Iron in PDB 8rc9: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H

Enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H

All present enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H:
1.2.1.2;

Protein crystallography data

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H, PDB code: 8rc9 was solved by G.Vilela-Alves, R.R.Manuel, 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) 97.19 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.18, 127.926, 149.467, 90, 90, 90
R / Rfree (%) 20.6 / 25.5

Other elements in 8rc9:

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H 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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H (pdb code 8rc9). 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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H, PDB code: 8rc9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8rc9

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Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:27.8
occ:1.00
 FE1 A:SF41103 0.0 27.8 1.0
S2 A:SF41103 2.3 27.4 1.0
S4 A:SF41103 2.3 26.8 1.0
SG A:CYS53 2.3 25.7 1.0
S3 A:SF41103 2.3 24.6 1.0
FE3 A:SF41103 2.8 27.0 1.0
FE4 A:SF41103 2.8 27.5 1.0
FE2 A:SF41103 2.8 27.1 1.0
CB A:CYS53 3.3 23.3 1.0
N A:CYS53 3.8 23.2 1.0
CA A:CYS53 3.8 23.0 1.0
S1 A:SF41103 3.9 26.9 1.0
O A:HOH1319 4.0 27.6 1.0
O A:CYS53 4.1 27.4 1.0
C A:CYS53 4.1 25.6 1.0
CB A:VAL55 4.2 19.6 1.0
CG2 A:VAL55 4.3 20.0 1.0
CD A:PRO234 4.5 22.8 1.0
N A:VAL55 4.6 22.2 1.0
SG A:CYS88 4.7 29.0 1.0
SG A:CYS57 4.8 26.6 1.0
SG A:CYS50 4.9 30.8 1.0
N A:ALA54 5.0 22.4 1.0
CA A:VAL55 5.0 21.4 1.0
C A:TYR52 5.0 26.6 1.0

Iron binding site 2 out of 16 in 8rc9

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Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:27.1
occ:1.00
 FE2 A:SF41103 0.0 27.1 1.0
S1 A:SF41103 2.3 26.9 1.0
SG A:CYS57 2.3 26.6 1.0
S3 A:SF41103 2.3 24.6 1.0
S4 A:SF41103 2.3 26.8 1.0
FE3 A:SF41103 2.7 27.0 1.0
FE4 A:SF41103 2.8 27.5 1.0
FE1 A:SF41103 2.8 27.8 1.0
CB A:CYS57 3.2 24.8 1.0
S2 A:SF41103 3.9 27.4 1.0
CD1 A:ILE235 4.2 25.6 1.0
N A:CYS57 4.3 22.7 1.0
CG1 A:ILE235 4.3 24.2 1.0
CA A:CYS57 4.3 23.9 1.0
CB A:VAL55 4.3 19.6 1.0
CB A:ILE235 4.4 25.4 1.0
CG1 A:VAL55 4.5 19.8 1.0
CB A:CYS50 4.6 26.6 1.0
SG A:CYS50 4.7 30.8 1.0
SG A:CYS53 4.8 25.7 1.0
CD2 A:LEU87 4.8 25.1 1.0

Iron binding site 3 out of 16 in 8rc9

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Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:27.0
occ:1.00
 FE3 A:SF41103 0.0 27.0 1.0
S4 A:SF41103 2.3 26.8 1.0
S1 A:SF41103 2.3 26.9 1.0
S2 A:SF41103 2.3 27.4 1.0
SG A:CYS50 2.3 30.8 1.0
FE2 A:SF41103 2.7 27.1 1.0
FE4 A:SF41103 2.7 27.5 1.0
FE1 A:SF41103 2.8 27.8 1.0
CB A:CYS50 3.2 26.6 1.0
S3 A:SF41103 3.9 24.6 1.0
CA A:GLY91 4.3 25.4 1.0
CB A:TYR52 4.3 25.5 1.0
N A:CYS53 4.3 23.2 1.0
N A:GLY91 4.4 24.5 1.0
SG A:CYS88 4.6 29.0 1.0
CA A:CYS50 4.6 26.3 1.0
CB A:CYS57 4.6 24.8 1.0
SG A:CYS57 4.7 26.6 1.0
N A:TYR52 4.9 25.7 1.0
SG A:CYS53 4.9 25.7 1.0
CA A:TYR52 4.9 25.9 1.0
CD2 A:TYR52 5.0 26.3 1.0
O A:CYS53 5.0 27.4 1.0

Iron binding site 4 out of 16 in 8rc9

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Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:27.5
occ:1.00
 FE4 A:SF41103 0.0 27.5 1.0
S1 A:SF41103 2.3 26.9 1.0
S2 A:SF41103 2.3 27.4 1.0
S3 A:SF41103 2.3 24.6 1.0
SG A:CYS88 2.3 29.0 1.0
FE3 A:SF41103 2.7 27.0 1.0
FE1 A:SF41103 2.8 27.8 1.0
FE2 A:SF41103 2.8 27.1 1.0
CB A:CYS88 3.2 30.4 1.0
S4 A:SF41103 3.9 26.8 1.0
N A:CYS88 3.9 27.3 1.0
CA A:CYS88 4.1 27.1 1.0
CD A:PRO234 4.4 22.8 1.0
CG A:PRO234 4.5 23.9 1.0
N A:GLY91 4.6 24.5 1.0
CD1 A:ILE235 4.6 25.6 1.0
NZ A:LYS90 4.6 31.0 1.0
C A:CYS88 4.7 27.8 1.0
O A:HOH1319 4.8 27.6 1.0
O A:CYS88 4.8 28.3 1.0
SG A:CYS53 4.8 25.7 1.0
SG A:CYS50 4.9 30.8 1.0
SG A:CYS57 4.9 26.6 1.0
CB A:PRO234 5.0 24.7 1.0
CA A:GLY91 5.0 25.4 1.0

Iron binding site 5 out of 16 in 8rc9

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Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:29.8
occ:1.00
 FE1 B:SF4301 0.0 29.8 1.0
S4 B:SF4301 2.3 29.0 1.0
S3 B:SF4301 2.3 30.1 1.0
S2 B:SF4301 2.3 29.4 1.0
SG B:CYS157 2.3 29.5 1.0
FE2 B:SF4301 2.7 30.3 1.0
FE3 B:SF4301 2.7 30.0 1.0
FE4 B:SF4301 2.8 31.6 1.0
CB B:CYS157 3.2 29.6 1.0
CA B:CYS157 3.7 29.5 1.0
S1 B:SF4301 3.9 30.1 1.0
OG1 B:THR159 3.9 25.8 1.0
CB B:THR161 4.1 30.4 1.0
CD B:PRO158 4.1 32.9 1.0
CG B:MET162 4.4 36.2 1.0
OG1 B:THR161 4.5 26.8 1.0
CG2 B:THR161 4.5 32.0 1.0
C B:CYS157 4.5 29.5 1.0
N B:PRO158 4.6 33.4 1.0
SG B:CYS15 4.7 28.9 1.0
SG B:CYS18 4.7 26.6 1.0
N B:CYS157 5.0 30.2 1.0
N B:MET162 5.0 33.5 1.0

Iron binding site 6 out of 16 in 8rc9

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Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.3
occ:1.00
 FE2 B:SF4301 0.0 30.3 1.0
SG B:CYS18 2.2 26.6 1.0
S4 B:SF4301 2.2 29.0 1.0
S3 B:SF4301 2.3 30.1 1.0
S1 B:SF4301 2.3 30.1 1.0
FE1 B:SF4301 2.7 29.8 1.0
FE4 B:SF4301 2.8 31.6 1.0
FE3 B:SF4301 2.8 30.0 1.0
CB B:CYS18 3.2 27.9 1.0
S2 B:SF4301 3.9 29.4 1.0
N B:CYS18 3.9 28.1 1.0
CA B:CYS18 4.2 27.3 1.0
CG B:PRO71 4.5 32.3 1.0
CB B:PRO71 4.8 33.2 1.0
N B:ARG16 4.8 30.7 1.0
SG B:CYS15 4.8 28.9 1.0
SG B:CYS12 4.8 29.6 1.0
CG2 B:VAL53 4.8 31.4 1.0
SG B:CYS157 4.9 29.5 1.0
N B:GLY17 4.9 28.3 1.0
CA B:ARG16 4.9 27.1 1.0

Iron binding site 7 out of 16 in 8rc9

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Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.0
occ:1.00
 FE3 B:SF4301 0.0 30.0 1.0
S2 B:SF4301 2.3 29.4 1.0
S4 B:SF4301 2.3 29.0 1.0
S1 B:SF4301 2.3 30.1 1.0
SG B:CYS15 2.4 28.9 1.0
FE1 B:SF4301 2.7 29.8 1.0
FE4 B:SF4301 2.7 31.6 1.0
FE2 B:SF4301 2.8 30.3 1.0
N B:CYS15 3.5 29.1 1.0
CB B:CYS15 3.6 29.9 1.0
N B:ARG16 3.7 30.7 1.0
S3 B:SF4301 3.9 30.1 1.0
CA B:CYS15 4.0 29.8 1.0
C B:CYS15 4.2 30.0 1.0
CD B:PRO158 4.3 32.9 1.0
N B:GLY17 4.3 28.3 1.0
OG1 B:THR13 4.4 29.2 1.0
C B:ALA14 4.5 27.9 1.0
SG B:CYS18 4.5 26.6 1.0
N B:ALA14 4.6 31.8 1.0
CA B:ARG16 4.7 27.1 1.0
CA B:ALA14 4.7 29.6 1.0
SG B:CYS12 4.8 29.6 1.0
SG B:CYS157 4.8 29.5 1.0
CG B:PRO158 4.9 31.7 1.0
N B:CYS18 4.9 28.1 1.0
C B:ARG16 5.0 28.1 1.0

Iron binding site 8 out of 16 in 8rc9

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Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:31.6
occ:1.00
 FE4 B:SF4301 0.0 31.6 1.0
S1 B:SF4301 2.3 30.1 1.0
S2 B:SF4301 2.3 29.4 1.0
S3 B:SF4301 2.3 30.1 1.0
SG B:CYS12 2.4 29.6 1.0
FE3 B:SF4301 2.7 30.0 1.0
FE2 B:SF4301 2.8 30.3 1.0
FE1 B:SF4301 2.8 29.8 1.0
CB B:CYS12 3.5 24.6 1.0
CA B:CYS12 3.8 25.1 1.0
S4 B:SF4301 3.9 29.0 1.0
N B:ALA14 4.1 31.8 1.0
N B:THR13 4.2 31.7 1.0
OG1 B:THR161 4.3 26.8 1.0
CG B:PRO71 4.4 32.3 1.0
CG2 B:THR161 4.4 32.0 1.0
C B:CYS12 4.4 30.5 1.0
CA B:ALA14 4.4 29.6 1.0
CB B:THR161 4.5 30.4 1.0
SG B:CYS18 4.7 26.6 1.0
N B:CYS15 4.7 29.1 1.0
OG1 B:THR159 4.8 25.8 1.0
SG B:CYS157 4.8 29.5 1.0

Iron binding site 9 out of 16 in 8rc9

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Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:53.9
occ:1.00
 FE1 B:SF4302 0.0 53.9 1.0
S3 B:SF4302 2.2 56.3 1.0
S2 B:SF4302 2.3 46.2 1.0
S4 B:SF4302 2.3 43.6 1.0
SG B:CYS77 2.5 48.9 1.0
FE4 B:SF4302 2.7 48.7 1.0
FE2 B:SF4302 2.8 53.7 1.0
FE3 B:SF4302 2.8 46.4 1.0
CB B:CYS77 3.5 51.0 1.0
N B:CYS77 3.9 48.1 1.0
S1 B:SF4302 3.9 43.8 1.0
CA B:CYS77 4.3 51.7 1.0
N B:HIS76 4.5 40.1 1.0
CB B:PRO80 4.5 54.9 1.0
SG B:CYS121 4.6 45.1 1.0
CD2 B:TYR123 4.6 45.9 1.0
CA B:PRO80 4.7 52.1 1.0
CD B:PRO81 4.8 52.1 1.0
CB B:ARG75 4.8 42.3 1.0
N B:ARG75 4.8 41.0 1.0
SG B:CYS74 4.9 45.7 1.0
CE2 B:TYR123 4.9 45.2 1.0
SG B:CYS82 4.9 55.1 1.0
C B:HIS76 5.0 44.1 1.0

Iron binding site 10 out of 16 in 8rc9

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Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H


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 Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 2 H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:53.7
occ:1.00
 FE2 B:SF4302 0.0 53.7 1.0
S4 B:SF4302 2.3 43.6 1.0
S3 B:SF4302 2.3 56.3 1.0
S1 B:SF4302 2.3 43.8 1.0
SG B:CYS82 2.4 55.1 1.0
FE4 B:SF4302 2.7 48.7 1.0
FE1 B:SF4302 2.8 53.9 1.0
FE3 B:SF4302 2.8 46.4 1.0
CB B:CYS82 3.2 59.8 1.0
S2 B:SF4302 3.9 46.2 1.0
CB B:PRO80 4.2 54.9 1.0
N B:CYS82 4.3 61.8 1.0
CA B:CYS82 4.3 60.6 1.0
CG1 B:VAL103 4.5 41.0 1.0
CE B:LYS137 4.6 50.0 1.0
SG B:CYS121 4.7 45.1 1.0
SG B:CYS74 4.8 45.7 1.0
CA B:PRO80 4.9 52.1 1.0

Reference:

G.Vilela-Alves, R.R.Manuel, A.Viegas, P.Carpentier, F.Biaso, B.Guigliarelli, I.C.Pereira, M.J.Romao, C.Mota. Substrate-Dependent Oxidative Inactivation of A W-Dependent Formate Dehydrogenase Involving Selenocysteine Displacement Chem Sci 2024.
ISSN: ESSN 2041-6539
Page generated: Sat Aug 10 16:36:24 2024

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