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Iron in PDB 1h0h: Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas

Enzymatic activity of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas

All present enzymatic activity of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas:
1.2.1.2;

Protein crystallography data

The structure of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas, PDB code: 1h0h was solved by H.C.A.Raaijmakers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.408, 110.398, 156.185, 90.00, 93.53, 90.00
R / Rfree (%) 16.7 / 20.1

Other elements in 1h0h:

The structure of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas also contains other interesting chemical elements:

Tungsten (W) 2 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas (pdb code 1h0h). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas, PDB code: 1h0h:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 1h0h

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Iron binding site 1 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1010

b:16.1
occ:1.00
FE1 A:SF41010 0.0 16.1 1.0
SG A:CYS54 2.3 15.6 1.0
S3 A:SF41010 2.3 16.8 1.0
S2 A:SF41010 2.3 16.8 1.0
S4 A:SF41010 2.4 17.4 1.0
FE4 A:SF41010 2.8 15.3 1.0
FE3 A:SF41010 2.8 15.4 1.0
FE2 A:SF41010 2.8 15.8 1.0
CB A:CYS54 3.4 15.8 1.0
N A:CYS54 3.7 15.0 1.0
S1 A:SF41010 4.0 18.1 1.0
CA A:CYS54 4.1 15.3 1.0
N A:GLY57 4.3 15.9 1.0
CD A:PRO200 4.3 16.6 1.0
CG A:PRO200 4.4 15.8 1.0
NZ A:LYS56 4.5 11.1 1.0
CB A:PRO200 4.6 15.8 1.0
CD1 A:ILE201 4.6 13.6 1.0
C A:CYS54 4.7 14.6 1.0
O A:HOH2053 4.8 14.8 1.0
SG A:CYS20 4.8 15.6 1.0
C A:LEU53 4.8 16.2 1.0
CA A:GLY57 4.8 16.1 1.0
SG A:CYS24 4.8 14.7 1.0
O A:CYS54 4.9 14.1 1.0
SG A:CYS17 4.9 15.9 1.0
CB A:LYS56 4.9 13.5 1.0

Iron binding site 2 out of 32 in 1h0h

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Iron binding site 2 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1010

b:15.8
occ:1.00
FE2 A:SF41010 0.0 15.8 1.0
SG A:CYS20 2.3 15.6 1.0
S3 A:SF41010 2.3 16.8 1.0
S1 A:SF41010 2.3 18.1 1.0
S4 A:SF41010 2.3 17.4 1.0
FE4 A:SF41010 2.8 15.3 1.0
FE3 A:SF41010 2.8 15.4 1.0
FE1 A:SF41010 2.8 16.1 1.0
CB A:CYS20 3.4 14.4 1.0
N A:CYS20 3.7 13.8 1.0
CA A:CYS20 3.9 14.2 1.0
S2 A:SF41010 4.0 16.8 1.0
CB A:VAL22 4.0 16.2 1.0
O A:CYS20 4.1 12.2 1.0
C A:CYS20 4.1 14.1 1.0
O A:HOH2053 4.1 14.8 1.0
CG2 A:VAL22 4.3 15.5 1.0
CD A:PRO200 4.4 16.6 1.0
N A:VAL22 4.5 16.1 1.0
SG A:CYS24 4.7 14.7 1.0
SG A:CYS54 4.8 15.6 1.0
SG A:CYS17 4.8 15.9 1.0
CA A:VAL22 4.9 14.4 1.0
N A:SER21 4.9 13.9 1.0
C A:TYR19 4.9 14.1 1.0

Iron binding site 3 out of 32 in 1h0h

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Iron binding site 3 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1010

b:15.4
occ:1.00
FE3 A:SF41010 0.0 15.4 1.0
SG A:CYS24 2.2 14.7 1.0
S4 A:SF41010 2.3 17.4 1.0
S1 A:SF41010 2.4 18.1 1.0
S2 A:SF41010 2.4 16.8 1.0
FE4 A:SF41010 2.7 15.3 1.0
FE2 A:SF41010 2.8 15.8 1.0
FE1 A:SF41010 2.8 16.1 1.0
CB A:CYS24 3.1 14.2 1.0
S3 A:SF41010 3.9 16.8 1.0
CB A:ILE201 4.2 14.2 1.0
N A:CYS24 4.2 16.3 1.0
CB A:VAL22 4.3 16.2 1.0
CG1 A:ILE201 4.3 15.0 1.0
CA A:CYS24 4.3 15.6 1.0
CD1 A:ILE201 4.4 13.6 1.0
CG1 A:VAL22 4.4 16.2 1.0
CB A:CYS17 4.6 13.4 1.0
SG A:CYS17 4.7 15.9 1.0
SG A:CYS20 4.8 15.6 1.0
CD2 A:LEU53 4.9 14.2 1.0
N A:CYS54 5.0 15.0 1.0
N A:ILE201 5.0 13.7 1.0
SG A:CYS54 5.0 15.6 1.0

Iron binding site 4 out of 32 in 1h0h

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Iron binding site 4 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1010

b:15.3
occ:1.00
FE4 A:SF41010 0.0 15.3 1.0
S3 A:SF41010 2.2 16.8 1.0
SG A:CYS17 2.3 15.9 1.0
S2 A:SF41010 2.4 16.8 1.0
S1 A:SF41010 2.4 18.1 1.0
FE3 A:SF41010 2.7 15.4 1.0
FE1 A:SF41010 2.8 16.1 1.0
FE2 A:SF41010 2.8 15.8 1.0
CB A:CYS17 3.1 13.4 1.0
S4 A:SF41010 3.9 17.4 1.0
CB A:TYR19 4.2 14.1 1.0
CA A:GLY57 4.2 16.1 1.0
N A:GLY57 4.2 15.9 1.0
N A:CYS20 4.4 13.8 1.0
CA A:CYS17 4.6 14.2 1.0
SG A:CYS24 4.6 14.7 1.0
SG A:CYS54 4.6 15.6 1.0
CB A:CYS24 4.6 14.2 1.0
N A:TYR19 4.7 11.7 1.0
CA A:TYR19 4.8 13.4 1.0
SG A:CYS20 4.9 15.6 1.0
CD2 A:TYR19 5.0 14.2 1.0

Iron binding site 5 out of 32 in 1h0h

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Iron binding site 5 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1011

b:19.6
occ:1.00
FE1 B:SF41011 0.0 19.6 1.0
SG B:CYS156 2.2 18.9 1.0
S4 B:SF41011 2.3 21.1 1.0
S2 B:SF41011 2.3 19.4 1.0
S3 B:SF41011 2.3 20.8 1.0
FE4 B:SF41011 2.7 19.0 1.0
FE2 B:SF41011 2.8 20.3 1.0
FE3 B:SF41011 2.8 19.4 1.0
CB B:CYS156 3.2 18.3 1.0
CA B:CYS156 3.7 16.6 1.0
S1 B:SF41011 3.9 18.2 1.0
CD B:PRO157 4.0 16.5 1.0
CB B:ALA160 4.1 19.1 1.0
OG1 B:THR158 4.3 18.2 1.0
CG B:MET161 4.4 18.1 1.0
C B:CYS156 4.4 16.1 1.0
N B:PRO157 4.5 15.8 1.0
SG B:CYS14 4.7 18.6 1.0
N B:MET161 4.8 19.0 1.0
SG B:CYS11 4.9 18.7 1.0
SG B:CYS17 4.9 19.1 1.0
N B:CYS156 4.9 17.1 1.0

Iron binding site 6 out of 32 in 1h0h

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Iron binding site 6 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1011

b:20.3
occ:1.00
FE2 B:SF41011 0.0 20.3 1.0
S3 B:SF41011 2.2 20.8 1.0
SG B:CYS17 2.3 19.1 1.0
S4 B:SF41011 2.3 21.1 1.0
S1 B:SF41011 2.3 18.2 1.0
FE3 B:SF41011 2.8 19.4 1.0
FE1 B:SF41011 2.8 19.6 1.0
FE4 B:SF41011 2.8 19.0 1.0
CB B:CYS17 3.2 15.6 1.0
N B:CYS17 3.8 15.8 1.0
S2 B:SF41011 3.9 19.4 1.0
CA B:CYS17 4.1 17.2 1.0
CG2 B:VAL52 4.4 15.4 1.0
CB B:PRO69 4.5 16.6 1.0
SG B:CYS11 4.6 18.7 1.0
SG B:CYS156 4.8 18.9 1.0
N B:GLY16 4.8 16.5 1.0
SG B:CYS14 4.8 18.6 1.0
CG B:MET161 4.9 18.1 1.0
N B:ARG15 4.9 13.9 1.0
CG B:PRO69 4.9 17.1 1.0
CB B:CYS156 5.0 18.3 1.0

Iron binding site 7 out of 32 in 1h0h

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Iron binding site 7 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1011

b:19.4
occ:1.00
FE3 B:SF41011 0.0 19.4 1.0
SG B:CYS11 2.2 18.7 1.0
S2 B:SF41011 2.3 19.4 1.0
S1 B:SF41011 2.3 18.2 1.0
S4 B:SF41011 2.4 21.1 1.0
FE2 B:SF41011 2.8 20.3 1.0
FE1 B:SF41011 2.8 19.6 1.0
FE4 B:SF41011 2.8 19.0 1.0
CB B:CYS11 3.1 16.1 1.0
CA B:CYS11 3.6 15.0 1.0
N B:ALA13 3.9 13.5 1.0
N B:THR12 3.9 14.9 1.0
S3 B:SF41011 3.9 20.8 1.0
C B:CYS11 4.1 14.1 1.0
CA B:ALA13 4.3 13.9 1.0
CB B:ALA160 4.6 19.1 1.0
N B:CYS14 4.6 12.8 1.0
CG B:PRO69 4.7 17.1 1.0
SG B:CYS17 4.8 19.1 1.0
SG B:CYS156 4.8 18.9 1.0
N B:CYS11 4.9 13.9 1.0
C B:THR12 4.9 14.3 1.0

Iron binding site 8 out of 32 in 1h0h

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Iron binding site 8 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1011

b:19.0
occ:1.00
FE4 B:SF41011 0.0 19.0 1.0
S1 B:SF41011 2.3 18.2 1.0
S3 B:SF41011 2.3 20.8 1.0
S2 B:SF41011 2.3 19.4 1.0
SG B:CYS14 2.4 18.6 1.0
FE1 B:SF41011 2.7 19.6 1.0
FE2 B:SF41011 2.8 20.3 1.0
FE3 B:SF41011 2.8 19.4 1.0
CB B:CYS14 3.5 14.4 1.0
N B:CYS14 3.5 12.8 1.0
N B:ARG15 3.8 13.9 1.0
CA B:CYS14 3.9 14.2 1.0
CD B:PRO157 3.9 16.5 1.0
S4 B:SF41011 4.0 21.1 1.0
N B:GLY16 4.1 16.5 1.0
C B:CYS14 4.2 14.4 1.0
C B:ALA13 4.5 14.8 1.0
OG1 B:THR12 4.5 15.8 1.0
N B:ALA13 4.5 13.5 1.0
CG B:PRO157 4.6 16.9 1.0
SG B:CYS156 4.7 18.9 1.0
CA B:ARG15 4.7 14.6 1.0
SG B:CYS17 4.7 19.1 1.0
N B:CYS17 4.7 15.8 1.0
CA B:ALA13 4.8 13.9 1.0
SG B:CYS11 4.8 18.7 1.0
CA B:GLY16 4.8 16.5 1.0
C B:ARG15 4.9 15.2 1.0
N B:THR12 4.9 14.9 1.0

Iron binding site 9 out of 32 in 1h0h

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Iron binding site 9 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1012

b:19.5
occ:1.00
FE1 B:SF41012 0.0 19.5 1.0
S4 B:SF41012 2.3 19.9 1.0
S2 B:SF41012 2.3 18.2 1.0
SG B:CYS140 2.3 17.5 1.0
S3 B:SF41012 2.4 17.3 1.0
FE3 B:SF41012 2.7 18.3 1.0
FE2 B:SF41012 2.7 18.3 1.0
FE4 B:SF41012 2.8 17.4 1.0
N B:CYS140 3.3 15.2 1.0
CB B:CYS140 3.3 15.7 1.0
CE1 B:HIS25 3.7 18.7 1.0
CA B:CYS140 3.7 15.6 1.0
S1 B:SF41012 3.9 19.9 1.0
C B:MET139 3.9 16.5 1.0
NE2 B:HIS25 4.1 18.4 1.0
CB B:PRO150 4.3 15.7 1.0
CA B:MET139 4.4 16.9 1.0
OD1 B:ASP138 4.4 15.4 1.0
N B:ALA151 4.5 13.8 1.0
N B:MET139 4.5 17.5 1.0
SG B:CYS152 4.6 18.4 1.0
O B:MET139 4.7 17.7 1.0
SG B:CYS21 4.7 16.3 1.0
SG B:CYS137 4.7 16.7 1.0
CA B:PRO150 4.8 14.8 1.0
ND1 B:HIS25 4.9 18.0 1.0
N B:CYS152 5.0 15.1 1.0

Iron binding site 10 out of 32 in 1h0h

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Iron binding site 10 out of 32 in the Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Tungsten Containing Formate Dehydrogenase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1012

b:18.3
occ:1.00
FE2 B:SF41012 0.0 18.3 1.0
S1 B:SF41012 2.2 19.9 1.0
S3 B:SF41012 2.3 17.3 1.0
SG B:CYS152 2.3 18.4 1.0
S4 B:SF41012 2.4 19.9 1.0
FE4 B:SF41012 2.7 17.4 1.0
FE1 B:SF41012 2.7 19.5 1.0
FE3 B:SF41012 2.8 18.3 1.0
CB B:CYS152 3.3 16.7 1.0
S2 B:SF41012 3.9 18.2 1.0
N B:CYS152 4.0 15.1 1.0
CA B:CYS152 4.2 17.3 1.0
NE2 B:GLN71 4.3 19.6 1.0
OE1 B:GLN71 4.5 18.6 1.0
CB B:PRO150 4.5 15.7 1.0
SG B:CYS140 4.6 17.5 1.0
CD B:GLN71 4.6 18.6 1.0
SG B:CYS21 4.8 16.3 1.0
CD B:LYS50 4.8 19.3 1.0
SG B:CYS137 4.8 16.7 1.0
CE B:LYS50 4.9 19.4 1.0
CB B:CYS21 4.9 13.9 1.0
CE2 B:PHE4 4.9 16.4 1.0

Reference:

H.C.A.Raaijmakers, S.Macieira, J.Dias, S.Teixeira, S.Bursakov, R.Huber, J.Moura, I.Moura, M.Romao. Gene Sequence and the 1.8 A Crystal Structure of the Tungsten-Containing Formate Dehydrogenase From Desulfovibrio Gigas Structure V. 10 1261 2002.
ISSN: ISSN 0969-2126
PubMed: 12220497
DOI: 10.1016/S0969-2126(02)00826-2
Page generated: Sun Dec 13 14:16:30 2020

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