Iron in PDB 6z9o: Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
Enzymatic activity of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
All present enzymatic activity of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld:
1.12.7.2;
Protein crystallography data
The structure of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld, PDB code: 6z9o
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)
|
50.98 /
1.53
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.096,
63.503,
109.942,
90.00,
104.74,
90.00
|
|
R / Rfree (%)
|
16.1 /
18.5
|
Other elements in 6z9o:
The structure of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld 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 Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
(pdb code 6z9o). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the
Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld, PDB code: 6z9o:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 1 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:19.0
occ:1.00
|
FE1
|
A:SF4301
|
0.0
|
19.0
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
21.9
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
23.6
|
1.0
|
|
SG
|
A:CYS238
|
2.3
|
19.7
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
21.9
|
1.0
|
|
FE4
|
A:SF4301
|
2.8
|
20.5
|
1.0
|
|
FE3
|
A:SF4301
|
2.8
|
21.6
|
1.0
|
|
FE2
|
A:SF4301
|
2.8
|
20.5
|
1.0
|
|
HB3
|
A:CYS238
|
3.0
|
25.6
|
1.0
|
|
CB
|
A:CYS238
|
3.2
|
21.2
|
1.0
|
|
HB2
|
A:CYS238
|
3.5
|
25.6
|
1.0
|
|
HB2
|
A:ARG233
|
3.7
|
23.8
|
1.0
|
|
HD3
|
A:PRO241
|
3.7
|
24.5
|
1.0
|
|
HA3
|
A:GLY240
|
3.8
|
22.9
|
1.0
|
|
H
|
A:GLY240
|
3.9
|
24.4
|
1.0
|
|
HG11
|
A:VAL260
|
3.9
|
26.8
|
1.0
|
|
S1
|
A:SF4301
|
4.0
|
24.4
|
1.0
|
|
H
|
A:ARG233
|
4.1
|
26.7
|
1.0
|
|
HG13
|
A:VAL260
|
4.2
|
26.8
|
1.0
|
|
HG22
|
A:VAL260
|
4.4
|
24.0
|
1.0
|
|
HG21
|
A:VAL260
|
4.4
|
24.0
|
1.0
|
|
CG1
|
A:VAL260
|
4.5
|
22.3
|
1.0
|
|
N
|
A:GLY240
|
4.5
|
20.3
|
1.0
|
|
CA
|
A:CYS238
|
4.5
|
20.2
|
1.0
|
|
CB
|
A:ARG233
|
4.6
|
19.8
|
1.0
|
|
HA
|
A:TYR234
|
4.6
|
28.0
|
1.0
|
|
CA
|
A:GLY240
|
4.6
|
19.1
|
1.0
|
|
CD
|
A:PRO241
|
4.6
|
20.4
|
1.0
|
|
SG
|
A:CYS232
|
4.7
|
23.3
|
1.0
|
|
HB2
|
A:HIS208
|
4.7
|
26.2
|
1.0
|
|
SG
|
A:CYS211
|
4.7
|
21.2
|
1.0
|
|
C
|
A:CYS238
|
4.8
|
20.3
|
1.0
|
|
ND1
|
A:HIS208
|
4.8
|
24.1
|
1.0
|
|
HB2
|
A:TYR234
|
4.8
|
31.8
|
1.0
|
|
CG2
|
A:VAL260
|
4.8
|
20.0
|
1.0
|
|
N
|
A:TYR234
|
4.8
|
23.5
|
1.0
|
|
N
|
A:ARG233
|
4.8
|
22.2
|
1.0
|
|
HB3
|
A:ARG233
|
4.9
|
23.8
|
1.0
|
|
O
|
A:CYS238
|
4.9
|
19.5
|
1.0
|
|
HA
|
A:HIS208
|
4.9
|
24.1
|
1.0
|
|
HD2
|
A:PRO241
|
4.9
|
24.5
|
1.0
|
|
H
|
A:TYR234
|
4.9
|
28.2
|
1.0
|
|
C
|
A:ARG233
|
4.9
|
22.2
|
1.0
|
|
HA
|
A:CYS238
|
5.0
|
24.4
|
1.0
|
|
HD3
|
A:ARG233
|
5.0
|
25.3
|
1.0
|
|
Iron binding site 2 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 2 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:20.5
occ:1.00
|
FE2
|
A:SF4301
|
0.0
|
20.5
|
1.0
|
|
ND1
|
A:HIS208
|
2.1
|
24.1
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
21.9
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
24.4
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
23.6
|
1.0
|
|
FE4
|
A:SF4301
|
2.7
|
20.5
|
1.0
|
|
FE3
|
A:SF4301
|
2.7
|
21.6
|
1.0
|
|
FE1
|
A:SF4301
|
2.8
|
19.0
|
1.0
|
|
CE1
|
A:HIS208
|
3.0
|
25.8
|
1.0
|
|
HB2
|
A:HIS208
|
3.1
|
26.2
|
1.0
|
|
CG
|
A:HIS208
|
3.1
|
21.1
|
1.0
|
|
HE1
|
A:HIS208
|
3.2
|
31.0
|
1.0
|
|
HA
|
A:HIS208
|
3.3
|
24.1
|
1.0
|
|
HD3
|
A:PRO241
|
3.4
|
24.5
|
1.0
|
|
CB
|
A:HIS208
|
3.5
|
21.8
|
1.0
|
|
HG3
|
A:PRO241
|
3.8
|
29.3
|
1.0
|
|
CA
|
A:HIS208
|
3.9
|
20.0
|
1.0
|
|
S2
|
A:SF4301
|
3.9
|
21.9
|
1.0
|
|
HB3
|
A:CYS211
|
4.1
|
27.0
|
1.0
|
|
NE2
|
A:HIS208
|
4.2
|
26.3
|
1.0
|
|
CD
|
A:PRO241
|
4.2
|
20.4
|
1.0
|
|
CD2
|
A:HIS208
|
4.2
|
25.1
|
1.0
|
|
HB2
|
A:CYS211
|
4.3
|
27.0
|
1.0
|
|
HA3
|
A:GLY240
|
4.3
|
22.9
|
1.0
|
|
HB2
|
A:TYR217
|
4.4
|
31.1
|
1.0
|
|
HD13
|
A:LEU214
|
4.4
|
33.1
|
1.0
|
|
HB3
|
A:HIS208
|
4.4
|
26.2
|
1.0
|
|
HD1
|
A:TYR217
|
4.4
|
36.7
|
1.0
|
|
CG
|
A:PRO241
|
4.4
|
24.3
|
1.0
|
|
CB
|
A:CYS211
|
4.5
|
22.4
|
1.0
|
|
O
|
A:HIS208
|
4.5
|
20.7
|
1.0
|
|
HD12
|
A:LEU214
|
4.6
|
33.1
|
1.0
|
|
SG
|
A:CYS211
|
4.6
|
21.2
|
1.0
|
|
SG
|
A:CYS232
|
4.7
|
23.3
|
1.0
|
|
CD1
|
A:TYR217
|
4.7
|
30.5
|
1.0
|
|
C
|
A:HIS208
|
4.7
|
22.5
|
1.0
|
|
N
|
A:PRO241
|
4.8
|
20.1
|
1.0
|
|
SG
|
A:CYS238
|
4.8
|
19.7
|
1.0
|
|
HA
|
A:LEU214
|
4.8
|
29.1
|
1.0
|
|
HB2
|
A:TYR234
|
4.9
|
31.8
|
1.0
|
|
HE2
|
A:HIS208
|
4.9
|
31.6
|
1.0
|
|
HG2
|
A:PRO241
|
4.9
|
29.3
|
1.0
|
|
HD2
|
A:PRO241
|
4.9
|
24.5
|
1.0
|
|
CG
|
A:TYR217
|
5.0
|
28.4
|
1.0
|
|
HD1
|
A:TYR234
|
5.0
|
32.5
|
1.0
|
|
CD1
|
A:LEU214
|
5.0
|
27.6
|
1.0
|
|
Iron binding site 3 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 3 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:21.6
occ:1.00
|
FE3
|
A:SF4301
|
0.0
|
21.6
|
1.0
|
|
SG
|
A:CYS232
|
2.3
|
23.3
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
21.9
|
1.0
|
|
S4
|
A:SF4301
|
2.3
|
23.6
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
24.4
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
20.5
|
1.0
|
|
FE4
|
A:SF4301
|
2.8
|
20.5
|
1.0
|
|
FE1
|
A:SF4301
|
2.8
|
19.0
|
1.0
|
|
H
|
A:ARG233
|
3.1
|
26.7
|
1.0
|
|
HB2
|
A:TYR217
|
3.4
|
31.1
|
1.0
|
|
CB
|
A:CYS232
|
3.5
|
25.1
|
1.0
|
|
HB2
|
A:CYS232
|
3.5
|
30.2
|
1.0
|
|
HD1
|
A:TYR217
|
3.7
|
36.7
|
1.0
|
|
HB2
|
A:TYR234
|
3.7
|
31.8
|
1.0
|
|
HA
|
A:CYS232
|
3.7
|
30.3
|
1.0
|
|
H
|
A:TYR234
|
3.8
|
28.2
|
1.0
|
|
N
|
A:ARG233
|
3.8
|
22.2
|
1.0
|
|
HB2
|
A:TYR213
|
3.9
|
32.0
|
1.0
|
|
S3
|
A:SF4301
|
3.9
|
21.9
|
1.0
|
|
CA
|
A:CYS232
|
4.1
|
25.2
|
1.0
|
|
N
|
A:TYR234
|
4.2
|
23.5
|
1.0
|
|
HB2
|
A:ARG233
|
4.2
|
23.8
|
1.0
|
|
HB3
|
A:CYS232
|
4.3
|
30.2
|
1.0
|
|
CB
|
A:TYR217
|
4.3
|
25.9
|
1.0
|
|
CD1
|
A:TYR217
|
4.3
|
30.5
|
1.0
|
|
C
|
A:CYS232
|
4.4
|
23.8
|
1.0
|
|
HE1
|
A:HIS208
|
4.4
|
31.0
|
1.0
|
|
ND1
|
A:HIS208
|
4.4
|
24.1
|
1.0
|
|
HB3
|
A:CYS238
|
4.5
|
25.6
|
1.0
|
|
CB
|
A:TYR234
|
4.6
|
26.4
|
1.0
|
|
O
|
A:TYR213
|
4.6
|
27.0
|
1.0
|
|
CA
|
A:ARG233
|
4.7
|
20.5
|
1.0
|
|
CG
|
A:TYR217
|
4.7
|
28.4
|
1.0
|
|
HB3
|
A:TYR217
|
4.7
|
31.1
|
1.0
|
|
HA
|
A:TYR234
|
4.7
|
28.0
|
1.0
|
|
CB
|
A:TYR213
|
4.8
|
26.6
|
1.0
|
|
C
|
A:ARG233
|
4.8
|
22.2
|
1.0
|
|
CE1
|
A:HIS208
|
4.8
|
25.8
|
1.0
|
|
CA
|
A:TYR234
|
4.8
|
23.3
|
1.0
|
|
HB3
|
A:TYR213
|
4.8
|
32.0
|
1.0
|
|
HD3
|
A:ARG233
|
4.8
|
25.3
|
1.0
|
|
HA
|
A:LEU214
|
4.8
|
29.1
|
1.0
|
|
SG
|
A:CYS211
|
4.8
|
21.2
|
1.0
|
|
SG
|
A:CYS238
|
4.9
|
19.7
|
1.0
|
|
HB3
|
A:TYR234
|
4.9
|
31.8
|
1.0
|
|
CB
|
A:ARG233
|
5.0
|
19.8
|
1.0
|
|
H
|
A:TYR217
|
5.0
|
33.1
|
1.0
|
|
C
|
A:TYR213
|
5.0
|
27.9
|
1.0
|
|
Iron binding site 4 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 4 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:20.5
occ:1.00
|
FE4
|
A:SF4301
|
0.0
|
20.5
|
1.0
|
|
SG
|
A:CYS211
|
2.2
|
21.2
|
1.0
|
|
S1
|
A:SF4301
|
2.3
|
24.4
|
1.0
|
|
S3
|
A:SF4301
|
2.3
|
21.9
|
1.0
|
|
S2
|
A:SF4301
|
2.3
|
21.9
|
1.0
|
|
FE2
|
A:SF4301
|
2.7
|
20.5
|
1.0
|
|
FE1
|
A:SF4301
|
2.8
|
19.0
|
1.0
|
|
FE3
|
A:SF4301
|
2.8
|
21.6
|
1.0
|
|
HB3
|
A:CYS211
|
3.0
|
27.0
|
1.0
|
|
CB
|
A:CYS211
|
3.1
|
22.4
|
1.0
|
|
HB2
|
A:CYS211
|
3.1
|
27.0
|
1.0
|
|
HB2
|
A:TYR213
|
3.3
|
32.0
|
1.0
|
|
HG11
|
A:VAL260
|
3.4
|
26.8
|
1.0
|
|
HD2
|
A:TYR213
|
3.6
|
31.1
|
1.0
|
|
S4
|
A:SF4301
|
3.9
|
23.6
|
1.0
|
|
HA
|
A:HIS208
|
3.9
|
24.1
|
1.0
|
|
H
|
A:TYR213
|
4.0
|
28.8
|
1.0
|
|
CG1
|
A:VAL260
|
4.3
|
22.3
|
1.0
|
|
CB
|
A:TYR213
|
4.3
|
26.6
|
1.0
|
|
HG13
|
A:VAL260
|
4.4
|
26.8
|
1.0
|
|
ND1
|
A:HIS208
|
4.5
|
24.1
|
1.0
|
|
CD2
|
A:TYR213
|
4.5
|
25.9
|
1.0
|
|
CA
|
A:CYS211
|
4.5
|
23.3
|
1.0
|
|
HG21
|
A:VAL260
|
4.6
|
24.0
|
1.0
|
|
HG12
|
A:VAL260
|
4.6
|
26.8
|
1.0
|
|
C
|
A:TYR213
|
4.6
|
27.9
|
1.0
|
|
N
|
A:TYR213
|
4.7
|
23.9
|
1.0
|
|
H
|
A:ARG233
|
4.7
|
26.7
|
1.0
|
|
HA
|
A:LEU214
|
4.7
|
29.1
|
1.0
|
|
CA
|
A:TYR213
|
4.7
|
24.9
|
1.0
|
|
N
|
A:LEU214
|
4.8
|
22.9
|
1.0
|
|
SG
|
A:CYS238
|
4.8
|
19.7
|
1.0
|
|
CA
|
A:HIS208
|
4.8
|
20.0
|
1.0
|
|
HG22
|
A:ILE207
|
4.8
|
26.6
|
1.0
|
|
HB3
|
A:TYR213
|
4.8
|
32.0
|
1.0
|
|
HA
|
A:CYS211
|
4.8
|
28.0
|
1.0
|
|
H
|
A:LEU214
|
4.9
|
27.6
|
1.0
|
|
CG
|
A:TYR213
|
4.9
|
25.1
|
1.0
|
|
SG
|
A:CYS232
|
4.9
|
23.3
|
1.0
|
|
HB2
|
A:HIS208
|
4.9
|
26.2
|
1.0
|
|
O
|
A:TYR213
|
5.0
|
27.0
|
1.0
|
|
C
|
A:CYS211
|
5.0
|
23.7
|
1.0
|
|
Iron binding site 5 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 5 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:18.9
occ:1.00
|
FE1
|
A:SF4302
|
0.0
|
18.9
|
1.0
|
|
SG
|
A:CYS268
|
2.3
|
17.6
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
19.4
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
19.0
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
19.2
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
19.1
|
1.0
|
|
FE2
|
A:SF4302
|
2.7
|
18.7
|
1.0
|
|
FE4
|
A:SF4302
|
2.8
|
18.0
|
1.0
|
|
H
|
A:CYS268
|
2.9
|
20.4
|
1.0
|
|
HB3
|
A:CYS268
|
3.3
|
21.2
|
1.0
|
|
CB
|
A:CYS268
|
3.4
|
17.6
|
1.0
|
|
HG13
|
A:VAL269
|
3.7
|
22.0
|
1.0
|
|
N
|
A:CYS268
|
3.7
|
17.0
|
1.0
|
|
HH12
|
B:ARG182
|
3.7
|
24.0
|
1.0
|
|
HH22
|
B:ARG182
|
3.7
|
23.4
|
1.0
|
|
S1
|
A:SF4302
|
3.9
|
18.0
|
1.0
|
|
CA
|
A:CYS268
|
4.0
|
17.4
|
1.0
|
|
NH1
|
B:ARG182
|
4.1
|
19.9
|
1.0
|
|
NH2
|
B:ARG182
|
4.1
|
19.4
|
1.0
|
|
H
|
A:VAL269
|
4.1
|
18.5
|
1.0
|
|
HB2
|
A:CYS268
|
4.2
|
21.2
|
1.0
|
|
CZ
|
B:ARG182
|
4.3
|
17.6
|
1.0
|
|
H
|
A:GLY267
|
4.5
|
21.6
|
1.0
|
|
HH2
|
A:TRP165
|
4.5
|
23.5
|
1.0
|
|
N
|
A:VAL269
|
4.5
|
15.4
|
1.0
|
|
HH11
|
B:ARG182
|
4.6
|
24.0
|
1.0
|
|
HH21
|
B:ARG182
|
4.6
|
23.4
|
1.0
|
|
C
|
A:CYS268
|
4.6
|
15.7
|
1.0
|
|
CG1
|
A:VAL269
|
4.6
|
18.3
|
1.0
|
|
H
|
A:ILE266
|
4.6
|
19.9
|
1.0
|
|
HG21
|
A:THR243
|
4.7
|
22.7
|
1.0
|
|
HG22
|
A:VAL269
|
4.7
|
20.6
|
1.0
|
|
HZ2
|
A:TRP252
|
4.7
|
19.9
|
1.0
|
|
H
|
A:CYS159
|
4.7
|
20.3
|
1.0
|
|
HG12
|
A:ILE266
|
4.8
|
22.4
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
18.4
|
1.0
|
|
C
|
A:GLY267
|
4.8
|
15.4
|
1.0
|
|
SG
|
A:CYS259
|
4.8
|
17.9
|
1.0
|
|
SG
|
A:CYS247
|
4.8
|
18.3
|
1.0
|
|
HG11
|
A:VAL269
|
4.9
|
22.0
|
1.0
|
|
N
|
A:GLY267
|
4.9
|
17.9
|
1.0
|
|
HG13
|
A:ILE266
|
4.9
|
22.4
|
1.0
|
|
HA
|
A:CYS268
|
4.9
|
20.9
|
1.0
|
|
HA2
|
A:GLY158
|
4.9
|
21.7
|
1.0
|
|
HA2
|
A:GLY267
|
5.0
|
20.6
|
1.0
|
|
Iron binding site 6 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 6 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:18.7
occ:1.00
|
FE2
|
A:SF4302
|
0.0
|
18.7
|
1.0
|
|
SG
|
A:CYS265
|
2.3
|
18.4
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
19.0
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
18.0
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
19.4
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
19.1
|
1.0
|
|
FE1
|
A:SF4302
|
2.7
|
18.9
|
1.0
|
|
FE4
|
A:SF4302
|
2.8
|
18.0
|
1.0
|
|
HB2
|
A:CYS265
|
3.2
|
22.2
|
1.0
|
|
CB
|
A:CYS265
|
3.3
|
18.4
|
1.0
|
|
H
|
A:GLY267
|
3.3
|
21.6
|
1.0
|
|
HA
|
A:CYS265
|
3.3
|
21.3
|
1.0
|
|
HD12
|
A:ILE207
|
3.4
|
39.6
|
1.0
|
|
HG21
|
A:THR243
|
3.5
|
22.7
|
1.0
|
|
HD11
|
A:ILE207
|
3.5
|
39.6
|
1.0
|
|
H
|
A:ILE266
|
3.6
|
19.9
|
1.0
|
|
H
|
A:CYS268
|
3.7
|
20.4
|
1.0
|
|
CD1
|
A:ILE207
|
3.8
|
33.0
|
1.0
|
|
HD13
|
A:ILE207
|
3.8
|
39.6
|
1.0
|
|
CA
|
A:CYS265
|
3.8
|
17.7
|
1.0
|
|
S2
|
A:SF4302
|
3.9
|
19.2
|
1.0
|
|
HB2
|
A:CYS259
|
4.0
|
24.3
|
1.0
|
|
N
|
A:GLY267
|
4.1
|
17.9
|
1.0
|
|
N
|
A:ILE266
|
4.1
|
16.5
|
1.0
|
|
HB3
|
A:CYS265
|
4.1
|
22.2
|
1.0
|
|
HA2
|
A:GLY267
|
4.2
|
20.6
|
1.0
|
|
C
|
A:CYS265
|
4.4
|
17.8
|
1.0
|
|
CG2
|
A:THR243
|
4.4
|
18.9
|
1.0
|
|
HG22
|
A:THR243
|
4.5
|
22.7
|
1.0
|
|
N
|
A:CYS268
|
4.5
|
17.0
|
1.0
|
|
CA
|
A:GLY267
|
4.6
|
17.1
|
1.0
|
|
CB
|
A:CYS259
|
4.7
|
20.2
|
1.0
|
|
SG
|
A:CYS259
|
4.7
|
17.9
|
1.0
|
|
HB3
|
A:CYS259
|
4.8
|
24.3
|
1.0
|
|
SG
|
A:CYS268
|
4.9
|
17.6
|
1.0
|
|
SG
|
A:CYS247
|
4.9
|
18.3
|
1.0
|
|
HG23
|
A:THR243
|
4.9
|
22.7
|
1.0
|
|
HB2
|
A:CYS247
|
4.9
|
21.6
|
1.0
|
|
HG23
|
A:VAL260
|
5.0
|
24.0
|
1.0
|
|
HG21
|
A:ILE207
|
5.0
|
26.6
|
1.0
|
|
HG12
|
A:ILE266
|
5.0
|
22.4
|
1.0
|
|
Iron binding site 7 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 7 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:19.1
occ:1.00
|
FE3
|
A:SF4302
|
0.0
|
19.1
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
19.2
|
1.0
|
|
SG
|
A:CYS259
|
2.3
|
17.9
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
18.0
|
1.0
|
|
S4
|
A:SF4302
|
2.3
|
19.4
|
1.0
|
|
FE4
|
A:SF4302
|
2.7
|
18.0
|
1.0
|
|
FE2
|
A:SF4302
|
2.7
|
18.7
|
1.0
|
|
FE1
|
A:SF4302
|
2.7
|
18.9
|
1.0
|
|
HB2
|
A:CYS259
|
2.8
|
24.3
|
1.0
|
|
CB
|
A:CYS259
|
3.1
|
20.2
|
1.0
|
|
HB3
|
A:CYS259
|
3.5
|
24.3
|
1.0
|
|
HE21
|
B:GLN187
|
3.5
|
22.6
|
1.0
|
|
S3
|
A:SF4302
|
3.8
|
19.0
|
1.0
|
|
H
|
A:CYS259
|
3.9
|
20.3
|
1.0
|
|
HA
|
A:CYS265
|
3.9
|
21.3
|
1.0
|
|
CZ
|
B:ARG182
|
4.2
|
17.6
|
1.0
|
|
NE2
|
B:GLN187
|
4.2
|
18.8
|
1.0
|
|
HE1
|
A:TRP252
|
4.3
|
21.3
|
1.0
|
|
NH2
|
B:ARG182
|
4.3
|
19.4
|
1.0
|
|
NH1
|
B:ARG182
|
4.4
|
19.9
|
1.0
|
|
CA
|
A:CYS259
|
4.4
|
16.7
|
1.0
|
|
H
|
A:ILE266
|
4.4
|
19.9
|
1.0
|
|
HE22
|
B:GLN187
|
4.4
|
22.6
|
1.0
|
|
NE
|
B:ARG182
|
4.4
|
19.4
|
1.0
|
|
HH22
|
B:ARG182
|
4.5
|
23.4
|
1.0
|
|
HD3
|
B:ARG182
|
4.5
|
23.0
|
1.0
|
|
HH21
|
B:ARG182
|
4.5
|
23.4
|
1.0
|
|
N
|
A:CYS259
|
4.5
|
16.8
|
1.0
|
|
HB2
|
A:CYS265
|
4.6
|
22.2
|
1.0
|
|
HH12
|
B:ARG182
|
4.6
|
24.0
|
1.0
|
|
SG
|
A:CYS247
|
4.6
|
18.3
|
1.0
|
|
HE
|
B:ARG182
|
4.6
|
23.4
|
1.0
|
|
NE1
|
A:TRP252
|
4.7
|
17.7
|
1.0
|
|
HH11
|
B:ARG182
|
4.7
|
24.0
|
1.0
|
|
SG
|
A:CYS268
|
4.7
|
17.6
|
1.0
|
|
SG
|
A:CYS265
|
4.7
|
18.4
|
1.0
|
|
HB3
|
A:CYS247
|
4.8
|
21.6
|
1.0
|
|
CA
|
A:CYS265
|
4.8
|
17.7
|
1.0
|
|
HG3
|
B:GLN187
|
4.8
|
23.7
|
1.0
|
|
HA
|
A:CYS259
|
4.9
|
20.1
|
1.0
|
|
HG12
|
A:ILE266
|
4.9
|
22.4
|
1.0
|
|
CB
|
A:CYS265
|
4.9
|
18.4
|
1.0
|
|
HG2
|
B:ARG182
|
5.0
|
22.4
|
1.0
|
|
CD
|
B:ARG182
|
5.0
|
19.1
|
1.0
|
|
HB2
|
A:CYS247
|
5.0
|
21.6
|
1.0
|
|
Iron binding site 8 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 8 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:18.0
occ:1.00
|
FE4
|
A:SF4302
|
0.0
|
18.0
|
1.0
|
|
S1
|
A:SF4302
|
2.3
|
18.0
|
1.0
|
|
SG
|
A:CYS247
|
2.3
|
18.3
|
1.0
|
|
S2
|
A:SF4302
|
2.3
|
19.2
|
1.0
|
|
S3
|
A:SF4302
|
2.3
|
19.0
|
1.0
|
|
FE3
|
A:SF4302
|
2.7
|
19.1
|
1.0
|
|
FE2
|
A:SF4302
|
2.8
|
18.7
|
1.0
|
|
FE1
|
A:SF4302
|
2.8
|
18.9
|
1.0
|
|
HB2
|
A:CYS247
|
3.2
|
21.6
|
1.0
|
|
CB
|
A:CYS247
|
3.3
|
17.9
|
1.0
|
|
HD11
|
A:ILE207
|
3.4
|
39.6
|
1.0
|
|
HB3
|
A:CYS247
|
3.4
|
21.6
|
1.0
|
|
HE1
|
A:TRP252
|
3.5
|
21.3
|
1.0
|
|
HD13
|
A:ILE207
|
3.7
|
39.6
|
1.0
|
|
HH2
|
A:TRP165
|
3.7
|
23.5
|
1.0
|
|
HB3
|
A:ALA245
|
3.9
|
19.8
|
1.0
|
|
S4
|
A:SF4302
|
3.9
|
19.4
|
1.0
|
|
CD1
|
A:ILE207
|
3.9
|
33.0
|
1.0
|
|
HD12
|
A:ILE207
|
4.3
|
39.6
|
1.0
|
|
NE1
|
A:TRP252
|
4.3
|
17.7
|
1.0
|
|
HB1
|
A:ALA245
|
4.4
|
19.8
|
1.0
|
|
H
|
A:CYS247
|
4.4
|
20.5
|
1.0
|
|
HZ2
|
A:TRP252
|
4.5
|
19.9
|
1.0
|
|
CB
|
A:ALA245
|
4.5
|
16.4
|
1.0
|
|
CH2
|
A:TRP165
|
4.6
|
19.5
|
1.0
|
|
HE3
|
A:TRP258
|
4.6
|
24.5
|
1.0
|
|
CA
|
A:CYS247
|
4.7
|
17.9
|
1.0
|
|
HB2
|
A:CYS259
|
4.7
|
24.3
|
1.0
|
|
SG
|
A:CYS259
|
4.7
|
17.9
|
1.0
|
|
HG13
|
A:VAL269
|
4.7
|
22.0
|
1.0
|
|
HZ2
|
A:TRP165
|
4.8
|
23.2
|
1.0
|
|
HB2
|
A:ALA245
|
4.8
|
19.8
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
18.4
|
1.0
|
|
SG
|
A:CYS268
|
4.8
|
17.6
|
1.0
|
|
HG21
|
A:THR243
|
4.8
|
22.7
|
1.0
|
|
N
|
A:CYS247
|
5.0
|
17.0
|
1.0
|
|
Iron binding site 9 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 9 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:13.4
occ:0.49
|
FE1
|
A:SF4303
|
0.0
|
13.4
|
0.5
|
|
FE1
|
A:6ML304
|
0.6
|
19.5
|
0.5
|
|
O12
|
A:6ML304
|
1.5
|
20.0
|
0.5
|
|
S3
|
A:6ML304
|
1.9
|
21.6
|
0.5
|
|
S2
|
A:SF4303
|
2.3
|
21.0
|
0.5
|
|
S4
|
A:SF4303
|
2.3
|
14.0
|
0.5
|
|
S3
|
A:SF4303
|
2.3
|
19.8
|
0.5
|
|
SG
|
A:CYS18
|
2.4
|
19.0
|
1.0
|
|
S2
|
A:6ML304
|
2.5
|
18.5
|
0.5
|
|
FE4
|
A:SF4303
|
2.7
|
21.1
|
0.5
|
|
FE3
|
A:SF4303
|
2.7
|
13.9
|
0.5
|
|
FE2
|
A:SF4303
|
2.8
|
12.8
|
0.5
|
|
FE3
|
A:6ML304
|
2.8
|
19.2
|
0.5
|
|
H
|
A:CYS18
|
2.8
|
21.8
|
1.0
|
|
FE2
|
A:6ML304
|
3.0
|
16.7
|
0.5
|
|
HB3
|
A:CYS18
|
3.1
|
22.6
|
1.0
|
|
O24
|
A:6ML304
|
3.3
|
18.4
|
0.5
|
|
CB
|
A:CYS18
|
3.3
|
18.7
|
1.0
|
|
H
|
A:GLY20
|
3.3
|
20.6
|
1.0
|
|
HE2
|
B:HIS185
|
3.4
|
24.8
|
1.0
|
|
FE4
|
A:6ML304
|
3.4
|
21.6
|
0.5
|
|
N
|
A:CYS18
|
3.5
|
18.1
|
1.0
|
|
HA3
|
A:GLY20
|
3.8
|
23.8
|
1.0
|
|
S1
|
A:SF4303
|
3.9
|
20.8
|
0.5
|
|
S4
|
A:6ML304
|
3.9
|
19.8
|
0.5
|
|
CA
|
A:CYS18
|
3.9
|
19.4
|
1.0
|
|
S1
|
A:6ML304
|
3.9
|
19.4
|
0.5
|
|
N
|
A:GLY20
|
4.1
|
17.1
|
1.0
|
|
OE2
|
A:GLU77
|
4.1
|
25.4
|
0.5
|
|
HB2
|
A:CYS18
|
4.2
|
22.6
|
1.0
|
|
HG3
|
B:ARG73
|
4.2
|
21.0
|
1.0
|
|
NE2
|
B:HIS185
|
4.2
|
20.6
|
1.0
|
|
H
|
A:CYS21
|
4.3
|
22.3
|
0.5
|
|
HA2
|
A:GLY17
|
4.3
|
27.3
|
1.0
|
|
C
|
A:CYS18
|
4.3
|
17.8
|
1.0
|
|
H
|
A:THR19
|
4.3
|
21.8
|
1.0
|
|
CA
|
A:GLY20
|
4.4
|
19.8
|
1.0
|
|
H
|
A:CYS21
|
4.4
|
22.3
|
0.5
|
|
N
|
A:THR19
|
4.5
|
18.1
|
1.0
|
|
HA
|
B:ARG73
|
4.6
|
20.4
|
1.0
|
|
O
|
A:HOH465
|
4.6
|
18.8
|
1.0
|
|
C
|
A:GLY17
|
4.6
|
18.6
|
1.0
|
|
SG
|
A:CYS21
|
4.7
|
20.8
|
0.5
|
|
HB3
|
B:ARG73
|
4.8
|
21.8
|
1.0
|
|
HA
|
A:CYS18
|
4.8
|
23.4
|
1.0
|
|
SG
|
A:CYS159
|
4.8
|
17.6
|
1.0
|
|
N
|
A:CYS21
|
4.9
|
18.5
|
0.5
|
|
O
|
B:ARG73
|
4.9
|
17.1
|
1.0
|
|
CA
|
A:GLY17
|
4.9
|
22.7
|
1.0
|
|
N
|
A:CYS21
|
4.9
|
18.5
|
0.5
|
|
CG
|
B:ARG73
|
4.9
|
17.4
|
1.0
|
|
HA3
|
A:GLY17
|
5.0
|
27.3
|
1.0
|
|
Iron binding site 10 out
of 18 in 6z9o
Go back to
Iron Binding Sites List in 6z9o
Iron binding site 10 out
of 18 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld
 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:12.8
occ:0.49
|
FE2
|
A:SF4303
|
0.0
|
12.8
|
0.5
|
|
FE4
|
A:6ML304
|
0.7
|
21.6
|
0.5
|
|
O24
|
A:6ML304
|
1.6
|
18.4
|
0.5
|
|
S3
|
A:6ML304
|
1.8
|
21.6
|
0.5
|
|
S1
|
A:SF4303
|
2.3
|
20.8
|
0.5
|
|
S3
|
A:SF4303
|
2.3
|
19.8
|
0.5
|
|
S4
|
A:SF4303
|
2.3
|
14.0
|
0.5
|
|
S4
|
A:6ML304
|
2.5
|
19.8
|
0.5
|
|
SG
|
A:CYS121
|
2.5
|
19.6
|
1.0
|
|
FE3
|
A:6ML304
|
2.7
|
19.2
|
0.5
|
|
FE3
|
A:SF4303
|
2.7
|
13.9
|
0.5
|
|
FE1
|
A:SF4303
|
2.8
|
13.4
|
0.5
|
|
FE4
|
A:SF4303
|
2.8
|
21.1
|
0.5
|
|
FE2
|
A:6ML304
|
3.0
|
16.7
|
0.5
|
|
HB2
|
A:CYS121
|
3.0
|
22.7
|
1.0
|
|
O12
|
A:6ML304
|
3.1
|
20.0
|
0.5
|
|
FE1
|
A:6ML304
|
3.3
|
19.5
|
0.5
|
|
CB
|
A:CYS121
|
3.4
|
18.9
|
1.0
|
|
H
|
A:CYS121
|
3.4
|
20.6
|
1.0
|
|
O
|
A:HOH413
|
3.7
|
19.3
|
1.0
|
|
HA2
|
A:GLY17
|
3.7
|
27.3
|
1.0
|
|
S2
|
A:6ML304
|
3.9
|
18.5
|
0.5
|
|
O
|
A:HOH465
|
3.9
|
18.8
|
1.0
|
|
S2
|
A:SF4303
|
3.9
|
21.0
|
0.5
|
|
H
|
A:CYS18
|
4.0
|
21.8
|
1.0
|
|
S1
|
A:6ML304
|
4.0
|
19.4
|
0.5
|
|
HB3
|
A:CYS121
|
4.1
|
22.7
|
1.0
|
|
N
|
A:CYS121
|
4.1
|
17.1
|
1.0
|
|
HA2
|
A:GLY78
|
4.2
|
23.0
|
1.0
|
|
O
|
A:HOH489
|
4.3
|
20.1
|
1.0
|
|
OE2
|
A:GLU77
|
4.3
|
25.4
|
0.5
|
|
CA
|
A:CYS121
|
4.4
|
17.2
|
1.0
|
|
HA3
|
A:GLY119
|
4.6
|
20.8
|
1.0
|
|
CA
|
A:GLY17
|
4.6
|
22.7
|
1.0
|
|
SG
|
A:CYS159
|
4.6
|
17.6
|
1.0
|
|
H
|
A:GLY78
|
4.7
|
23.8
|
1.0
|
|
N
|
A:CYS18
|
4.7
|
18.1
|
1.0
|
|
HA3
|
A:GLY17
|
4.8
|
27.3
|
1.0
|
|
H
|
A:THR120
|
4.8
|
21.2
|
1.0
|
|
HB3
|
A:CYS18
|
4.8
|
22.6
|
1.0
|
|
SG
|
A:CYS21
|
4.8
|
20.8
|
0.5
|
|
O
|
A:GLN16
|
4.9
|
20.8
|
1.0
|
|
HA
|
A:CYS121
|
4.9
|
20.7
|
1.0
|
|
HA
|
A:CYS159
|
5.0
|
19.7
|
1.0
|
|
H
|
A:ALA122
|
5.0
|
21.7
|
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 17:30:02 2024
|
