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

Go back to Iron Binding Sites List in 8rc9
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

Go back to Iron Binding Sites List in 8rc9
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

Go back to Iron Binding Sites List in 8rc9
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

Go back to Iron Binding Sites List in 8rc9
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

Go back to Iron Binding Sites List in 8rc9
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

Go back to Iron Binding Sites List in 8rc9
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

Go back to Iron Binding Sites List in 8rc9
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

Go back to Iron Binding Sites List in 8rc9
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

Go back to Iron Binding Sites List in 8rc9
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

Go back to Iron Binding Sites List in 8rc9
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

Last articles

W in 8QLN
W in 8RJA
V in 8WTN
Te in 8QLN
Re in 9GHX
Rb in 8Z5C
Ni in 9C0T
Ni in 9C0S
Ni in 9GP1
Ni in 9FYO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy