Iron in PDB 8rc8: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 0 Min

Enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 0 Min

All present enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 0 Min:
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 0 Min, PDB code: 8rc8 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) 47.90 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.988, 124.345, 149.899, 90, 90, 90
R / Rfree (%) 18.1 / 22

Other elements in 8rc8:

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Exposed to Air For 0 Min 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 0 Min (pdb code 8rc8). 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 0 Min, PDB code: 8rc8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:20.9
occ:1.00
 FE1 A:SF41103 0.0 20.9 1.0
S4 A:SF41103 2.3 19.4 1.0
S2 A:SF41103 2.3 19.6 1.0
S3 A:SF41103 2.3 20.3 1.0
SG A:CYS53 2.3 19.2 1.0
FE3 A:SF41103 2.8 19.8 1.0
FE4 A:SF41103 2.8 19.2 1.0
FE2 A:SF41103 2.8 19.5 1.0
CB A:CYS53 3.4 19.5 1.0
N A:CYS53 3.8 19.1 1.0
CA A:CYS53 3.9 19.3 1.0
S1 A:SF41103 3.9 19.7 1.0
O A:HOH1360 4.0 16.6 1.0
CB A:VAL55 4.0 18.7 1.0
C A:CYS53 4.1 21.4 1.0
CG2 A:VAL55 4.2 17.8 1.0
O A:CYS53 4.2 19.2 1.0
N A:VAL55 4.6 17.4 1.0
CD A:PRO234 4.6 18.2 1.0
SG A:CYS50 4.8 21.5 1.0
SG A:CYS88 4.8 20.7 1.0
SG A:CYS57 4.8 20.2 1.0
CA A:VAL55 4.9 17.9 1.0
N A:ALA54 4.9 20.2 1.0
CG1 A:VAL55 5.0 18.8 1.0

Iron binding site 2 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:19.5
occ:1.00
 FE2 A:SF41103 0.0 19.5 1.0
S4 A:SF41103 2.3 19.4 1.0
S1 A:SF41103 2.3 19.7 1.0
SG A:CYS57 2.3 20.2 1.0
S3 A:SF41103 2.3 20.3 1.0
FE3 A:SF41103 2.7 19.8 1.0
FE1 A:SF41103 2.8 20.9 1.0
FE4 A:SF41103 2.8 19.2 1.0
CB A:CYS57 3.2 21.3 1.0
S2 A:SF41103 3.9 19.6 1.0
CD1 A:ILE235 4.1 18.4 1.0
CB A:VAL55 4.3 18.7 1.0
N A:CYS57 4.3 19.9 1.0
CG1 A:ILE235 4.3 18.7 1.0
CG1 A:VAL55 4.3 18.8 1.0
CB A:ILE235 4.4 18.6 1.0
CA A:CYS57 4.4 19.7 1.0
SG A:CYS50 4.7 21.5 1.0
CB A:CYS50 4.7 20.6 1.0
SG A:CYS53 4.9 19.2 1.0
CD2 A:LEU87 4.9 20.5 1.0
CG2 A:VAL55 4.9 17.8 1.0

Iron binding site 3 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:19.8
occ:1.00
 FE3 A:SF41103 0.0 19.8 1.0
S4 A:SF41103 2.3 19.4 1.0
S1 A:SF41103 2.3 19.7 1.0
SG A:CYS50 2.3 21.5 1.0
S2 A:SF41103 2.3 19.6 1.0
FE2 A:SF41103 2.7 19.5 1.0
FE4 A:SF41103 2.7 19.2 1.0
FE1 A:SF41103 2.8 20.9 1.0
CB A:CYS50 3.2 20.6 1.0
S3 A:SF41103 3.9 20.3 1.0
CA A:GLY91 4.2 21.1 1.0
N A:GLY91 4.3 21.3 1.0
CB A:TYR52 4.3 20.2 1.0
N A:CYS53 4.4 19.1 1.0
CA A:CYS50 4.6 20.8 1.0
SG A:CYS57 4.7 20.2 1.0
SG A:CYS88 4.7 20.7 1.0
CB A:CYS57 4.7 21.3 1.0
N A:TYR52 4.8 22.3 1.0
SG A:CYS53 4.9 19.2 1.0
CA A:TYR52 5.0 21.5 1.0

Iron binding site 4 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:19.2
occ:1.00
 FE4 A:SF41103 0.0 19.2 1.0
S1 A:SF41103 2.3 19.7 1.0
S3 A:SF41103 2.3 20.3 1.0
S2 A:SF41103 2.3 19.6 1.0
SG A:CYS88 2.3 20.7 1.0
FE3 A:SF41103 2.7 19.8 1.0
FE1 A:SF41103 2.8 20.9 1.0
FE2 A:SF41103 2.8 19.5 1.0
CB A:CYS88 3.3 22.3 1.0
N A:CYS88 3.9 20.9 1.0
S4 A:SF41103 3.9 19.4 1.0
CA A:CYS88 4.1 22.4 1.0
CD A:PRO234 4.3 18.2 1.0
N A:GLY91 4.4 21.3 1.0
CD1 A:ILE235 4.5 18.4 1.0
NZ A:LYS90 4.5 19.9 1.0
CG A:PRO234 4.6 16.9 1.0
O A:HOH1360 4.6 16.6 1.0
C A:CYS88 4.7 21.5 1.0
SG A:CYS53 4.8 19.2 1.0
SG A:CYS50 4.9 21.5 1.0
O A:CYS88 4.9 22.6 1.0
CA A:GLY91 4.9 21.1 1.0
CB A:PRO234 4.9 17.8 1.0
CE A:LYS90 4.9 21.5 1.0
SG A:CYS57 5.0 20.2 1.0
CB A:LYS90 5.0 22.4 1.0

Iron binding site 5 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:20.1
occ:1.00
 FE1 B:SF4301 0.0 20.1 1.0
S3 B:SF4301 2.3 22.3 1.0
S4 B:SF4301 2.3 22.2 1.0
S2 B:SF4301 2.3 21.2 1.0
SG B:CYS157 2.3 21.6 1.0
FE2 B:SF4301 2.8 23.3 1.0
FE3 B:SF4301 2.8 20.9 1.0
FE4 B:SF4301 2.8 22.2 1.0
CB B:CYS157 3.3 20.1 1.0
CA B:CYS157 3.8 19.9 1.0
OG1 B:THR159 3.9 19.4 1.0
S1 B:SF4301 3.9 22.7 1.0
CD B:PRO158 4.1 21.1 1.0
CB B:THR161 4.1 20.7 1.0
CG B:MET162 4.3 26.1 1.0
OG1 B:THR161 4.4 22.2 1.0
C B:CYS157 4.5 19.9 1.0
N B:PRO158 4.5 20.5 1.0
CG2 B:THR161 4.6 19.4 1.0
SG B:CYS15 4.7 20.5 1.0
SG B:CYS18 4.9 21.4 1.0
N B:THR159 4.9 20.1 1.0
N B:MET162 5.0 23.7 1.0

Iron binding site 6 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:23.3
occ:1.00
 FE2 B:SF4301 0.0 23.3 1.0
S4 B:SF4301 2.3 22.2 1.0
S3 B:SF4301 2.3 22.3 1.0
S1 B:SF4301 2.3 22.7 1.0
SG B:CYS18 2.3 21.4 1.0
FE3 B:SF4301 2.7 20.9 1.0
FE1 B:SF4301 2.8 20.1 1.0
FE4 B:SF4301 2.8 22.2 1.0
CB B:CYS18 3.3 24.4 1.0
O B:HOH437 3.9 20.4 1.0
S2 B:SF4301 3.9 21.2 1.0
N B:CYS18 3.9 21.7 1.0
CA B:CYS18 4.3 23.3 1.0
CG B:PRO71 4.4 25.2 1.0
N B:GLY17 4.7 19.6 1.0
N B:ARG16 4.7 20.9 1.0
SG B:CYS15 4.7 20.5 1.0
CB B:PRO71 4.7 22.3 1.0
CA B:ARG16 4.8 20.3 1.0
SG B:CYS12 4.8 21.5 1.0
CG2 B:VAL53 4.9 19.8 1.0
SG B:CYS157 4.9 21.6 1.0

Iron binding site 7 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:20.9
occ:1.00
 FE3 B:SF4301 0.0 20.9 1.0
S2 B:SF4301 2.3 21.2 1.0
S4 B:SF4301 2.3 22.2 1.0
S1 B:SF4301 2.3 22.7 1.0
SG B:CYS15 2.4 20.5 1.0
FE2 B:SF4301 2.7 23.3 1.0
FE4 B:SF4301 2.8 22.2 1.0
FE1 B:SF4301 2.8 20.1 1.0
N B:CYS15 3.5 20.8 1.0
CB B:CYS15 3.6 22.5 1.0
N B:ARG16 3.7 20.9 1.0
S3 B:SF4301 3.9 22.3 1.0
CA B:CYS15 3.9 21.6 1.0
CD B:PRO158 4.2 21.1 1.0
N B:GLY17 4.2 19.6 1.0
C B:CYS15 4.3 19.2 1.0
OG1 B:THR13 4.4 19.9 1.0
C B:ALA14 4.5 21.3 1.0
N B:ALA14 4.6 21.1 1.0
CA B:ARG16 4.6 20.3 1.0
CG B:PRO158 4.6 22.2 1.0
SG B:CYS18 4.7 21.4 1.0
CA B:ALA14 4.7 19.6 1.0
SG B:CYS12 4.7 21.5 1.0
SG B:CYS157 4.8 21.6 1.0
C B:ARG16 4.9 19.5 1.0
CA B:GLY17 4.9 20.1 1.0
N B:CYS18 4.9 21.7 1.0
N B:THR13 5.0 21.6 1.0

Iron binding site 8 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:22.2
occ:1.00
 FE4 B:SF4301 0.0 22.2 1.0
S2 B:SF4301 2.3 21.2 1.0
S1 B:SF4301 2.3 22.7 1.0
S3 B:SF4301 2.3 22.3 1.0
SG B:CYS12 2.4 21.5 1.0
FE3 B:SF4301 2.8 20.9 1.0
FE2 B:SF4301 2.8 23.3 1.0
FE1 B:SF4301 2.8 20.1 1.0
CB B:CYS12 3.5 17.6 1.0
CA B:CYS12 3.9 19.2 1.0
S4 B:SF4301 3.9 22.2 1.0
N B:ALA14 4.1 21.1 1.0
N B:THR13 4.2 21.6 1.0
CG B:PRO71 4.3 25.2 1.0
OG1 B:THR161 4.3 22.2 1.0
CG2 B:THR161 4.4 19.4 1.0
CB B:THR161 4.5 20.7 1.0
C B:CYS12 4.5 18.8 1.0
CA B:ALA14 4.5 19.6 1.0
N B:CYS15 4.8 20.8 1.0
OG1 B:THR159 4.8 19.4 1.0
SG B:CYS18 4.9 21.4 1.0
SG B:CYS157 4.9 21.6 1.0

Iron binding site 9 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:35.3
occ:1.00
 FE1 B:SF4302 0.0 35.3 1.0
SG B:CYS77 2.2 33.5 1.0
S3 B:SF4302 2.3 35.0 1.0
S2 B:SF4302 2.3 32.6 1.0
S4 B:SF4302 2.3 31.2 1.0
FE4 B:SF4302 2.7 34.0 1.0
FE2 B:SF4302 2.7 32.9 1.0
FE3 B:SF4302 2.8 31.6 1.0
CB B:CYS77 3.4 31.7 1.0
N B:CYS77 3.9 30.4 1.0
S1 B:SF4302 3.9 32.3 1.0
CA B:CYS77 4.3 32.3 1.0
CD2 B:TYR123 4.5 32.7 1.0
N B:HIS76 4.6 28.4 1.0
SG B:CYS121 4.6 36.3 1.0
CD B:PRO81 4.6 37.3 1.0
SG B:CYS74 4.7 29.7 1.0
CE2 B:TYR123 4.8 33.0 1.0
N B:ARG75 4.8 26.0 1.0
CA B:PRO80 4.8 39.0 1.0
CB B:PRO80 4.9 41.9 1.0
CB B:ARG75 4.9 24.8 1.0
SG B:CYS82 4.9 35.0 1.0
C B:HIS76 4.9 25.1 1.0

Iron binding site 10 out of 16 in 8rc8

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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 0 Min


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 0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:32.9
occ:1.00
 FE2 B:SF4302 0.0 32.9 1.0
S4 B:SF4302 2.3 31.2 1.0
S1 B:SF4302 2.3 32.3 1.0
S3 B:SF4302 2.3 35.0 1.0
SG B:CYS82 2.4 35.0 1.0
FE1 B:SF4302 2.7 35.3 1.0
FE3 B:SF4302 2.7 31.6 1.0
FE4 B:SF4302 2.7 34.0 1.0
CB B:CYS82 3.2 32.4 1.0
S2 B:SF4302 3.9 32.6 1.0
N B:CYS82 4.2 38.8 1.0
CA B:CYS82 4.3 36.3 1.0
CB B:PRO80 4.4 41.9 1.0
CG1 B:VAL103 4.5 38.3 1.0
CE B:LYS137 4.7 29.7 1.0
SG B:CYS74 4.8 29.7 1.0
SG B:CYS77 4.8 33.5 1.0
SG B:CYS121 4.8 36.3 1.0
CA B:PRO80 4.9 39.0 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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