Iron in PDB 8rcc: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 Min

Enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 Min

All present enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 Min:
1.2.1.2;

Protein crystallography data

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 Min, PDB code: 8rcc was solved by G.Vilela-Alves, P.Carpentier, 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) 95.84 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.81, 124.401, 150.307, 90, 90, 90
R / Rfree (%) 19.4 / 24.4

Other elements in 8rcc:

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min (pdb code 8rcc). 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min, PDB code: 8rcc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8rcc

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Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min 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
SG A:CYS53 2.2 21.2 1.0
S4 A:SF41103 2.3 21.3 1.0
S3 A:SF41103 2.3 20.5 1.0
S2 A:SF41103 2.3 21.5 1.0
FE2 A:SF41103 2.7 21.3 1.0
FE4 A:SF41103 2.8 22.5 1.0
FE3 A:SF41103 2.8 23.6 1.0
CB A:CYS53 3.3 19.1 1.0
N A:CYS53 3.8 20.0 1.0
CA A:CYS53 3.9 19.7 1.0
S1 A:SF41103 3.9 22.6 1.0
O A:CYS53 4.0 18.7 1.0
CB A:VAL55 4.0 19.5 1.0
C A:CYS53 4.1 20.1 1.0
O A:HOH1218 4.2 21.0 1.0
CG2 A:VAL55 4.3 19.4 1.0
CD A:PRO234 4.6 19.1 1.0
N A:VAL55 4.6 19.9 1.0
SG A:CYS57 4.7 20.9 1.0
SG A:CYS88 4.7 21.1 1.0
SG A:CYS50 4.8 19.6 1.0
CG1 A:VAL55 4.9 20.2 1.0
CA A:VAL55 4.9 20.1 1.0
C A:TYR52 5.0 21.0 1.0

Iron binding site 2 out of 16 in 8rcc

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Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:21.3
occ:1.00
 FE2 A:SF41103 0.0 21.3 1.0
SG A:CYS57 2.2 20.9 1.0
S1 A:SF41103 2.2 22.6 1.0
S4 A:SF41103 2.3 21.3 1.0
S3 A:SF41103 2.3 20.5 1.0
FE3 A:SF41103 2.7 23.6 1.0
FE1 A:SF41103 2.7 21.8 1.0
FE4 A:SF41103 2.7 22.5 1.0
CB A:CYS57 3.2 19.1 1.0
S2 A:SF41103 3.9 21.5 1.0
CG1 A:VAL55 4.2 20.2 1.0
CD1 A:ILE235 4.2 17.6 1.0
N A:CYS57 4.3 17.4 1.0
CB A:VAL55 4.3 19.5 1.0
CA A:CYS57 4.4 18.5 1.0
CB A:ILE235 4.4 17.6 1.0
CG1 A:ILE235 4.4 17.3 1.0
SG A:CYS50 4.6 19.6 1.0
CB A:CYS50 4.6 19.1 1.0
SG A:CYS53 4.7 21.2 1.0
SG A:CYS88 4.9 21.1 1.0
CD2 A:LEU87 5.0 21.8 1.0

Iron binding site 3 out of 16 in 8rcc

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Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:23.6
occ:1.00
 FE3 A:SF41103 0.0 23.6 1.0
SG A:CYS50 2.2 19.6 1.0
S4 A:SF41103 2.3 21.3 1.0
S1 A:SF41103 2.3 22.6 1.0
S2 A:SF41103 2.3 21.5 1.0
FE2 A:SF41103 2.7 21.3 1.0
FE4 A:SF41103 2.7 22.5 1.0
FE1 A:SF41103 2.8 21.8 1.0
CB A:CYS50 3.2 19.1 1.0
S3 A:SF41103 3.9 20.5 1.0
CB A:TYR52 4.2 22.7 1.0
N A:GLY91 4.3 19.3 1.0
CA A:GLY91 4.3 19.7 1.0
N A:CYS53 4.4 20.0 1.0
SG A:CYS88 4.5 21.1 1.0
SG A:CYS57 4.5 20.9 1.0
CA A:CYS50 4.6 20.5 1.0
CB A:CYS57 4.6 19.1 1.0
CD2 A:TYR52 4.8 23.3 1.0
N A:TYR52 4.8 24.3 1.0
CA A:TYR52 4.9 23.0 1.0
SG A:CYS53 4.9 21.2 1.0
O A:CYS53 4.9 18.7 1.0

Iron binding site 4 out of 16 in 8rcc

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Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:22.5
occ:1.00
 FE4 A:SF41103 0.0 22.5 1.0
S1 A:SF41103 2.3 22.6 1.0
SG A:CYS88 2.3 21.1 1.0
S2 A:SF41103 2.3 21.5 1.0
S3 A:SF41103 2.3 20.5 1.0
FE2 A:SF41103 2.7 21.3 1.0
FE3 A:SF41103 2.7 23.6 1.0
FE1 A:SF41103 2.8 21.8 1.0
CB A:CYS88 3.2 23.6 1.0
N A:CYS88 3.8 22.0 1.0
S4 A:SF41103 3.9 21.3 1.0
CA A:CYS88 4.0 22.7 1.0
CD A:PRO234 4.3 19.1 1.0
NZ A:LYS90 4.4 19.2 1.0
CG A:PRO234 4.5 19.0 1.0
N A:GLY91 4.5 19.3 1.0
CD1 A:ILE235 4.6 17.6 1.0
C A:CYS88 4.6 22.7 1.0
O A:HOH1218 4.7 21.0 1.0
O A:CYS88 4.8 22.6 1.0
SG A:CYS53 4.8 21.2 1.0
CB A:PRO234 4.8 18.7 1.0
SG A:CYS57 4.8 20.9 1.0
SG A:CYS50 4.8 19.6 1.0
CE A:LYS90 4.9 20.0 1.0
CB A:LYS90 5.0 19.8 1.0

Iron binding site 5 out of 16 in 8rcc

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Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3302

b:23.5
occ:1.00
 FE1 B:SF43302 0.0 23.5 1.0
S4 B:SF43302 2.3 22.3 1.0
SG B:CYS157 2.3 20.3 1.0
S3 B:SF43302 2.3 21.3 1.0
S2 B:SF43302 2.3 24.7 1.0
FE2 B:SF43302 2.7 22.5 1.0
FE3 B:SF43302 2.7 25.1 1.0
FE4 B:SF43302 2.8 21.7 1.0
CB B:CYS157 3.2 21.5 1.0
OG1 B:THR159 3.7 30.9 1.0
CA B:CYS157 3.7 22.2 1.0
S1 B:SF43302 3.9 22.9 1.0
CB B:THR161 4.1 23.7 1.0
CG B:MET162 4.2 28.9 1.0
CD B:PRO158 4.3 22.2 1.0
OG1 B:THR161 4.5 21.6 1.0
CG2 B:THR161 4.5 23.9 1.0
C B:CYS157 4.5 23.7 1.0
SG B:CYS15 4.7 23.2 1.0
N B:PRO158 4.7 23.4 1.0
SG B:CYS18 4.9 19.8 1.0
N B:MET162 4.9 27.7 1.0
N B:CYS157 4.9 24.0 1.0
CB B:THR159 4.9 28.8 1.0

Iron binding site 6 out of 16 in 8rcc

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Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3302

b:22.5
occ:1.00
 FE2 B:SF43302 0.0 22.5 1.0
S3 B:SF43302 2.3 21.3 1.0
S4 B:SF43302 2.3 22.3 1.0
S1 B:SF43302 2.3 22.9 1.0
SG B:CYS18 2.3 19.8 1.0
FE1 B:SF43302 2.7 23.5 1.0
FE4 B:SF43302 2.7 21.7 1.0
FE3 B:SF43302 2.8 25.1 1.0
CB B:CYS18 3.2 21.5 1.0
S2 B:SF43302 3.9 24.7 1.0
N B:CYS18 3.9 22.4 1.0
CA B:CYS18 4.2 22.2 1.0
N B:ARG16 4.6 22.3 1.0
CG B:PRO71 4.6 28.8 1.0
CB B:PRO71 4.7 28.4 1.0
N B:GLY17 4.7 23.5 1.0
CA B:ARG16 4.7 23.8 1.0
SG B:CYS15 4.7 23.2 1.0
CG2 B:VAL53 4.7 23.7 1.0
SG B:CYS12 4.8 26.2 1.0
SG B:CYS157 4.8 20.3 1.0
C B:ARG16 4.9 23.0 1.0

Iron binding site 7 out of 16 in 8rcc

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Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3302

b:25.1
occ:1.00
 FE3 B:SF43302 0.0 25.1 1.0
S2 B:SF43302 2.3 24.7 1.0
S1 B:SF43302 2.3 22.9 1.0
S4 B:SF43302 2.3 22.3 1.0
SG B:CYS15 2.3 23.2 1.0
FE1 B:SF43302 2.7 23.5 1.0
FE2 B:SF43302 2.8 22.5 1.0
FE4 B:SF43302 2.8 21.7 1.0
CB B:CYS15 3.6 21.3 1.0
N B:CYS15 3.6 21.1 1.0
N B:ARG16 3.7 22.3 1.0
S3 B:SF43302 3.9 21.3 1.0
CA B:CYS15 4.0 21.6 1.0
C B:CYS15 4.2 20.8 1.0
N B:GLY17 4.2 23.5 1.0
OG1 B:THR13 4.3 25.0 1.0
CD B:PRO158 4.4 22.2 1.0
C B:ALA14 4.5 19.5 1.0
N B:ALA14 4.5 19.1 1.0
CA B:ARG16 4.6 23.8 1.0
SG B:CYS157 4.7 20.3 1.0
SG B:CYS18 4.7 19.8 1.0
CA B:ALA14 4.8 19.3 1.0
SG B:CYS12 4.8 26.2 1.0
C B:ARG16 4.9 23.0 1.0
N B:THR13 4.9 20.8 1.0
N B:CYS18 4.9 22.4 1.0

Iron binding site 8 out of 16 in 8rcc

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Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3302

b:21.7
occ:1.00
 FE4 B:SF43302 0.0 21.7 1.0
S3 B:SF43302 2.3 21.3 1.0
S1 B:SF43302 2.3 22.9 1.0
S2 B:SF43302 2.3 24.7 1.0
SG B:CYS12 2.4 26.2 1.0
FE2 B:SF43302 2.7 22.5 1.0
FE3 B:SF43302 2.8 25.1 1.0
FE1 B:SF43302 2.8 23.5 1.0
CB B:CYS12 3.4 24.7 1.0
CA B:CYS12 3.7 24.3 1.0
S4 B:SF43302 3.9 22.3 1.0
N B:ALA14 4.0 19.1 1.0
N B:THR13 4.1 20.8 1.0
C B:CYS12 4.3 22.8 1.0
CG2 B:THR161 4.4 23.9 1.0
OG1 B:THR161 4.4 21.6 1.0
CA B:ALA14 4.5 19.3 1.0
CB B:THR161 4.6 23.7 1.0
OG1 B:THR159 4.6 30.9 1.0
CG B:PRO71 4.7 28.8 1.0
SG B:CYS157 4.8 20.3 1.0
N B:CYS15 4.8 21.1 1.0
SG B:CYS18 4.9 19.8 1.0
SG B:CYS15 5.0 23.2 1.0

Iron binding site 9 out of 16 in 8rcc

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Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3303

b:42.0
occ:1.00
 FE1 B:SF43303 0.0 42.0 1.0
SG B:CYS77 2.3 31.7 1.0
S2 B:SF43303 2.3 41.7 1.0
S4 B:SF43303 2.3 38.1 1.0
S3 B:SF43303 2.3 37.4 1.0
FE4 B:SF43303 2.7 39.0 1.0
FE2 B:SF43303 2.8 40.8 1.0
FE3 B:SF43303 2.8 36.6 1.0
CB B:CYS77 3.6 31.8 1.0
S1 B:SF43303 3.9 35.3 1.0
N B:CYS77 4.0 34.1 1.0
CD B:PRO81 4.3 46.0 1.0
CA B:CYS77 4.4 33.1 1.0
N B:HIS76 4.5 34.2 1.0
CD2 B:TYR123 4.6 37.5 1.0
SG B:CYS74 4.6 40.2 1.0
CB B:ARG75 4.6 35.4 1.0
N B:ARG75 4.6 34.9 1.0
SG B:CYS121 4.7 49.1 1.0
SG B:CYS82 4.8 45.9 1.0
CE2 B:TYR123 4.9 36.9 1.0
C B:HIS76 5.0 33.3 1.0
CA B:PRO80 5.0 45.5 1.0
C B:ARG75 5.0 34.0 1.0
CA B:HIS76 5.0 33.1 1.0

Iron binding site 10 out of 16 in 8rcc

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Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Aerobic Soaked with 48 Bar CO2 For 1 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 - Aerobic Soaked with 48 Bar CO2 For 1 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3303

b:40.8
occ:1.00
 FE2 B:SF43303 0.0 40.8 1.0
S4 B:SF43303 2.3 38.1 1.0
SG B:CYS82 2.3 45.9 1.0
S3 B:SF43303 2.3 37.4 1.0
S1 B:SF43303 2.3 35.3 1.0
FE3 B:SF43303 2.7 36.6 1.0
FE4 B:SF43303 2.7 39.0 1.0
FE1 B:SF43303 2.8 42.0 1.0
CB B:CYS82 3.1 43.9 1.0
S2 B:SF43303 3.9 41.7 1.0
N B:CYS82 4.2 46.5 1.0
CA B:CYS82 4.3 46.8 1.0
CG1 B:VAL103 4.4 32.4 1.0
CB B:PRO80 4.6 45.6 1.0
SG B:CYS74 4.7 40.2 1.0
SG B:CYS121 4.7 49.1 1.0
SG B:CYS77 4.8 31.7 1.0
CE B:LYS137 4.9 40.9 1.0
CB B:CYS121 5.0 44.0 1.0
CD B:PRO81 5.0 46.0 1.0
CA B:PRO80 5.0 45.5 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 16:38:31 2024

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