|
11.1
|
1.0
|
|
H
|
A:ILE266
|
4.4
|
13.0
|
1.0
|
|
NH1
|
B:ARG182
|
4.5
|
10.9
|
1.0
|
|
HE
|
B:ARG182
|
4.5
|
14.3
|
1.0
|
|
N
|
A:CYS259
|
4.5
|
10.9
|
1.0
|
|
HH21
|
B:ARG182
|
4.5
|
15.3
|
1.0
|
|
HH22
|
B:ARG182
|
4.6
|
15.3
|
1.0
|
|
SG
|
A:CYS247
|
4.6
|
11.7
|
1.0
|
|
NE1
|
A:TRP252
|
4.7
|
10.2
|
1.0
|
|
HH11
|
B:ARG182
|
4.7
|
13.1
|
1.0
|
|
SG
|
A:CYS268
|
4.7
|
10.7
|
1.0
|
|
HH12
|
B:ARG182
|
4.7
|
13.1
|
1.0
|
|
HB3
|
A:CYS247
|
4.8
|
14.1
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
11.3
|
1.0
|
|
CD
|
B:ARG182
|
4.8
|
11.5
|
1.0
|
|
HB2
|
A:CYS265
|
4.8
|
13.5
|
1.0
|
|
HG3
|
B:GLN187
|
4.8
|
12.9
|
1.0
|
|
CA
|
A:CYS265
|
4.8
|
11.0
|
1.0
|
|
HG12
|
A:ILE266
|
4.9
|
13.2
|
1.0
|
|
HA
|
A:CYS259
|
4.9
|
13.3
|
1.0
|
|
Iron binding site 8 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 8 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:11.3
occ:1.00
|
FE4
|
A:SF4302
|
0.0
|
11.3
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
11.6
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
11.5
|
1.0
|
|
SG
|
A:CYS247
|
2.3
|
11.7
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
11.2
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
11.0
|
1.0
|
|
FE2
|
A:SF4302
|
2.7
|
11.0
|
1.0
|
|
FE1
|
A:SF4302
|
2.8
|
10.6
|
1.0
|
|
HB2
|
A:CYS247
|
3.2
|
14.1
|
1.0
|
|
CB
|
A:CYS247
|
3.3
|
11.8
|
1.0
|
|
HD12
|
A:ILE207
|
3.4
|
16.6
|
0.5
|
|
HB3
|
A:CYS247
|
3.4
|
14.1
|
1.0
|
|
HE1
|
A:TRP252
|
3.5
|
12.2
|
1.0
|
|
HD12
|
A:ILE207
|
3.8
|
19.3
|
0.5
|
|
HH2
|
A:TRP165
|
3.8
|
14.6
|
1.0
|
|
HB3
|
A:ALA245
|
3.9
|
16.2
|
1.0
|
|
S4
|
A:SF4302
|
3.9
|
10.8
|
1.0
|
|
HD13
|
A:ILE207
|
3.9
|
16.6
|
0.5
|
|
HD11
|
A:ILE207
|
4.1
|
19.3
|
0.5
|
|
CD1
|
A:ILE207
|
4.1
|
13.9
|
0.5
|
|
HB2
|
A:ALA245
|
4.2
|
16.2
|
1.0
|
|
NE1
|
A:TRP252
|
4.2
|
10.2
|
1.0
|
|
CD1
|
A:ILE207
|
4.4
|
16.1
|
0.5
|
|
CB
|
A:ALA245
|
4.4
|
13.5
|
1.0
|
|
H
|
A:CYS247
|
4.5
|
15.6
|
1.0
|
|
HZ2
|
A:TRP252
|
4.5
|
12.8
|
1.0
|
|
HD11
|
A:ILE207
|
4.6
|
16.6
|
0.5
|
|
CH2
|
A:TRP165
|
4.6
|
12.2
|
1.0
|
|
HE3
|
A:TRP258
|
4.6
|
15.6
|
1.0
|
|
SG
|
A:CYS259
|
4.7
|
11.1
|
1.0
|
|
HG13
|
A:VAL269
|
4.7
|
11.5
|
1.0
|
|
HB2
|
A:CYS259
|
4.7
|
13.5
|
1.0
|
|
CA
|
A:CYS247
|
4.7
|
12.9
|
1.0
|
|
HB1
|
A:ALA245
|
4.7
|
16.2
|
1.0
|
|
HZ2
|
A:TRP165
|
4.8
|
14.3
|
1.0
|
|
HG22
|
A:THR243
|
4.8
|
15.3
|
1.0
|
|
SG
|
A:CYS268
|
4.8
|
10.7
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
11.3
|
1.0
|
|
HG13
|
A:ILE207
|
4.9
|
20.0
|
0.5
|
|
CE2
|
A:TRP252
|
5.0
|
10.2
|
1.0
|
|
Iron binding site 9 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 9 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:9.6
occ:0.59
|
FE1
|
A:SF4303
|
0.0
|
9.6
|
0.6
|
|
FE1
|
A:6ML304
|
0.4
|
7.8
|
0.4
|
|
O12
|
A:6ML304
|
1.5
|
8.7
|
0.4
|
|
S2
|
A:SF4303
|
2.3
|
9.1
|
0.6
|
|
S3
|
A:6ML304
|
2.3
|
8.6
|
0.4
|
|
S4
|
A:SF4303
|
2.3
|
8.8
|
0.6
|
|
S3
|
A:SF4303
|
2.3
|
10.2
|
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
|
9.9
|
0.6
|
|
FE3
|
A:6ML304
|
2.7
|
9.2
|
0.4
|
|
FE3
|
A:SF4303
|
2.7
|
8.2
|
0.6
|
|
FE2
|
A:SF4303
|
2.7
|
9.7
|
0.6
|
|
H
|
A:CYS18
|
2.8
|
10.8
|
1.0
|
|
FE2
|
A:6ML304
|
2.9
|
9.7
|
0.4
|
|
FE4
|
A:6ML304
|
3.1
|
8.8
|
0.4
|
|
HB3
|
A:CYS18
|
3.3
|
10.0
|
1.0
|
|
H
|
A:GLY20
|
3.3
|
12.1
|
1.0
|
|
CB
|
A:CYS18
|
3.4
|
8.4
|
1.0
|
|
O24
|
A:6ML304
|
3.4
|
9.9
|
0.4
|
|
HE2
|
B:HIS185
|
3.4
|
11.9
|
1.0
|
|
N
|
A:CYS18
|
3.6
|
8.9
|
1.0
|
|
HA3
|
A:GLY20
|
3.7
|
12.1
|
1.0
|
|
S1
|
A:SF4303
|
3.8
|
9.5
|
0.6
|
|
S1
|
A:6ML304
|
3.9
|
10.7
|
0.4
|
|
CA
|
A:CYS18
|
3.9
|
8.1
|
1.0
|
|
S4
|
A:6ML304
|
4.0
|
8.9
|
0.4
|
|
N
|
A:GLY20
|
4.0
|
10.1
|
1.0
|
|
H
|
A:CYS21
|
4.2
|
12.7
|
0.4
|
|
HB2
|
A:CYS18
|
4.2
|
10.0
|
1.0
|
|
HG3
|
B:ARG73
|
4.2
|
9.2
|
1.0
|
|
H
|
A:CYS21
|
4.2
|
13.1
|
0.6
|
|
NE2
|
B:HIS185
|
4.2
|
9.9
|
1.0
|
|
CA
|
A:GLY20
|
4.3
|
10.0
|
1.0
|
|
C
|
A:CYS18
|
4.4
|
8.4
|
1.0
|
|
HA2
|
A:GLY17
|
4.4
|
13.1
|
1.0
|
|
H
|
A:THR19
|
4.4
|
10.3
|
1.0
|
|
N
|
A:THR19
|
4.5
|
8.6
|
1.0
|
|
O
|
B:HOH795
|
4.6
|
11.7
|
1.0
|
|
HA
|
B:ARG73
|
4.6
|
9.5
|
1.0
|
|
C
|
A:GLY17
|
4.7
|
9.9
|
1.0
|
|
HB3
|
B:ARG73
|
4.7
|
9.5
|
1.0
|
|
N
|
A:CYS21
|
4.7
|
10.5
|
0.4
|
|
N
|
A:CYS21
|
4.7
|
10.9
|
0.6
|
|
SG
|
A:CYS21
|
4.8
|
10.1
|
0.6
|
|
HA
|
A:CYS18
|
4.8
|
9.8
|
1.0
|
|
SG
|
A:CYS159
|
4.8
|
9.5
|
1.0
|
|
SG
|
A:CYS121
|
4.9
|
10.4
|
1.0
|
|
O
|
B:ARG73
|
4.9
|
8.2
|
1.0
|
|
CA
|
A:GLY17
|
4.9
|
10.9
|
1.0
|
|
C
|
A:GLY20
|
4.9
|
10.1
|
1.0
|
|
CG
|
B:ARG73
|
4.9
|
7.6
|
1.0
|
|
HG2
|
B:ARG73
|
5.0
|
9.2
|
1.0
|
|
Iron binding site 10 out
of 36 in 6z8j
Go back to
Iron Binding Sites List in 6z8j
Iron binding site 10 out
of 36 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:9.7
occ:0.59
|
FE2
|
A:SF4303
|
0.0
|
9.7
|
0.6
|
|
FE4
|
A:6ML304
|
0.4
|
8.8
|
0.4
|
|
O24
|
A:6ML304
|
1.8
|
9.9
|
0.4
|
|
S3
|
A:6ML304
|
2.1
|
8.6
|
0.4
|
|
S4
|
A:SF4303
|
2.3
|
8.8
|
0.6
|
|
S1
|
A:SF4303
|
2.3
|
9.5
|
0.6
|
|
S3
|
A:SF4303
|
2.3
|
10.2
|
0.6
|
|
SG
|
A:CYS121
|
2.4
|
10.4
|
1.0
|
|
S4
|
A:6ML304
|
2.5
|
8.9
|
0.4
|
|
FE3
|
A:6ML304
|
2.6
|
9.2
|
0.4
|
|
FE3
|
A:SF4303
|
2.7
|
8.2
|
0.6
|
|
FE1
|
A:SF4303
|
2.7
|
9.6
|
0.6
|
|
FE4
|
A:SF4303
|
2.8
|
9.9
|
0.6
|
|
FE1
|
A:6ML304
|
3.0
|
7.8
|
0.4
|
|
FE2
|
A:6ML304
|
3.0
|
9.7
|
0.4
|
|
HB2
|
A:CYS121
|
3.1
|
12.6
|
1.0
|
|
O12
|
A:6ML304
|
3.2
|
8.7
|
0.4
|
|
CB
|
A:CYS121
|
3.4
|
10.4
|
1.0
|
|
H
|
A:CYS121
|
3.4
|
10.3
|
1.0
|
|
O
|
A:HOH411
|
3.8
|
9.7
|
1.0
|
|
HA2
|
A:GLY17
|
3.8
|
13.1
|
1.0
|
|
S2
|
A:SF4303
|
3.9
|
9.1
|
0.6
|
|
O
|
B:HOH795
|
3.9
|
11.7
|
1.0
|
|
H
|
A:CYS18
|
4.0
|
10.8
|
1.0
|
|
S2
|
A:6ML304
|
4.0
|
8.0
|
0.4
|
|
HB3
|
A:CYS121
|
4.1
|
12.6
|
1.0
|
|
S1
|
A:6ML304
|
4.1
|
10.7
|
0.4
|
|
O
|
A:HOH547
|
4.1
|
11.8
|
1.0
|
|
N
|
A:CYS121
|
4.1
|
8.6
|
1.0
|
|
HA2
|
A:GLY78
|
4.2
|
12.2
|
1.0
|
|
CA
|
A:CYS121
|
4.3
|
9.9
|
1.0
|
|
SG
|
A:CYS159
|
4.6
|
9.5
|
1.0
|
|
HA3
|
A:GLY119
|
4.6
|
10.3
|
1.0
|
|
H
|
A:GLY78
|
4.7
|
13.7
|
1.0
|
|
N
|
A:CYS18
|
4.7
|
8.9
|
1.0
|
|
CA
|
A:GLY17
|
4.7
|
10.9
|
1.0
|
|
SG
|
A:CYS21
|
4.8
|
10.1
|
0.6
|
|
HA
|
A:CYS121
|
4.8
|
11.9
|
1.0
|
|
O
|
A:GLN16
|
4.9
|
11.0
|
1.0
|
|
HA3
|
A:GLY17
|
4.9
|
13.1
|
1.0
|
|
HB3
|
A:CYS18
|
4.9
|
10.0
|
1.0
|
|
HA
|
A:CYS159
|
4.9
|
11.5
|
1.0
|
|
SG
|
A:CYS18
|
5.0
|
10.5
|
1.0
|
|
H
|
A:THR120
|
5.0
|
9.9
|
1.0
|
|
Reference:
S.Zacarias,
A.Temporao,
P.Carpentier,
P.Van Der Linden,
I.A.C.Pereira,
P.M.Matias.
Exploring the Gas Access Routes in A [Nifese] Hydrogenase Using Crystals Pressurized with Krypton and Oxygen. J.Biol.Inorg.Chem. V. 25 863 2020.
ISSN: ESSN 1432-1327
PubMed: 32865640
DOI: 10.1007/S00775-020-01814-Y
Page generated: Wed Aug 7 16:58:45 2024
|
