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Copper 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
Iron (Fe) 8 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form, PDB code: 1n5w:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 1n5w

Go back to Copper Binding Sites List in 1n5w
Copper binding site 1 out of 2 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


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 Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu3921

b:12.1
occ:0.90
CU B:CUM3921 0.0 12.1 0.9
S B:CUM3921 2.2 9.7 1.0
SG B:CYS388 2.2 9.4 1.0
O B:HOH4334 2.4 24.7 1.0
N B:CYS388 3.1 9.0 1.0
CB B:CYS388 3.3 11.4 1.0
OM2 B:CUM3921 3.4 11.3 1.0
N B:ALA385 3.4 9.1 1.0
N B:SER389 3.5 9.0 1.0
CA B:CYS388 3.5 9.3 1.0
C B:ALA385 3.6 9.6 1.0
CA B:ALA385 3.6 10.5 1.0
OE2 B:GLU763 3.7 10.1 1.0
MO B:CUM3921 3.7 10.4 1.0
O B:ALA385 3.8 10.1 1.0
CG1 B:VAL384 3.8 12.1 1.0
C B:CYS388 3.9 9.1 1.0
C B:VAL384 4.1 9.8 1.0
N B:ARG387 4.2 8.4 1.0
N B:PHE390 4.2 8.5 1.0
N B:TYR386 4.2 9.3 1.0
C B:ARG387 4.2 8.3 1.0
CA B:ARG387 4.5 9.0 1.0
CA B:SER389 4.5 8.6 1.0
O B:HOH4547 4.6 30.0 1.0
CA B:VAL384 4.6 9.6 1.0
O B:VAL384 4.8 12.1 1.0
CB B:VAL384 4.8 10.7 1.0
C B:TYR386 4.8 8.8 1.0
OM1 B:CUM3921 4.9 9.6 1.0
C B:SER389 4.9 10.3 1.0
O B:CYS388 4.9 10.2 1.0
CD B:GLU763 4.9 9.3 1.0

Copper binding site 2 out of 2 in 1n5w

Go back to Copper Binding Sites List in 1n5w
Copper binding site 2 out of 2 in the Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form


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 Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu4921

b:12.6
occ:0.90
CU E:CUM4921 0.0 12.6 0.9
S E:CUM4921 2.2 10.1 1.0
SG E:CYS388 2.2 10.4 1.0
O E:HOH5313 2.5 28.4 1.0
N E:CYS388 3.1 9.9 1.0
CB E:CYS388 3.3 10.6 1.0
OM2 E:CUM4921 3.4 10.9 1.0
N E:ALA385 3.4 9.4 1.0
N E:SER389 3.5 9.6 1.0
CA E:CYS388 3.6 9.8 1.0
CA E:ALA385 3.6 9.6 1.0
C E:ALA385 3.6 9.8 1.0
OE2 E:GLU763 3.7 11.6 1.0
O E:ALA385 3.7 10.8 1.0
MO E:CUM4921 3.7 10.8 1.0
CG1 E:VAL384 3.8 10.6 1.0
C E:CYS388 3.9 10.5 1.0
C E:VAL384 4.1 9.7 1.0
N E:PHE390 4.2 10.4 1.0
N E:TYR386 4.2 8.9 1.0
N E:ARG387 4.2 10.3 1.0
C E:ARG387 4.2 8.6 1.0
CA E:ARG387 4.5 7.7 1.0
CA E:SER389 4.5 8.8 1.0
CA E:VAL384 4.6 11.1 1.0
O E:VAL384 4.7 11.7 1.0
CB E:VAL384 4.8 12.0 1.0
C E:TYR386 4.8 10.3 1.0
C E:SER389 4.9 9.4 1.0
OM1 E:CUM4921 4.9 10.8 1.0
O E:CYS388 4.9 9.6 1.0
CD E:GLU763 4.9 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: Sun Dec 13 11:00:36 2020

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