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Iron in PDB 1n5w: Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form

Enzymatic activity of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form

All present enzymatic activity of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form:
1.2.99.2;

Protein crystallography data

The structure of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form, PDB code: 1n5w was solved by H.Dobbek, L.Gremer, R.Kiefersauer, R.Huber, O.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.295, 132.088, 159.825, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 17.1

Other elements in 1n5w:

The structure of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Copper (Cu) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form (pdb code 1n5w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form, PDB code: 1n5w:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1n5w

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Iron binding site 1 out of 8 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3907

b:8.8
occ:1.00
FE1 A:FES3907 0.0 8.8 1.0
S2 A:FES3907 2.3 8.1 1.0
S1 A:FES3907 2.3 8.2 1.0
SG A:CYS102 2.3 8.1 1.0
SG A:CYS139 2.4 8.3 1.0
FE2 A:FES3907 2.7 9.3 1.0
CB A:CYS139 3.3 9.4 1.0
CB A:CYS102 3.4 8.7 1.0
N A:CYS102 3.6 9.3 1.0
CA A:CYS102 3.9 8.0 1.0
O B:HOH3935 4.0 10.4 1.0
N A:GLY103 4.0 10.3 1.0
N A:CYS139 4.0 8.0 1.0
N A:TYR104 4.2 8.3 1.0
C A:CYS102 4.3 8.7 1.0
CA A:CYS139 4.3 7.7 1.0
SG A:CYS137 4.4 8.1 1.0
C A:GLN101 4.7 8.1 1.0
SG A:CYS105 4.7 8.7 1.0
N A:CYS105 4.8 9.0 1.0
N A:ARG138 4.8 8.8 1.0
N A:GLN101 4.8 8.2 1.0
CB A:TYR104 4.8 10.4 1.0
CA A:GLY103 4.9 9.4 1.0
C A:ARG138 5.0 8.0 1.0

Iron binding site 2 out of 8 in 1n5w

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Iron binding site 2 out of 8 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3907

b:9.3
occ:1.00
FE2 A:FES3907 0.0 9.3 1.0
S2 A:FES3907 2.2 8.1 1.0
S1 A:FES3907 2.2 8.2 1.0
SG A:CYS105 2.3 8.7 1.0
SG A:CYS137 2.4 8.1 1.0
FE1 A:FES3907 2.7 8.8 1.0
CB A:CYS105 3.4 9.9 1.0
CB A:CYS137 3.4 9.0 1.0
CA A:CYS137 3.8 8.7 1.0
N A:CYS105 4.0 9.0 1.0
N A:ARG138 4.1 8.8 1.0
N A:CYS139 4.3 8.0 1.0
CA A:CYS105 4.3 8.3 1.0
CB A:CYS139 4.4 9.4 1.0
C A:CYS137 4.4 9.7 1.0
O A:HOH3912 4.4 9.8 1.0
SG A:CYS139 4.5 8.3 1.0
SG A:CYS102 4.7 8.1 1.0
CG2 A:THR140 4.8 10.7 1.0
CA A:CYS139 4.9 7.7 1.0
C A:CYS105 5.0 9.8 1.0
N A:TYR104 5.0 8.3 1.0
O A:LEU136 5.0 10.9 1.0

Iron binding site 3 out of 8 in 1n5w

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Iron binding site 3 out of 8 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3908

b:9.7
occ:1.00
FE1 A:FES3908 0.0 9.7 1.0
S1 A:FES3908 2.2 8.9 1.0
S2 A:FES3908 2.3 9.5 1.0
SG A:CYS47 2.3 8.8 1.0
SG A:CYS42 2.4 9.1 1.0
FE2 A:FES3908 2.7 9.6 1.0
CB A:CYS47 3.5 9.7 1.0
N A:CYS47 3.5 9.5 1.0
CB A:CYS42 3.5 10.6 1.0
N A:CYS42 3.5 10.1 1.0
CA A:CYS47 3.8 8.7 1.0
N A:GLY48 3.8 9.3 1.0
CA A:CYS42 3.9 11.3 1.0
O A:CYS42 4.0 11.8 1.0
O A:HOH3954 4.0 24.4 1.0
C A:CYS42 4.2 9.9 1.0
C A:GLY41 4.2 10.2 1.0
N A:GLY41 4.2 10.1 1.0
C A:CYS47 4.2 9.6 1.0
SG A:CYS62 4.4 9.6 1.0
N A:HIS46 4.4 11.1 1.0
CA A:GLY41 4.5 9.2 1.0
N A:ALA49 4.6 9.4 1.0
C A:HIS46 4.6 8.8 1.0
C A:SER45 4.7 11.5 1.0
SG A:CYS50 4.7 8.7 1.0
CA A:SER45 4.7 10.3 1.0
N A:SER45 4.8 9.6 1.0
CA A:GLY48 4.8 10.7 1.0
O A:GLY41 5.0 10.9 1.0

Iron binding site 4 out of 8 in 1n5w

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Iron binding site 4 out of 8 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3908

b:9.6
occ:1.00
FE2 A:FES3908 0.0 9.6 1.0
S2 A:FES3908 2.2 9.5 1.0
S1 A:FES3908 2.2 8.9 1.0
SG A:CYS50 2.3 8.7 1.0
SG A:CYS62 2.3 9.6 1.0
FE1 A:FES3908 2.7 9.7 1.0
CB A:CYS62 3.3 10.6 1.0
CB A:CYS50 3.4 9.2 1.0
O A:HOH3954 4.0 24.4 1.0
N A:CYS62 4.3 10.7 1.0
N A:CYS50 4.3 9.0 1.0
CA A:CYS62 4.4 12.0 1.0
CB A:LYS60 4.4 9.2 1.0
SG A:CYS47 4.5 8.8 1.0
CA A:CYS50 4.5 10.4 1.0
N A:GLY48 4.6 9.3 1.0
SG A:CYS42 4.6 9.1 1.0
CG A:LYS60 4.8 9.6 1.0
N A:ALA49 4.8 9.4 1.0
CA A:SER45 4.9 10.3 1.0
CA A:GLY48 4.9 10.7 1.0

Iron binding site 5 out of 8 in 1n5w

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Iron binding site 5 out of 8 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe4907

b:9.1
occ:1.00
FE1 D:FES4907 0.0 9.1 1.0
S2 D:FES4907 2.3 7.8 1.0
S1 D:FES4907 2.3 8.5 1.0
SG D:CYS102 2.3 8.2 1.0
SG D:CYS139 2.3 8.5 1.0
FE2 D:FES4907 2.7 8.8 1.0
CB D:CYS139 3.3 7.9 1.0
CB D:CYS102 3.5 9.9 1.0
N D:CYS102 3.6 8.7 1.0
CA D:CYS102 3.9 9.6 1.0
N D:GLY103 4.0 10.1 1.0
O E:HOH4928 4.0 11.1 1.0
N D:CYS139 4.0 8.0 1.0
N D:TYR104 4.2 8.8 1.0
C D:CYS102 4.3 10.3 1.0
CA D:CYS139 4.3 9.1 1.0
SG D:CYS137 4.4 8.0 1.0
C D:GLN101 4.6 9.8 1.0
N D:CYS105 4.7 8.3 1.0
N D:ARG138 4.8 9.0 1.0
SG D:CYS105 4.8 8.0 1.0
N D:GLN101 4.8 10.2 1.0
CB D:TYR104 4.8 9.2 1.0
CA D:GLY103 4.9 9.1 1.0
C D:ARG138 5.0 8.0 1.0
C D:GLY103 5.0 9.0 1.0
CB D:GLN101 5.0 10.4 1.0

Iron binding site 6 out of 8 in 1n5w

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Iron binding site 6 out of 8 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe4907

b:8.8
occ:1.00
FE2 D:FES4907 0.0 8.8 1.0
S1 D:FES4907 2.2 8.5 1.0
S2 D:FES4907 2.2 7.8 1.0
SG D:CYS105 2.3 8.0 1.0
SG D:CYS137 2.4 8.0 1.0
FE1 D:FES4907 2.7 9.1 1.0
CB D:CYS105 3.4 9.4 1.0
CB D:CYS137 3.4 8.4 1.0
CA D:CYS137 3.8 8.8 1.0
N D:CYS105 4.0 8.3 1.0
N D:ARG138 4.1 9.0 1.0
CA D:CYS105 4.2 8.8 1.0
N D:CYS139 4.2 8.0 1.0
O D:HOH4919 4.4 10.4 1.0
C D:CYS137 4.4 8.4 1.0
CB D:CYS139 4.4 7.9 1.0
SG D:CYS139 4.5 8.5 1.0
SG D:CYS102 4.7 8.2 1.0
CG2 D:THR140 4.8 10.3 1.0
CA D:CYS139 4.9 9.1 1.0
C D:CYS105 4.9 8.8 1.0
N D:TYR104 5.0 8.8 1.0

Iron binding site 7 out of 8 in 1n5w

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Iron binding site 7 out of 8 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe4908

b:9.3
occ:1.00
FE1 D:FES4908 0.0 9.3 1.0
S2 D:FES4908 2.3 8.7 1.0
S1 D:FES4908 2.3 8.9 1.0
SG D:CYS47 2.3 8.8 1.0
SG D:CYS42 2.4 8.7 1.0
FE2 D:FES4908 2.7 9.4 1.0
CB D:CYS47 3.4 9.1 1.0
N D:CYS47 3.5 8.3 1.0
CB D:CYS42 3.5 11.2 1.0
N D:CYS42 3.5 9.1 1.0
CA D:CYS47 3.9 9.0 1.0
N D:GLY48 3.9 9.1 1.0
CA D:CYS42 3.9 9.8 1.0
O D:CYS42 4.0 10.2 1.0
C D:CYS42 4.2 10.9 1.0
N D:GLY41 4.2 9.8 1.0
O D:HOH4969 4.2 14.8 1.0
C D:GLY41 4.2 8.7 1.0
C D:CYS47 4.3 8.7 1.0
SG D:CYS62 4.4 8.9 1.0
N D:HIS46 4.4 9.6 1.0
CA D:GLY41 4.5 9.9 1.0
N D:ALA49 4.6 9.4 1.0
C D:HIS46 4.6 8.9 1.0
SG D:CYS50 4.7 8.8 1.0
CA D:SER45 4.7 8.4 1.0
C D:SER45 4.7 8.4 1.0
N D:SER45 4.8 10.5 1.0
CA D:GLY48 4.9 10.0 1.0

Iron binding site 8 out of 8 in 1n5w

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Iron binding site 8 out of 8 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe4908

b:9.4
occ:1.00
FE2 D:FES4908 0.0 9.4 1.0
S2 D:FES4908 2.2 8.7 1.0
S1 D:FES4908 2.2 8.9 1.0
SG D:CYS50 2.3 8.8 1.0
SG D:CYS62 2.4 8.9 1.0
FE1 D:FES4908 2.7 9.3 1.0
CB D:CYS62 3.3 10.8 1.0
CB D:CYS50 3.4 10.0 1.0
O D:HOH4969 4.1 14.8 1.0
N D:CYS62 4.2 10.5 1.0
N D:CYS50 4.3 9.1 1.0
CA D:CYS62 4.3 10.5 1.0
SG D:CYS47 4.4 8.8 1.0
CA D:CYS50 4.5 8.8 1.0
CB D:LYS60 4.5 9.4 1.0
SG D:CYS42 4.6 8.7 1.0
N D:GLY48 4.6 9.1 1.0
N D:ALA49 4.8 9.4 1.0
CG D:LYS60 4.9 8.8 1.0
CA D:SER45 4.9 8.4 1.0
CA D:GLY48 5.0 10.0 1.0

Reference:

H.Dobbek, L.Gremer, R.Kiefersauer, R.Huber, O.Meyer. Catalysis at A Dinuclear [Cusmo(=O)Oh] Cluster in A Co Dehydrogenase Resolved at 1.1-A Resolution Proc.Natl.Acad.Sci.Usa V. 99 15971 2002.
ISSN: ISSN 0027-8424
PubMed: 12475995
DOI: 10.1073/PNAS.212640899
Page generated: Sat Aug 3 11:25:13 2024

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