Atomistry » Iron » PDB 6rsk-6sv1 » 6sdr
Atomistry »
  Iron »
    PDB 6rsk-6sv1 »
      6sdr »

Iron in PDB 6sdr: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form

Enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form

All present enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form:
1.2.1.2;

Protein crystallography data

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form, PDB code: 6sdr was solved by A.R.Oliveira, C.Mota, C.Mourato, R.M.Domingos, M.F.A.Santos, D.Gesto, B.Guigliarelli, T.Santos-Silva, M.J.Romao, I.C.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.36 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.593, 127.644, 148.213, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.6

Other elements in 6sdr:

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form 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 - Oxidized Form (pdb code 6sdr). 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 - Oxidized Form, PDB code: 6sdr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:16.9
occ:1.00
FE1 A:SF41103 0.0 16.9 1.0
S3 A:SF41103 2.2 14.3 1.0
S4 A:SF41103 2.3 18.3 1.0
S2 A:SF41103 2.3 17.7 1.0
SG A:CYS53 2.4 18.7 1.0
FE4 A:SF41103 2.7 16.9 1.0
FE2 A:SF41103 2.7 18.4 1.0
FE3 A:SF41103 2.7 18.9 1.0
CB A:CYS53 3.5 14.4 1.0
N A:CYS53 3.7 16.9 1.0
CB A:VAL55 3.8 24.2 1.0
S1 A:SF41103 3.8 20.9 1.0
CA A:CYS53 3.9 15.1 1.0
O A:HOH1357 4.0 15.1 1.0
O A:CYS53 4.0 16.9 1.0
CG2 A:VAL55 4.1 20.4 1.0
C A:CYS53 4.1 20.0 1.0
N A:VAL55 4.4 20.2 1.0
CD A:PRO234 4.5 17.1 1.0
CA A:VAL55 4.7 16.7 1.0
SG A:CYS50 4.7 17.0 1.0
SG A:CYS88 4.8 15.7 1.0
SG A:CYS57 4.8 18.0 1.0
CG1 A:VAL55 4.8 19.2 1.0
C A:TYR52 4.9 27.6 1.0
N A:ALA54 4.9 18.7 1.0

Iron binding site 2 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:18.4
occ:1.00
FE2 A:SF41103 0.0 18.4 1.0
SG A:CYS57 2.3 18.0 1.0
S4 A:SF41103 2.3 18.3 1.0
S1 A:SF41103 2.3 20.9 1.0
S3 A:SF41103 2.3 14.3 1.0
FE3 A:SF41103 2.7 18.9 1.0
FE1 A:SF41103 2.7 16.9 1.0
FE4 A:SF41103 2.8 16.9 1.0
CB A:CYS57 3.2 18.4 1.0
CD1 A:ILE235 3.8 24.3 1.0
S2 A:SF41103 3.9 17.7 1.0
CB A:VAL55 4.0 24.2 1.0
CG1 A:VAL55 4.0 19.2 1.0
N A:CYS57 4.2 18.3 1.0
CG1 A:ILE235 4.3 15.8 1.0
CA A:CYS57 4.3 21.4 1.0
CB A:ILE235 4.3 14.2 1.0
SG A:CYS50 4.6 17.0 1.0
CB A:CYS50 4.7 18.0 1.0
CG2 A:VAL55 4.7 20.4 1.0
SG A:CYS53 4.8 18.7 1.0
CD2 A:LEU87 4.9 19.5 1.0
N A:GLY56 5.0 14.9 1.0

Iron binding site 3 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:18.9
occ:1.00
FE3 A:SF41103 0.0 18.9 1.0
S1 A:SF41103 2.2 20.9 1.0
SG A:CYS50 2.2 17.0 1.0
S4 A:SF41103 2.3 18.3 1.0
S2 A:SF41103 2.3 17.7 1.0
FE2 A:SF41103 2.7 18.4 1.0
FE4 A:SF41103 2.7 16.9 1.0
FE1 A:SF41103 2.7 16.9 1.0
CB A:CYS50 3.2 18.0 1.0
S3 A:SF41103 3.9 14.3 1.0
CB A:TYR52 4.2 16.9 1.0
CA A:GLY91 4.2 29.8 1.0
N A:GLY91 4.3 25.0 1.0
N A:CYS53 4.3 16.9 1.0
SG A:CYS88 4.6 15.7 1.0
SG A:CYS57 4.6 18.0 1.0
CA A:CYS50 4.6 18.9 1.0
CB A:CYS57 4.7 18.4 1.0
N A:TYR52 4.7 17.5 1.0
CD2 A:TYR52 4.8 23.4 1.0
CA A:TYR52 4.8 17.0 1.0
SG A:CYS53 4.9 18.7 1.0
C A:TYR52 5.0 27.6 1.0
O A:CYS53 5.0 16.9 1.0

Iron binding site 4 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:16.9
occ:1.00
FE4 A:SF41103 0.0 16.9 1.0
S1 A:SF41103 2.3 20.9 1.0
S2 A:SF41103 2.3 17.7 1.0
S3 A:SF41103 2.3 14.3 1.0
SG A:CYS88 2.3 15.7 1.0
FE1 A:SF41103 2.7 16.9 1.0
FE3 A:SF41103 2.7 18.9 1.0
FE2 A:SF41103 2.8 18.4 1.0
CB A:CYS88 3.3 18.3 1.0
S4 A:SF41103 3.9 18.3 1.0
N A:CYS88 3.9 19.6 1.0
CA A:CYS88 4.1 20.9 1.0
CD1 A:ILE235 4.2 24.3 1.0
CD A:PRO234 4.2 17.1 1.0
NZ A:LYS90 4.4 15.8 1.0
N A:GLY91 4.4 25.0 1.0
CG A:PRO234 4.5 20.6 1.0
O A:HOH1357 4.5 15.1 1.0
C A:CYS88 4.7 22.5 1.0
SG A:CYS53 4.8 18.7 1.0
SG A:CYS50 4.8 17.0 1.0
O A:CYS88 4.8 18.7 1.0
CB A:PRO234 4.9 16.0 1.0
SG A:CYS57 4.9 18.0 1.0
CA A:GLY91 4.9 29.8 1.0
CE A:LYS90 5.0 20.2 1.0

Iron binding site 5 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:19.7
occ:1.00
FE1 B:SF4301 0.0 19.7 1.0
S3 B:SF4301 2.3 24.3 1.0
S4 B:SF4301 2.3 24.4 1.0
S2 B:SF4301 2.3 23.0 1.0
SG B:CYS157 2.3 25.5 1.0
FE2 B:SF4301 2.7 21.5 1.0
FE4 B:SF4301 2.7 22.2 1.0
FE3 B:SF4301 2.8 22.1 1.0
CB B:CYS157 3.3 22.0 1.0
OG1 B:THR159 3.8 16.9 1.0
CA B:CYS157 3.8 18.3 1.0
S1 B:SF4301 3.9 18.6 1.0
CB B:THR161 4.0 22.7 1.0
CG B:MET162 4.3 25.4 1.0
CD B:PRO158 4.3 16.1 1.0
OG1 B:THR161 4.4 26.1 1.0
CG2 B:THR161 4.5 19.8 1.0
C B:CYS157 4.6 22.5 1.0
SG B:CYS15 4.6 19.8 1.0
N B:PRO158 4.7 18.1 1.0
SG B:CYS18 4.8 28.4 1.0
SG B:CYS12 4.9 21.5 1.0
N B:THR159 5.0 20.5 1.0

Iron binding site 6 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:21.5
occ:1.00
FE2 B:SF4301 0.0 21.5 1.0
S4 B:SF4301 2.3 24.4 1.0
SG B:CYS18 2.3 28.4 1.0
S3 B:SF4301 2.3 24.3 1.0
S1 B:SF4301 2.3 18.6 1.0
FE1 B:SF4301 2.7 19.7 1.0
FE3 B:SF4301 2.7 22.1 1.0
FE4 B:SF4301 2.7 22.2 1.0
CB B:CYS18 3.2 20.1 1.0
O B:HOH444 3.8 21.1 1.0
N B:CYS18 3.8 20.9 1.0
S2 B:SF4301 3.9 23.0 1.0
CA B:CYS18 4.2 20.0 1.0
CG B:PRO71 4.4 24.9 1.0
N B:ARG16 4.5 21.5 1.0
SG B:CYS15 4.6 19.8 1.0
N B:GLY17 4.7 18.1 1.0
CA B:ARG16 4.7 25.3 1.0
SG B:CYS12 4.7 21.5 1.0
SG B:CYS157 4.8 25.5 1.0
CB B:PRO71 4.8 24.2 1.0
CG2 B:VAL53 4.9 31.3 1.0
C B:ARG16 5.0 25.5 1.0
C B:GLY17 5.0 25.5 1.0

Iron binding site 7 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:22.1
occ:1.00
FE3 B:SF4301 0.0 22.1 1.0
S1 B:SF4301 2.3 18.6 1.0
S2 B:SF4301 2.3 23.0 1.0
S4 B:SF4301 2.3 24.4 1.0
SG B:CYS15 2.3 19.8 1.0
FE2 B:SF4301 2.7 21.5 1.0
FE4 B:SF4301 2.7 22.2 1.0
FE1 B:SF4301 2.8 19.7 1.0
N B:CYS15 3.4 27.4 1.0
CB B:CYS15 3.4 23.1 1.0
N B:ARG16 3.6 21.5 1.0
CA B:CYS15 3.8 16.7 1.0
S3 B:SF4301 3.9 24.3 1.0
C B:CYS15 4.0 20.1 1.0
N B:GLY17 4.2 18.1 1.0
C B:ALA14 4.4 27.1 1.0
CD B:PRO158 4.4 16.1 1.0
OG1 B:THR13 4.5 23.0 1.0
CA B:ARG16 4.5 25.3 1.0
N B:ALA14 4.5 17.5 1.0
SG B:CYS12 4.7 21.5 1.0
SG B:CYS18 4.7 28.4 1.0
CA B:ALA14 4.8 22.6 1.0
SG B:CYS157 4.8 25.5 1.0
N B:CYS18 4.9 20.9 1.0
C B:ARG16 4.9 25.5 1.0
N B:THR13 5.0 20.5 1.0

Iron binding site 8 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form 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 23.0 1.0
SG B:CYS12 2.3 21.5 1.0
S3 B:SF4301 2.3 24.3 1.0
S1 B:SF4301 2.3 18.6 1.0
FE1 B:SF4301 2.7 19.7 1.0
FE3 B:SF4301 2.7 22.1 1.0
FE2 B:SF4301 2.7 21.5 1.0
CB B:CYS12 3.4 21.7 1.0
CA B:CYS12 3.8 19.1 1.0
S4 B:SF4301 3.9 24.4 1.0
N B:ALA14 4.0 17.5 1.0
N B:THR13 4.1 20.5 1.0
C B:CYS12 4.4 20.1 1.0
CG B:PRO71 4.4 24.9 1.0
OG1 B:THR161 4.4 26.1 1.0
CA B:ALA14 4.5 22.6 1.0
CG2 B:THR161 4.5 19.8 1.0
N B:CYS15 4.5 27.4 1.0
CB B:THR161 4.6 22.7 1.0
SG B:CYS18 4.8 28.4 1.0
OG1 B:THR159 4.8 16.9 1.0
SG B:CYS157 4.9 25.5 1.0
C B:THR13 5.0 19.4 1.0
C B:ALA14 5.0 27.1 1.0

Iron binding site 9 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:41.3
occ:1.00
FE1 B:SF4302 0.0 41.3 1.0
S3 B:SF4302 2.3 39.9 1.0
S2 B:SF4302 2.3 41.8 1.0
S4 B:SF4302 2.3 37.0 1.0
SG B:CYS77 2.4 47.0 1.0
FE4 B:SF4302 2.7 41.0 1.0
FE2 B:SF4302 2.8 40.7 1.0
FE3 B:SF4302 2.8 40.5 1.0
CB B:CYS77 3.6 45.5 1.0
N B:CYS77 3.7 42.0 1.0
S1 B:SF4302 3.9 45.6 1.0
CA B:CYS77 4.2 45.0 1.0
N B:HIS76 4.3 33.9 1.0
CB B:PRO80 4.5 48.9 1.0
CD2 B:TYR123 4.6 44.1 1.0
SG B:CYS74 4.6 36.7 1.0
SG B:CYS121 4.7 40.6 1.0
CA B:HIS76 4.7 34.9 1.0
C B:HIS76 4.7 38.6 1.0
CB B:ARG75 4.7 32.7 1.0
CD B:PRO81 4.7 43.5 1.0
CA B:PRO80 4.7 45.5 1.0
N B:ARG75 4.7 37.6 1.0
SG B:CYS82 4.8 43.1 1.0
CE2 B:TYR123 4.9 42.2 1.0
C B:ARG75 4.9 40.5 1.0

Iron binding site 10 out of 16 in 6sdr

Go back to Iron Binding Sites List in 6sdr
Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form


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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:40.7
occ:1.00
FE2 B:SF4302 0.0 40.7 1.0
S1 B:SF4302 2.3 45.6 1.0
S3 B:SF4302 2.3 39.9 1.0
S4 B:SF4302 2.3 37.0 1.0
SG B:CYS82 2.3 43.1 1.0
FE4 B:SF4302 2.7 41.0 1.0
FE3 B:SF4302 2.7 40.5 1.0
FE1 B:SF4302 2.8 41.3 1.0
CB B:CYS82 3.1 42.8 1.0
S2 B:SF4302 3.9 41.8 1.0
CB B:PRO80 4.2 48.9 1.0
N B:CYS82 4.2 52.5 1.0
CA B:CYS82 4.2 53.8 1.0
CG1 B:VAL103 4.5 42.3 1.0
CE B:LYS137 4.7 40.5 1.0
SG B:CYS74 4.7 36.7 1.0
CB B:CYS121 4.8 43.8 1.0
SG B:CYS121 4.8 40.6 1.0
CA B:PRO80 4.8 45.5 1.0
SG B:CYS77 4.9 47.0 1.0
CD B:LYS137 5.0 49.8 1.0
CZ B:PHE105 5.0 47.4 1.0

Reference:

A.R.Oliveira, C.Mota, C.Mourato, R.M.Domingos, M.F.A.Santos, D.Gesto, B.Guigliarelli, T.Santos-Silva, M.J.Romao, I.C.Pereira. Towards the Mechanistic Understanding of Enzymatic CO2 Reduction Acs Catalysis 2020.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.0C00086
Page generated: Sun Dec 13 17:05:47 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy