Atomistry » Iron » PDB 2zqx-30sj » 30gj
Atomistry »
  Iron »
    PDB 2zqx-30sj »
      30gj »

Iron in PDB 30gj: W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography

Enzymatic activity of W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography

All present enzymatic activity of W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography:
1.2.1.2;

Protein crystallography data

The structure of W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography, PDB code: 30gj was solved by G.Vilela-Alves, G.Martins, D.Von Stetten, P.Mehrabi, I.C.Pereira, M.J.Romao, A.R.Pearson, C.Mota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.79 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.5, 129.6, 151.9, 90, 90, 90
R / Rfree (%) 18.5 / 22.2

Other elements in 30gj:

The structure of W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography 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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography (pdb code 30gj). 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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography, PDB code: 30gj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:13.9
occ:1.00
 FE1 A:SF41103 0.0 13.9 1.0
SG A:CYS53 2.2 13.7 1.0
S2 A:SF41103 2.3 13.9 1.0
S4 A:SF41103 2.3 14.2 1.0
S3 A:SF41103 2.3 14.5 1.0
FE4 A:SF41103 2.7 13.4 1.0
FE3 A:SF41103 2.7 15.4 1.0
FE2 A:SF41103 2.8 14.6 1.0
CB A:CYS53 3.4 13.4 1.0
N A:CYS53 3.7 14.4 1.0
CA A:CYS53 3.8 14.9 1.0
S1 A:SF41103 3.9 14.0 1.0
O A:CYS53 3.9 16.3 1.0
C A:CYS53 4.1 14.9 1.0
O A:HOH1271 4.2 13.2 1.0
CB A:VAL55 4.2 13.3 1.0
CG2 A:VAL55 4.3 13.3 1.0
CD A:PRO234 4.5 16.3 1.0
SG A:CYS88 4.6 14.6 1.0
N A:VAL55 4.7 13.5 1.0
SG A:CYS50 4.7 14.7 1.0
SG A:CYS57 4.8 14.6 1.0
C A:TYR52 4.8 15.4 1.0
N A:ALA54 5.0 15.2 1.0

Iron binding site 2 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:14.6
occ:1.00
 FE2 A:SF41103 0.0 14.6 1.0
S1 A:SF41103 2.3 14.0 1.0
SG A:CYS57 2.3 14.6 1.0
S3 A:SF41103 2.3 14.5 1.0
S4 A:SF41103 2.3 14.2 1.0
FE3 A:SF41103 2.7 15.4 1.0
FE4 A:SF41103 2.8 13.4 1.0
FE1 A:SF41103 2.8 13.9 1.0
CB A:CYS57 3.1 15.0 1.0
S2 A:SF41103 3.9 13.9 1.0
CD1 A:ILE235 4.1 17.2 1.0
N A:CYS57 4.3 14.8 1.0
CA A:CYS57 4.3 15.1 1.0
CB A:VAL55 4.3 13.3 1.0
CG1 A:ILE235 4.4 16.4 1.0
CG1 A:VAL55 4.5 13.9 1.0
CB A:ILE235 4.5 16.0 1.0
CB A:CYS50 4.6 15.2 1.0
SG A:CYS50 4.6 14.7 1.0
SG A:CYS53 4.7 13.7 1.0
SG A:CYS88 4.9 14.6 1.0
CD2 A:LEU87 4.9 15.5 1.0
CG2 A:VAL55 5.0 13.3 1.0

Iron binding site 3 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:15.4
occ:1.00
 FE3 A:SF41103 0.0 15.4 1.0
SG A:CYS50 2.2 14.7 1.0
S2 A:SF41103 2.3 13.9 1.0
S4 A:SF41103 2.3 14.2 1.0
S1 A:SF41103 2.3 14.0 1.0
FE2 A:SF41103 2.7 14.6 1.0
FE1 A:SF41103 2.7 13.9 1.0
FE4 A:SF41103 2.7 13.4 1.0
CB A:CYS50 3.1 15.2 1.0
S3 A:SF41103 3.9 14.5 1.0
CB A:TYR52 4.3 15.0 1.0
N A:GLY91 4.4 17.0 1.0
CA A:GLY91 4.4 17.3 1.0
N A:CYS53 4.4 14.4 1.0
CA A:CYS50 4.5 14.7 1.0
CB A:CYS57 4.5 15.0 1.0
SG A:CYS88 4.6 14.6 1.0
SG A:CYS57 4.6 14.6 1.0
N A:TYR52 4.8 14.5 1.0
SG A:CYS53 4.8 13.7 1.0
O A:CYS53 4.9 16.3 1.0
CA A:TYR52 4.9 15.0 1.0
CD2 A:TYR52 4.9 15.0 1.0
C A:CYS50 5.0 14.8 1.0
C A:TYR52 5.0 15.4 1.0

Iron binding site 4 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:13.4
occ:1.00
 FE4 A:SF41103 0.0 13.4 1.0
SG A:CYS88 2.2 14.6 1.0
S1 A:SF41103 2.2 14.0 1.0
S2 A:SF41103 2.3 13.9 1.0
S3 A:SF41103 2.3 14.5 1.0
FE1 A:SF41103 2.7 13.9 1.0
FE3 A:SF41103 2.7 15.4 1.0
FE2 A:SF41103 2.8 14.6 1.0
CB A:CYS88 3.3 15.4 1.0
N A:CYS88 3.8 14.3 1.0
S4 A:SF41103 3.9 14.2 1.0
CA A:CYS88 4.1 15.0 1.0
CD A:PRO234 4.3 16.3 1.0
CD1 A:ILE235 4.4 17.2 1.0
N A:GLY91 4.5 17.0 1.0
CG A:PRO234 4.6 16.8 1.0
NZ A:LYS90 4.6 15.2 1.0
SG A:CYS53 4.6 13.7 1.0
C A:CYS88 4.7 17.1 1.0
O A:HOH1271 4.7 13.2 1.0
SG A:CYS50 4.8 14.7 1.0
O A:CYS88 4.9 15.9 1.0
SG A:CYS57 4.9 14.6 1.0
CB A:PRO234 5.0 16.3 1.0
C A:LEU87 5.0 15.1 1.0

Iron binding site 5 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:16.8
occ:1.00
 FE1 B:SF4301 0.0 16.8 1.0
S4 B:SF4301 2.3 15.8 1.0
S3 B:SF4301 2.3 16.5 1.0
SG B:CYS157 2.3 15.0 1.0
S2 B:SF4301 2.3 16.0 1.0
FE2 B:SF4301 2.7 17.2 1.0
FE3 B:SF4301 2.8 15.4 1.0
FE4 B:SF4301 2.8 16.7 1.0
CB B:CYS157 3.1 14.8 1.0
CA B:CYS157 3.8 15.2 1.0
S1 B:SF4301 3.9 16.0 1.0
OG1 B:THR159 4.0 15.7 1.0
CB B:THR161 4.1 17.8 1.0
CD B:PRO158 4.2 17.6 1.0
CG B:MET162 4.3 20.4 1.0
CG2 B:THR161 4.4 17.7 1.0
C B:CYS157 4.5 15.7 1.0
N B:PRO158 4.6 16.0 1.0
OG1 B:THR161 4.7 18.2 1.0
SG B:CYS15 4.7 16.3 1.0
SG B:CYS18 4.8 18.0 1.0
SG B:CYS12 4.9 17.7 1.0
N B:CYS157 5.0 15.1 1.0

Iron binding site 6 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:17.2
occ:1.00
 FE2 B:SF4301 0.0 17.2 1.0
SG B:CYS18 2.3 18.0 1.0
S3 B:SF4301 2.3 16.5 1.0
S4 B:SF4301 2.3 15.8 1.0
S1 B:SF4301 2.3 16.0 1.0
FE1 B:SF4301 2.7 16.8 1.0
FE3 B:SF4301 2.8 15.4 1.0
FE4 B:SF4301 2.8 16.7 1.0
CB B:CYS18 3.2 18.5 1.0
S2 B:SF4301 3.9 16.0 1.0
N B:CYS18 3.9 17.2 1.0
O B:HOH409 4.0 21.0 1.0
CA B:CYS18 4.2 17.9 1.0
CG B:PRO71 4.6 20.7 1.0
N B:GLY17 4.6 15.4 1.0
SG B:CYS15 4.7 16.3 1.0
N B:ARG16 4.8 16.8 1.0
SG B:CYS12 4.8 17.7 1.0
CB B:PRO71 4.8 19.4 1.0
CA B:ARG16 4.9 18.7 1.0
SG B:CYS157 4.9 15.0 1.0
CG2 B:VAL53 5.0 20.6 1.0

Iron binding site 7 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:15.4
occ:1.00
 FE3 B:SF4301 0.0 15.4 1.0
S2 B:SF4301 2.2 16.0 1.0
S1 B:SF4301 2.3 16.0 1.0
S4 B:SF4301 2.3 15.8 1.0
SG B:CYS15 2.3 16.3 1.0
FE4 B:SF4301 2.7 16.7 1.0
FE1 B:SF4301 2.8 16.8 1.0
FE2 B:SF4301 2.8 17.2 1.0
N B:CYS15 3.5 15.9 1.0
CB B:CYS15 3.6 16.6 1.0
N B:ARG16 3.8 16.8 1.0
S3 B:SF4301 3.9 16.5 1.0
CA B:CYS15 3.9 17.2 1.0
N B:GLY17 4.1 15.4 1.0
C B:CYS15 4.2 17.1 1.0
CD B:PRO158 4.4 17.6 1.0
OG1 B:THR13 4.4 17.7 1.0
C B:ALA14 4.5 18.3 1.0
N B:ALA14 4.6 17.2 1.0
CA B:ARG16 4.7 18.7 1.0
SG B:CYS18 4.7 18.0 1.0
SG B:CYS12 4.7 17.7 1.0
CA B:ALA14 4.8 18.3 1.0
SG B:CYS157 4.8 15.0 1.0
C B:ARG16 4.9 16.9 1.0
N B:CYS18 4.9 17.2 1.0
CA B:GLY17 5.0 16.2 1.0
CG B:PRO158 5.0 17.6 1.0

Iron binding site 8 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:16.7
occ:1.00
 FE4 B:SF4301 0.0 16.7 1.0
S1 B:SF4301 2.2 16.0 1.0
S2 B:SF4301 2.3 16.0 1.0
SG B:CYS12 2.3 17.7 1.0
S3 B:SF4301 2.3 16.5 1.0
FE3 B:SF4301 2.7 15.4 1.0
FE2 B:SF4301 2.8 17.2 1.0
FE1 B:SF4301 2.8 16.8 1.0
CB B:CYS12 3.5 17.6 1.0
CA B:CYS12 3.9 18.0 1.0
S4 B:SF4301 3.9 15.8 1.0
N B:ALA14 4.1 17.2 1.0
N B:THR13 4.2 18.9 1.0
CG2 B:THR161 4.4 17.7 1.0
C B:CYS12 4.4 19.1 1.0
CA B:ALA14 4.4 18.3 1.0
CG B:PRO71 4.5 20.7 1.0
CB B:THR161 4.6 17.8 1.0
OG1 B:THR161 4.6 18.2 1.0
N B:CYS15 4.7 15.9 1.0
SG B:CYS18 4.8 18.0 1.0
SG B:CYS157 4.8 15.0 1.0
OG1 B:THR159 5.0 15.7 1.0

Iron binding site 9 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:26.7
occ:1.00
 FE1 B:SF4302 0.0 26.7 1.0
S3 B:SF4302 2.3 29.6 1.0
S4 B:SF4302 2.3 25.9 1.0
S2 B:SF4302 2.3 27.4 1.0
SG B:CYS77 2.3 27.3 1.0
FE2 B:SF4302 2.7 27.5 1.0
FE4 B:SF4302 2.7 28.1 1.0
FE3 B:SF4302 2.8 24.6 1.0
CB B:CYS77 3.4 28.7 1.0
N B:CYS77 3.9 27.6 1.0
S1 B:SF4302 3.9 28.9 1.0
CA B:CYS77 4.3 28.1 1.0
N B:HIS76 4.6 23.0 1.0
CD2 B:TYR123 4.6 28.7 1.0
SG B:CYS121 4.7 26.2 1.0
CD B:PRO81 4.7 33.5 1.0
SG B:CYS74 4.7 24.9 1.0
CB B:PRO80 4.7 34.0 1.0
SG B:CYS82 4.8 26.9 1.0
CE2 B:TYR123 4.8 28.8 1.0
CA B:PRO80 4.9 34.6 1.0
N B:ARG75 4.9 21.5 1.0
C B:HIS76 5.0 26.1 1.0
CB B:ARG75 5.0 24.1 1.0

Iron binding site 10 out of 16 in 30gj

Go back to Iron Binding Sites List in 30gj
Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography


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 Nitratidesulfovibrio Vulgaris (Desulfovibrio Vulgaris) - Ambient Temperature, Serial Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:27.5
occ:1.00
 FE2 B:SF4302 0.0 27.5 1.0
S4 B:SF4302 2.2 25.9 1.0
S1 B:SF4302 2.3 28.9 1.0
S3 B:SF4302 2.3 29.6 1.0
SG B:CYS82 2.4 26.9 1.0
FE1 B:SF4302 2.7 26.7 1.0
FE4 B:SF4302 2.7 28.1 1.0
FE3 B:SF4302 2.7 24.6 1.0
CB B:CYS82 3.1 26.1 1.0
S2 B:SF4302 3.9 27.4 1.0
N B:CYS82 4.2 29.4 1.0
CA B:CYS82 4.2 29.2 1.0
CB B:PRO80 4.3 34.0 1.0
CG1 B:VAL103 4.6 28.6 1.0
SG B:CYS74 4.7 24.9 1.0
SG B:CYS121 4.8 26.2 1.0
CE B:LYS137 4.8 27.1 1.0
SG B:CYS77 4.9 27.3 1.0
CA B:PRO80 4.9 34.6 1.0

Reference:

G.Vilela-Alves, G.Martins, D.Von Stetten, P.Mehrabi, I.A.C.Pereira, M.J.Romao, A.R.Pearson, C.Mota. Room-Temperature Crystal Structure of A Metal-Dependent W-Formate Dehydrogenase By Serial Synchrotron Crystallography. Acta Crystallogr D Struct 2026BIOL.
ISSN: ISSN 2059-7983
PubMed: 42572941
DOI: 10.1107/S2059798326006923
Page generated: Sun Oct 4 10:31:40 2026

Last articles

Zn in 9ZLY
Zn in 9ZPK
Zn in 9ZPL
Zn in 9ZM2
Zn in 9ZO4
Zn in 9ZO5
Zn in 9ZOH
Zn in 9ZOF
Zn in 9ZIQ
Zn in 9ZD4
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy