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Iron in PDB 9qm1: W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite

Enzymatic activity of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite

All present enzymatic activity of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite:
1.2.1.2;

Protein crystallography data

The structure of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite, PDB code: 9qm1 was solved by G.Vilela-Alves, A.R.Oliveira, I.C.Pereira, M.J.Romao, C.Mota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.93 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.8, 122.511, 146.697, 90, 90, 90
R / Rfree (%) 21.4 / 26.7

Other elements in 9qm1:

The structure of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite also contains other interesting chemical elements:

Tungsten (W) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite (pdb code 9qm1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite, PDB code: 9qm1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 9qm1

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Iron binding site 1 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1214

b:15.6
occ:1.00
 FE1 A:SF41214 0.0 15.6 1.0
SG A:CYS53 2.2 16.7 1.0
S3 A:SF41214 2.3 17.7 1.0
S2 A:SF41214 2.3 19.8 1.0
S4 A:SF41214 2.3 18.2 1.0
FE4 A:SF41214 2.7 16.2 1.0
FE2 A:SF41214 2.7 18.1 1.0
FE3 A:SF41214 2.7 20.1 1.0
CB A:CYS53 3.3 17.3 1.0
N A:CYS53 3.7 22.4 1.0
CA A:CYS53 3.8 16.1 1.0
O A:HOH1431 3.8 20.0 1.0
S1 A:SF41214 3.9 17.6 1.0
O A:CYS53 3.9 23.5 1.0
C A:CYS53 4.0 15.6 1.0
CB A:VAL55 4.1 15.0 1.0
CG2 A:VAL55 4.3 16.6 1.0
SG A:CYS57 4.6 17.8 1.0
SG A:CYS88 4.6 16.6 1.0
N A:VAL55 4.7 18.0 1.0
CD A:PRO234 4.7 15.8 1.0
SG A:CYS50 4.7 20.4 1.0
C A:TYR52 4.9 26.5 1.0
N A:ALA54 5.0 17.8 1.0
CA A:VAL55 5.0 21.2 1.0
CB A:TYR52 5.0 21.8 1.0

Iron binding site 2 out of 16 in 9qm1

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Iron binding site 2 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1214

b:18.1
occ:1.00
 FE2 A:SF41214 0.0 18.1 1.0
SG A:CYS57 2.1 17.8 1.0
S4 A:SF41214 2.3 18.2 1.0
S3 A:SF41214 2.3 17.7 1.0
S1 A:SF41214 2.3 17.6 1.0
FE3 A:SF41214 2.7 20.1 1.0
FE1 A:SF41214 2.7 15.6 1.0
FE4 A:SF41214 2.8 16.2 1.0
CB A:CYS57 3.1 20.8 1.0
S2 A:SF41214 3.9 19.8 1.0
CD1 A:ILE235 4.0 20.0 1.0
N A:CYS57 4.3 24.1 1.0
CG1 A:ILE235 4.3 16.8 1.0
CA A:CYS57 4.3 24.5 1.0
CB A:VAL55 4.3 15.0 1.0
CB A:ILE235 4.3 14.4 1.0
CG1 A:VAL55 4.4 14.1 1.0
SG A:CYS53 4.7 16.7 1.0
CB A:CYS50 4.7 15.0 1.0
SG A:CYS50 4.7 20.4 1.0
CD2 A:LEU87 4.8 17.4 1.0
SG A:CYS88 4.9 16.6 1.0

Iron binding site 3 out of 16 in 9qm1

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Iron binding site 3 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1214

b:20.1
occ:1.00
 FE3 A:SF41214 0.0 20.1 1.0
S2 A:SF41214 2.3 19.8 1.0
S4 A:SF41214 2.3 18.2 1.0
S1 A:SF41214 2.3 17.6 1.0
SG A:CYS50 2.3 20.4 1.0
FE2 A:SF41214 2.7 18.1 1.0
FE4 A:SF41214 2.7 16.2 1.0
FE1 A:SF41214 2.7 15.6 1.0
CB A:CYS50 3.1 15.0 1.0
S3 A:SF41214 3.9 17.7 1.0
CB A:TYR52 4.1 21.8 1.0
CA A:GLY91 4.2 30.1 1.0
N A:GLY91 4.3 19.5 1.0
N A:CYS53 4.3 22.4 1.0
SG A:CYS57 4.5 17.8 1.0
SG A:CYS88 4.5 16.6 1.0
CB A:CYS57 4.6 20.8 1.0
CA A:CYS50 4.6 12.8 1.0
SG A:CYS53 4.8 16.7 1.0
N A:TYR52 4.8 14.2 1.0
CA A:TYR52 4.8 16.6 1.0
O A:CYS53 4.9 23.5 1.0
CD2 A:TYR52 4.9 23.6 1.0
C A:TYR52 5.0 26.5 1.0

Iron binding site 4 out of 16 in 9qm1

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Iron binding site 4 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1214

b:16.2
occ:1.00
 FE4 A:SF41214 0.0 16.2 1.0
SG A:CYS88 2.2 16.6 1.0
S2 A:SF41214 2.3 19.8 1.0
S3 A:SF41214 2.3 17.7 1.0
S1 A:SF41214 2.3 17.6 1.0
FE1 A:SF41214 2.7 15.6 1.0
FE3 A:SF41214 2.7 20.1 1.0
FE2 A:SF41214 2.8 18.1 1.0
CB A:CYS88 3.3 24.3 1.0
S4 A:SF41214 3.9 18.2 1.0
N A:CYS88 3.9 14.4 1.0
CA A:CYS88 4.1 18.7 1.0
O A:HOH1431 4.4 20.0 1.0
CD A:PRO234 4.4 15.8 1.0
NZ A:LYS90 4.4 15.5 1.0
N A:GLY91 4.4 19.5 1.0
CD1 A:ILE235 4.5 20.0 1.0
CG A:PRO234 4.5 15.7 1.0
SG A:CYS53 4.7 16.7 1.0
C A:CYS88 4.7 14.6 1.0
SG A:CYS57 4.8 17.8 1.0
SG A:CYS50 4.9 20.4 1.0
CB A:PRO234 4.9 14.8 1.0
CA A:GLY91 4.9 30.1 1.0
O A:CYS88 5.0 18.7 1.0
CE A:LYS90 5.0 19.9 1.0

Iron binding site 5 out of 16 in 9qm1

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Iron binding site 5 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:17.1
occ:1.00
 FE1 B:SF4301 0.0 17.1 1.0
SG B:CYS157 2.2 21.2 1.0
S3 B:SF4301 2.3 13.1 1.0
S4 B:SF4301 2.3 17.0 1.0
S2 B:SF4301 2.3 17.5 1.0
FE2 B:SF4301 2.7 15.0 1.0
FE4 B:SF4301 2.7 14.3 1.0
FE3 B:SF4301 2.8 16.8 1.0
CB B:CYS157 3.2 26.1 1.0
CA B:CYS157 3.8 26.3 1.0
S1 B:SF4301 3.9 13.5 1.0
OG1 B:THR159 4.0 17.7 1.0
CB B:THR161 4.1 13.2 1.0
CG B:MET162 4.2 18.1 1.0
CD B:PRO158 4.3 26.6 1.0
CG2 B:THR161 4.5 15.1 1.0
C B:CYS157 4.5 20.4 1.0
OG1 B:THR161 4.6 19.0 1.0
SG B:CYS15 4.7 16.3 1.0
N B:PRO158 4.7 19.5 1.0
SG B:CYS18 4.8 14.1 1.0
SG B:CYS12 5.0 15.2 1.0

Iron binding site 6 out of 16 in 9qm1

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Iron binding site 6 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:15.0
occ:1.00
 FE2 B:SF4301 0.0 15.0 1.0
S4 B:SF4301 2.3 17.0 1.0
S3 B:SF4301 2.3 13.1 1.0
SG B:CYS18 2.3 14.1 1.0
S1 B:SF4301 2.3 13.5 1.0
FE1 B:SF4301 2.7 17.1 1.0
FE3 B:SF4301 2.7 16.8 1.0
FE4 B:SF4301 2.7 14.3 1.0
CB B:CYS18 3.3 8.7 1.0
O B:HOH442 3.8 14.2 1.0
S2 B:SF4301 3.9 17.5 1.0
N B:CYS18 3.9 15.7 1.0
CA B:CYS18 4.2 13.4 1.0
CG B:PRO71 4.4 11.7 1.0
CB B:PRO71 4.5 15.4 1.0
N B:GLY17 4.6 12.8 1.0
SG B:CYS15 4.7 16.3 1.0
N B:ARG16 4.7 14.3 1.0
SG B:CYS12 4.8 15.2 1.0
SG B:CYS157 4.8 21.2 1.0
CA B:ARG16 4.8 21.2 1.0
CG2 B:VAL53 4.9 23.4 1.0

Iron binding site 7 out of 16 in 9qm1

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Iron binding site 7 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:16.8
occ:1.00
 FE3 B:SF4301 0.0 16.8 1.0
S1 B:SF4301 2.3 13.5 1.0
S2 B:SF4301 2.3 17.5 1.0
S4 B:SF4301 2.3 17.0 1.0
SG B:CYS15 2.4 16.3 1.0
FE2 B:SF4301 2.7 15.0 1.0
FE4 B:SF4301 2.8 14.3 1.0
FE1 B:SF4301 2.8 17.1 1.0
N B:CYS15 3.5 15.9 1.0
CB B:CYS15 3.6 17.6 1.0
N B:ARG16 3.8 14.3 1.0
S3 B:SF4301 3.9 13.1 1.0
CA B:CYS15 4.0 9.8 1.0
N B:GLY17 4.1 12.8 1.0
C B:CYS15 4.2 16.3 1.0
OG1 B:THR13 4.4 12.3 1.0
CD B:PRO158 4.4 26.6 1.0
C B:ALA14 4.5 13.6 1.0
N B:ALA14 4.6 13.1 1.0
SG B:CYS18 4.6 14.1 1.0
CA B:ARG16 4.6 21.2 1.0
SG B:CYS157 4.7 21.2 1.0
CA B:ALA14 4.7 12.5 1.0
SG B:CYS12 4.8 15.2 1.0
CA B:GLY17 4.9 21.0 1.0
N B:CYS18 4.9 15.7 1.0
C B:ARG16 4.9 29.7 1.0

Iron binding site 8 out of 16 in 9qm1

Go back to Iron Binding Sites List in 9qm1
Iron binding site 8 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:14.3
occ:1.00
 FE4 B:SF4301 0.0 14.3 1.0
S2 B:SF4301 2.3 17.5 1.0
S1 B:SF4301 2.3 13.5 1.0
S3 B:SF4301 2.3 13.1 1.0
SG B:CYS12 2.3 15.2 1.0
FE2 B:SF4301 2.7 15.0 1.0
FE1 B:SF4301 2.7 17.1 1.0
FE3 B:SF4301 2.8 16.8 1.0
CB B:CYS12 3.5 16.8 1.0
CA B:CYS12 3.8 15.3 1.0
S4 B:SF4301 3.9 17.0 1.0
N B:ALA14 4.1 13.1 1.0
N B:THR13 4.2 17.4 1.0
CG B:PRO71 4.3 11.7 1.0
C B:CYS12 4.4 12.7 1.0
CG2 B:THR161 4.4 15.1 1.0
CA B:ALA14 4.5 12.5 1.0
OG1 B:THR161 4.5 19.0 1.0
CB B:THR161 4.6 13.2 1.0
SG B:CYS157 4.7 21.2 1.0
N B:CYS15 4.8 15.9 1.0
SG B:CYS18 4.8 14.1 1.0
OG1 B:THR159 5.0 17.7 1.0

Iron binding site 9 out of 16 in 9qm1

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Iron binding site 9 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:19.8
occ:1.00
 FE1 B:SF4302 0.0 19.8 1.0
SG B:CYS77 2.2 24.8 1.0
S3 B:SF4302 2.3 23.2 1.0
S4 B:SF4302 2.3 20.8 1.0
S2 B:SF4302 2.3 18.8 1.0
FE4 B:SF4302 2.7 18.9 1.0
FE2 B:SF4302 2.7 20.6 1.0
FE3 B:SF4302 2.8 18.2 1.0
CB B:CYS77 3.4 17.7 1.0
N B:CYS77 3.8 15.8 1.0
S1 B:SF4302 3.9 21.2 1.0
CA B:CYS77 4.2 14.8 1.0
N B:HIS76 4.5 19.6 1.0
CD2 B:TYR123 4.5 24.5 1.0
SG B:CYS121 4.5 21.2 1.0
SG B:CYS74 4.6 19.1 1.0
CD B:PRO81 4.7 26.8 1.0
CE2 B:TYR123 4.8 25.4 1.0
N B:ARG75 4.8 15.5 1.0
CB B:PRO80 4.8 19.1 1.0
CB B:ARG75 4.8 15.9 1.0
SG B:CYS82 4.8 25.2 1.0
C B:HIS76 4.8 15.9 1.0
CA B:PRO80 4.8 26.8 1.0
CA B:HIS76 4.9 18.5 1.0
C B:ARG75 5.0 22.8 1.0

Iron binding site 10 out of 16 in 9qm1

Go back to Iron Binding Sites List in 9qm1
Iron binding site 10 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris - Soaked with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:20.6
occ:1.00
 FE2 B:SF4302 0.0 20.6 1.0
S1 B:SF4302 2.3 21.2 1.0
S4 B:SF4302 2.3 20.8 1.0
S3 B:SF4302 2.3 23.2 1.0
SG B:CYS82 2.4 25.2 1.0
FE4 B:SF4302 2.7 18.9 1.0
FE3 B:SF4302 2.7 18.2 1.0
FE1 B:SF4302 2.7 19.8 1.0
CB B:CYS82 3.1 18.8 1.0
S2 B:SF4302 3.9 18.8 1.0
N B:CYS82 4.2 19.7 1.0
CA B:CYS82 4.2 17.1 1.0
CB B:PRO80 4.3 19.1 1.0
CG1 B:VAL103 4.4 20.9 1.0
SG B:CYS74 4.6 19.1 1.0
CE B:LYS137 4.7 21.6 1.0
SG B:CYS121 4.7 21.2 1.0
CZ B:PHE105 4.8 17.1 1.0
SG B:CYS77 4.8 24.8 1.0
CE1 B:PHE105 4.9 24.7 1.0
CA B:PRO80 4.9 26.8 1.0

Reference:

A.R.Oliveira, G.Vilela-Alves, C.Mota, V.Fourmond, C.Leger, F.Biaso, B.Guigliarelli, M.J.Romao, I.C.Pereira. The Role of Selenocysteine in Catalysis and Oxygen Tolerance of A W‐Dependent Formate Dehydrogenase Acs Catalysis 2025.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.5C02382
Page generated: Fri Aug 8 08:13:36 2025

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