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Iron in PDB 30gk: W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01

Enzymatic activity of W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01

All present enzymatic activity of W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01:
1.2.1.2;

Protein crystallography data

The structure of W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01, PDB code: 30gk was solved by G.Vilela-Alves, G.Martins, D.Von Stetten, P.Mehrabi, I.C.Pereira, M.J.Romao, A.R.Pearson, C.Mota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.52 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.898, 127.884, 149.398, 90, 90, 90
R / Rfree (%) 21.2 / 25.1

Other elements in 30gk:

The structure of W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 (pdb code 30gk). 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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01, PDB code: 30gk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 30gk

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Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:21.8
occ:1.00
 FE1 A:SF41103 0.0 21.8 1.0
S2 A:SF41103 2.3 23.7 1.0
S4 A:SF41103 2.3 23.2 1.0
S3 A:SF41103 2.3 22.2 1.0
SG A:CYS53 2.3 23.3 1.0
FE4 A:SF41103 2.7 22.8 1.0
FE3 A:SF41103 2.7 23.3 1.0
FE2 A:SF41103 2.8 22.6 1.0
CB A:CYS53 3.4 23.9 1.0
N A:CYS53 3.7 25.1 1.0
CA A:CYS53 3.9 24.0 1.0
O A:CYS53 3.9 24.4 1.0
S1 A:SF41103 3.9 23.8 1.0
O A:HOH1471 4.0 19.0 1.0
CB A:VAL55 4.0 22.3 1.0
C A:CYS53 4.1 23.8 1.0
CG2 A:VAL55 4.1 22.7 1.0
CD A:PRO234 4.5 21.6 1.0
N A:VAL55 4.6 22.1 1.0
SG A:CYS88 4.6 24.6 1.0
SG A:CYS50 4.7 23.9 1.0
SG A:CYS57 4.7 21.9 1.0
C A:TYR52 4.9 25.8 1.0
CA A:VAL55 4.9 22.3 1.0
N A:ALA54 4.9 22.9 1.0
CB A:TYR52 5.0 25.9 1.0

Iron binding site 2 out of 16 in 30gk

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Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:22.6
occ:1.00
 FE2 A:SF41103 0.0 22.6 1.0
SG A:CYS57 2.2 21.9 1.0
S1 A:SF41103 2.3 23.8 1.0
S4 A:SF41103 2.3 23.2 1.0
S3 A:SF41103 2.3 22.2 1.0
FE3 A:SF41103 2.7 23.3 1.0
FE4 A:SF41103 2.7 22.8 1.0
FE1 A:SF41103 2.8 21.8 1.0
CB A:CYS57 3.1 22.4 1.0
S2 A:SF41103 3.9 23.7 1.0
CD1 A:ILE235 4.1 22.6 1.0
CB A:VAL55 4.2 22.3 1.0
N A:CYS57 4.2 22.1 1.0
CA A:CYS57 4.3 22.9 1.0
CG1 A:VAL55 4.3 22.1 1.0
CG1 A:ILE235 4.4 22.2 1.0
CB A:ILE235 4.4 22.5 1.0
CB A:CYS50 4.6 24.7 1.0
SG A:CYS50 4.6 23.9 1.0
SG A:CYS53 4.8 23.3 1.0
CG2 A:VAL55 4.8 22.7 1.0
CD2 A:LEU87 4.8 25.1 1.0
SG A:CYS88 4.8 24.6 1.0

Iron binding site 3 out of 16 in 30gk

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Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:23.3
occ:1.00
 FE3 A:SF41103 0.0 23.3 1.0
S4 A:SF41103 2.3 23.2 1.0
SG A:CYS50 2.3 23.9 1.0
S2 A:SF41103 2.3 23.7 1.0
S1 A:SF41103 2.3 23.8 1.0
FE2 A:SF41103 2.7 22.6 1.0
FE4 A:SF41103 2.7 22.8 1.0
FE1 A:SF41103 2.7 21.8 1.0
CB A:CYS50 3.1 24.7 1.0
S3 A:SF41103 3.9 22.2 1.0
CA A:GLY91 4.2 27.6 1.0
CB A:TYR52 4.2 25.9 1.0
N A:GLY91 4.2 26.4 1.0
N A:CYS53 4.4 25.1 1.0
SG A:CYS88 4.5 24.6 1.0
CB A:CYS57 4.5 22.4 1.0
CA A:CYS50 4.6 24.9 1.0
SG A:CYS57 4.6 21.9 1.0
N A:TYR52 4.8 25.6 1.0
O A:CYS53 4.8 24.4 1.0
CA A:TYR52 4.8 25.6 1.0
CD2 A:TYR52 4.9 26.7 1.0
SG A:CYS53 4.9 23.3 1.0
C A:TYR52 5.0 25.8 1.0

Iron binding site 4 out of 16 in 30gk

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Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:22.8
occ:1.00
 FE4 A:SF41103 0.0 22.8 1.0
SG A:CYS88 2.2 24.6 1.0
S1 A:SF41103 2.3 23.8 1.0
S3 A:SF41103 2.3 22.2 1.0
S2 A:SF41103 2.3 23.7 1.0
FE3 A:SF41103 2.7 23.3 1.0
FE1 A:SF41103 2.7 21.8 1.0
FE2 A:SF41103 2.7 22.6 1.0
CB A:CYS88 3.3 25.4 1.0
S4 A:SF41103 3.9 23.2 1.0
N A:CYS88 3.9 26.0 1.0
CA A:CYS88 4.1 26.1 1.0
CD A:PRO234 4.3 21.6 1.0
N A:GLY91 4.4 26.4 1.0
CG A:PRO234 4.4 22.0 1.0
NZ A:LYS90 4.5 25.5 1.0
CD1 A:ILE235 4.5 22.6 1.0
O A:HOH1471 4.6 19.0 1.0
C A:CYS88 4.7 25.9 1.0
CB A:PRO234 4.7 21.5 1.0
SG A:CYS53 4.7 23.3 1.0
SG A:CYS57 4.8 21.9 1.0
SG A:CYS50 4.8 23.9 1.0
CA A:GLY91 4.9 27.6 1.0
O A:CYS88 4.9 26.6 1.0
CE A:LYS90 5.0 25.3 1.0

Iron binding site 5 out of 16 in 30gk

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Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:26.3
occ:1.00
 FE1 B:SF4301 0.0 26.3 1.0
S3 B:SF4301 2.3 26.3 1.0
S4 B:SF4301 2.3 26.4 1.0
SG B:CYS157 2.3 28.0 1.0
S2 B:SF4301 2.3 25.8 1.0
FE2 B:SF4301 2.7 27.0 1.0
FE3 B:SF4301 2.7 25.5 1.0
FE4 B:SF4301 2.8 25.6 1.0
CB B:CYS157 3.2 28.4 1.0
CA B:CYS157 3.8 27.4 1.0
S1 B:SF4301 3.9 26.1 1.0
OG1 B:THR159 3.9 24.7 1.0
CB B:THR161 4.1 29.0 1.0
CD B:PRO158 4.1 28.2 1.0
CG B:MET162 4.3 31.6 1.0
OG1 B:THR161 4.5 29.4 1.0
CG2 B:THR161 4.5 29.1 1.0
C B:CYS157 4.5 27.6 1.0
N B:PRO158 4.6 27.2 1.0
SG B:CYS15 4.7 26.4 1.0
SG B:CYS18 4.7 28.9 1.0
SG B:CYS12 4.9 25.5 1.0
N B:MET162 5.0 30.8 1.0

Iron binding site 6 out of 16 in 30gk

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Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:27.0
occ:1.00
 FE2 B:SF4301 0.0 27.0 1.0
SG B:CYS18 2.2 28.9 1.0
S4 B:SF4301 2.2 26.4 1.0
S3 B:SF4301 2.3 26.3 1.0
S1 B:SF4301 2.3 26.1 1.0
FE1 B:SF4301 2.7 26.3 1.0
FE3 B:SF4301 2.7 25.5 1.0
FE4 B:SF4301 2.8 25.6 1.0
CB B:CYS18 3.2 27.9 1.0
O B:HOH436 3.8 32.4 1.0
S2 B:SF4301 3.9 25.8 1.0
N B:CYS18 3.9 26.9 1.0
CA B:CYS18 4.2 27.8 1.0
CG B:PRO71 4.4 32.9 1.0
N B:ARG16 4.7 27.3 1.0
SG B:CYS15 4.7 26.4 1.0
N B:GLY17 4.7 25.9 1.0
CB B:PRO71 4.7 33.2 1.0
SG B:CYS157 4.8 28.0 1.0
SG B:CYS12 4.8 25.5 1.0
CG2 B:VAL53 4.8 32.4 1.0
CA B:ARG16 4.8 26.8 1.0
CG B:MET162 5.0 31.6 1.0

Iron binding site 7 out of 16 in 30gk

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Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:25.5
occ:1.00
 FE3 B:SF4301 0.0 25.5 1.0
S2 B:SF4301 2.3 25.8 1.0
S1 B:SF4301 2.3 26.1 1.0
S4 B:SF4301 2.3 26.4 1.0
SG B:CYS15 2.4 26.4 1.0
FE4 B:SF4301 2.7 25.6 1.0
FE2 B:SF4301 2.7 27.0 1.0
FE1 B:SF4301 2.7 26.3 1.0
N B:CYS15 3.5 26.7 1.0
CB B:CYS15 3.5 26.8 1.0
N B:ARG16 3.7 27.3 1.0
S3 B:SF4301 3.9 26.3 1.0
CA B:CYS15 3.9 26.8 1.0
C B:CYS15 4.2 27.3 1.0
N B:GLY17 4.2 25.9 1.0
CD B:PRO158 4.3 28.2 1.0
OG1 B:THR13 4.4 26.4 1.0
C B:ALA14 4.5 26.4 1.0
SG B:CYS18 4.5 28.9 1.0
N B:ALA14 4.5 26.1 1.0
CA B:ARG16 4.6 26.8 1.0
CA B:ALA14 4.7 26.4 1.0
SG B:CYS12 4.7 25.5 1.0
SG B:CYS157 4.8 28.0 1.0
CG B:PRO158 4.8 27.8 1.0
C B:ARG16 4.9 25.9 1.0
N B:CYS18 4.9 26.9 1.0
CA B:GLY17 5.0 25.9 1.0
N B:THR13 5.0 26.1 1.0

Iron binding site 8 out of 16 in 30gk

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Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:25.6
occ:1.00
 FE4 B:SF4301 0.0 25.6 1.0
S2 B:SF4301 2.3 25.8 1.0
S1 B:SF4301 2.3 26.1 1.0
SG B:CYS12 2.3 25.5 1.0
S3 B:SF4301 2.3 26.3 1.0
FE3 B:SF4301 2.7 25.5 1.0
FE2 B:SF4301 2.8 27.0 1.0
FE1 B:SF4301 2.8 26.3 1.0
CB B:CYS12 3.5 25.5 1.0
CA B:CYS12 3.8 25.6 1.0
S4 B:SF4301 3.9 26.4 1.0
N B:ALA14 4.0 26.1 1.0
N B:THR13 4.2 26.1 1.0
CG B:PRO71 4.3 32.9 1.0
C B:CYS12 4.4 26.2 1.0
CA B:ALA14 4.4 26.4 1.0
CG2 B:THR161 4.5 29.1 1.0
OG1 B:THR161 4.5 29.4 1.0
CB B:THR161 4.6 29.0 1.0
N B:CYS15 4.7 26.7 1.0
SG B:CYS18 4.7 28.9 1.0
SG B:CYS157 4.8 28.0 1.0
OG1 B:THR159 4.9 24.7 1.0

Iron binding site 9 out of 16 in 30gk

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Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:44.3
occ:1.00
 FE1 B:SF4302 0.0 44.3 1.0
SG B:CYS77 2.2 50.2 1.0
S3 B:SF4302 2.3 48.2 1.0
S4 B:SF4302 2.3 43.0 1.0
S2 B:SF4302 2.3 44.2 1.0
FE4 B:SF4302 2.7 46.5 1.0
FE2 B:SF4302 2.7 47.3 1.0
FE3 B:SF4302 2.8 43.1 1.0
CB B:CYS77 3.4 48.5 1.0
N B:CYS77 3.7 45.9 1.0
S1 B:SF4302 3.9 44.8 1.0
CA B:CYS77 4.2 48.2 1.0
N B:HIS76 4.5 40.2 1.0
SG B:CYS121 4.5 47.7 1.0
CD2 B:TYR123 4.6 43.0 1.0
CD B:PRO81 4.6 56.6 1.0
CB B:PRO80 4.7 58.4 1.0
SG B:CYS74 4.7 40.2 1.0
CA B:PRO80 4.7 58.0 1.0
CB B:ARG75 4.8 39.9 1.0
N B:ARG75 4.8 39.1 1.0
C B:HIS76 4.8 42.6 1.0
SG B:CYS82 4.9 53.9 1.0
CA B:HIS76 4.9 41.8 1.0
CE2 B:TYR123 4.9 42.2 1.0

Iron binding site 10 out of 16 in 30gk

Go back to Iron Binding Sites List in 30gk
Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01


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 From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Same Batch Ssx 2025/04/01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:47.3
occ:1.00
 FE2 B:SF4302 0.0 47.3 1.0
S4 B:SF4302 2.3 43.0 1.0
S3 B:SF4302 2.3 48.2 1.0
S1 B:SF4302 2.3 44.8 1.0
SG B:CYS82 2.4 53.9 1.0
FE1 B:SF4302 2.7 44.3 1.0
FE4 B:SF4302 2.7 46.5 1.0
FE3 B:SF4302 2.7 43.1 1.0
CB B:CYS82 3.1 55.1 1.0
S2 B:SF4302 3.9 44.2 1.0
N B:CYS82 4.2 57.4 1.0
CA B:CYS82 4.2 56.8 1.0
CB B:PRO80 4.2 58.4 1.0
CG1 B:VAL103 4.5 49.1 1.0
SG B:CYS121 4.6 47.7 1.0
SG B:CYS74 4.7 40.2 1.0
CE B:LYS137 4.8 44.9 1.0
SG B:CYS77 4.8 50.2 1.0
CA B:PRO80 4.8 58.0 1.0

Reference:

G.Vilela-Alves, G.Martins, D.Von Stetten, P.Mehrabi, I.A.C.Pereira, M.J.Romao, A.R.Pearson, C.Mota. Room-Temperature Crystal Structure of A Metal-Dependent W-Formate Dehydrogenase By Serial Synchrotron Crystallography. Acta Crystallogr D Struct 2026BIOL.
ISSN: ISSN 2059-7983
PubMed: 42572941
DOI: 10.1107/S2059798326006923
Page generated: Sun Oct 4 10:31:40 2026

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