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Copper in PDB 1n62: Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State

Enzymatic activity of Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State

All present enzymatic activity of Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State:
1.2.99.2;

Protein crystallography data

The structure of Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State, PDB code: 1n62 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) 17.80 / 1.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.860, 130.019, 156.231, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.2

Other elements in 1n62:

The structure of Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Iron (Fe) 8 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State (pdb code 1n62). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State, PDB code: 1n62:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 1n62

Go back to Copper Binding Sites List in 1n62
Copper binding site 1 out of 2 in the Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu3921

b:11.4
occ:0.68
CU B:CUB3921 0.0 11.4 0.7
NZ B:CUB3921 1.8 13.8 1.0
SG B:CYS388 2.0 10.8 1.0
CZ B:CUB3921 2.7 12.9 1.0
C1Z B:CUB3921 2.9 16.8 1.0
CG1 B:VAL384 3.0 12.5 1.0
S B:CUB3921 3.1 11.6 0.9
CB B:CYS388 3.2 11.6 1.0
N B:SER389 3.2 10.2 1.0
N B:PHE390 3.3 10.0 1.0
N B:ALA385 3.4 10.3 1.0
N B:CYS388 3.4 9.9 1.0
CA B:CYS388 3.5 10.1 1.0
C B:CYS388 3.6 10.3 1.0
C B:VAL384 3.8 10.4 1.0
OM2 B:CUB3921 3.9 12.7 1.0
C2Z B:CUB3921 3.9 19.0 1.0
CA B:ALA385 3.9 10.6 1.0
O B:ALA385 4.0 10.6 1.0
CA B:VAL384 4.0 11.2 1.0
CB B:VAL384 4.0 12.8 1.0
CA B:PHE390 4.0 10.5 1.0
C B:ALA385 4.1 10.2 1.0
CA B:SER389 4.1 10.4 1.0
C3Z B:CUB3921 4.1 17.9 1.0
C B:SER389 4.1 10.2 1.0
OE2 B:GLU763 4.2 11.8 1.0
O B:CYS388 4.4 10.7 1.0
O B:VAL384 4.5 12.3 1.0
CG2 B:VAL384 4.5 14.0 1.0
N B:ARG391 4.7 9.8 1.0
C B:ARG387 4.7 9.8 1.0
CD1 B:PHE390 4.9 12.8 1.0
N B:TYR386 4.9 9.9 1.0
C B:PHE390 4.9 9.8 1.0

Copper binding site 2 out of 2 in 1n62

Go back to Copper Binding Sites List in 1n62
Copper binding site 2 out of 2 in the Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu4921

b:11.4
occ:0.68
CU E:CUB4921 0.0 11.4 0.7
NZ E:CUB4921 1.8 15.3 1.0
SG E:CYS388 2.0 11.4 1.0
CZ E:CUB4921 2.6 13.1 1.0
C1Z E:CUB4921 2.9 15.8 1.0
CG1 E:VAL384 3.0 14.5 1.0
S E:CUB4921 3.1 12.1 0.9
CB E:CYS388 3.2 11.5 1.0
N E:SER389 3.2 10.5 1.0
N E:PHE390 3.3 10.7 1.0
N E:ALA385 3.4 10.7 1.0
N E:CYS388 3.4 10.9 1.0
CA E:CYS388 3.5 10.6 1.0
C E:CYS388 3.5 10.5 1.0
C E:VAL384 3.8 11.6 1.0
OM2 E:CUB4921 3.9 12.5 1.0
CA E:ALA385 3.9 11.2 1.0
C2Z E:CUB4921 4.0 16.7 1.0
CA E:VAL384 4.0 11.6 1.0
O E:ALA385 4.0 10.9 1.0
CA E:PHE390 4.0 10.9 1.0
CB E:VAL384 4.0 12.6 1.0
CA E:SER389 4.1 11.2 1.0
C E:ALA385 4.1 10.4 1.0
C3Z E:CUB4921 4.1 17.5 1.0
C E:SER389 4.1 11.0 1.0
OE2 E:GLU763 4.2 12.3 1.0
O E:CYS388 4.3 11.2 1.0
O E:VAL384 4.5 13.3 1.0
CG2 E:VAL384 4.6 13.4 1.0
N E:ARG391 4.6 10.9 1.0
C E:ARG387 4.7 10.7 1.0
C E:PHE390 4.9 11.1 1.0
N E:TYR386 4.9 10.4 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: Wed Oct 28 14:16:04 2020
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