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Copper in PDB 3n9h: Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha

Enzymatic activity of Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha

All present enzymatic activity of Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha:
1.4.3.21;

Protein crystallography data

The structure of Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha, PDB code: 3n9h was solved by Z.Chen, S.Datta, J.L.Dubois, J.P.Klinman, F.S.Mathews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.10 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 138.910, 147.150, 233.760, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 19.8

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha (pdb code 3n9h). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha, PDB code: 3n9h:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3n9h

Go back to Copper Binding Sites List in 3n9h
Copper binding site 1 out of 6 in the Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:31.2
occ:1.00
 NE2 A:HIS456 2.2 27.3 1.0
ND1 A:HIS624 2.2 23.2 1.0
NE2 A:HIS458 2.2 23.9 1.0
O A:HOH1497 2.8 30.2 1.0
CD2 A:HIS458 2.9 23.1 1.0
CG A:HIS624 3.1 22.6 1.0
CE1 A:HIS456 3.1 26.6 1.0
CD2 A:HIS456 3.1 26.3 1.0
CE1 A:HIS624 3.2 23.2 1.0
CB A:HIS624 3.3 20.4 1.0
CE1 A:HIS458 3.3 24.6 1.0
O2 A:TPQ405 4.2 47.9 1.0
CG A:HIS458 4.2 23.9 1.0
ND1 A:HIS456 4.2 27.0 1.0
CD2 A:HIS624 4.2 24.1 1.0
NE2 A:HIS624 4.3 24.4 1.0
CG A:HIS456 4.3 25.0 1.0
ND1 A:HIS458 4.3 26.5 1.0
O A:HOH1499 4.4 30.2 1.0
CD1 A:LEU425 4.4 35.4 1.0
O A:HOH1053 4.5 45.1 1.0
CE A:MET634 4.7 41.8 1.0
CD1 A:ILE622 4.7 24.1 1.0
C3 A:TPQ405 4.8 52.1 1.0
CA A:HIS624 4.9 20.2 1.0
C2 A:TPQ405 4.9 49.3 1.0
SD A:MET634 4.9 46.8 1.0

Copper binding site 2 out of 6 in 3n9h

Go back to Copper Binding Sites List in 3n9h
Copper binding site 2 out of 6 in the Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:31.2
occ:1.00
 NE2 B:HIS456 2.2 27.3 1.0
ND1 B:HIS624 2.2 23.2 1.0
NE2 B:HIS458 2.2 23.9 1.0
O B:HOH1497 2.8 30.2 1.0
CD2 B:HIS458 2.9 23.1 1.0
CG B:HIS624 3.1 22.6 1.0
CE1 B:HIS456 3.1 26.6 1.0
CD2 B:HIS456 3.1 26.3 1.0
CE1 B:HIS624 3.2 23.2 1.0
CB B:HIS624 3.3 20.4 1.0
CE1 B:HIS458 3.3 24.6 1.0
O2 B:TPQ405 4.2 47.9 1.0
CG B:HIS458 4.2 23.9 1.0
ND1 B:HIS456 4.2 27.0 1.0
CD2 B:HIS624 4.2 24.1 1.0
NE2 B:HIS624 4.3 24.4 1.0
CG B:HIS456 4.3 25.0 1.0
ND1 B:HIS458 4.3 26.5 1.0
O B:HOH1499 4.4 30.2 1.0
CD1 B:LEU425 4.4 35.4 1.0
O B:HOH1053 4.5 45.1 1.0
CE B:MET634 4.7 41.8 1.0
CD1 B:ILE622 4.7 24.1 1.0
C3 B:TPQ405 4.8 52.1 1.0
CA B:HIS624 4.9 20.2 1.0
C2 B:TPQ405 4.9 49.3 1.0
SD B:MET634 4.9 46.8 1.0

Copper binding site 3 out of 6 in 3n9h

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Copper binding site 3 out of 6 in the Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu701

b:31.2
occ:1.00
 NE2 C:HIS456 2.2 27.3 1.0
ND1 C:HIS624 2.2 23.2 1.0
NE2 C:HIS458 2.2 23.9 1.0
O C:HOH1497 2.8 30.2 1.0
CD2 C:HIS458 2.9 23.1 1.0
CG C:HIS624 3.1 22.6 1.0
CE1 C:HIS456 3.1 26.6 1.0
CD2 C:HIS456 3.1 26.3 1.0
CE1 C:HIS624 3.2 23.2 1.0
CB C:HIS624 3.3 20.4 1.0
CE1 C:HIS458 3.3 24.6 1.0
O2 C:TPQ405 4.2 47.9 1.0
CG C:HIS458 4.2 23.9 1.0
ND1 C:HIS456 4.2 27.0 1.0
CD2 C:HIS624 4.2 24.1 1.0
NE2 C:HIS624 4.3 24.4 1.0
CG C:HIS456 4.3 25.0 1.0
ND1 C:HIS458 4.3 26.5 1.0
O C:HOH1499 4.4 30.2 1.0
CD1 C:LEU425 4.4 35.4 1.0
O C:HOH1053 4.5 45.1 1.0
CE C:MET634 4.7 41.8 1.0
CD1 C:ILE622 4.7 24.1 1.0
C3 C:TPQ405 4.8 52.1 1.0
CA C:HIS624 4.9 20.2 1.0
C2 C:TPQ405 4.9 49.3 1.0
SD C:MET634 4.9 46.8 1.0

Copper binding site 4 out of 6 in 3n9h

Go back to Copper Binding Sites List in 3n9h
Copper binding site 4 out of 6 in the Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu701

b:31.2
occ:1.00
 NE2 D:HIS456 2.2 27.3 1.0
ND1 D:HIS624 2.2 23.2 1.0
NE2 D:HIS458 2.2 23.9 1.0
O D:HOH1497 2.8 30.2 1.0
CD2 D:HIS458 2.9 23.1 1.0
CG D:HIS624 3.1 22.6 1.0
CE1 D:HIS456 3.1 26.6 1.0
CD2 D:HIS456 3.1 26.3 1.0
CE1 D:HIS624 3.2 23.2 1.0
CB D:HIS624 3.3 20.4 1.0
CE1 D:HIS458 3.3 24.6 1.0
O2 D:TPQ405 4.2 47.9 1.0
CG D:HIS458 4.2 23.9 1.0
ND1 D:HIS456 4.2 27.0 1.0
CD2 D:HIS624 4.2 24.1 1.0
NE2 D:HIS624 4.3 24.4 1.0
CG D:HIS456 4.3 25.0 1.0
ND1 D:HIS458 4.3 26.5 1.0
O D:HOH1499 4.4 30.2 1.0
CD1 D:LEU425 4.4 35.4 1.0
O D:HOH1053 4.5 45.1 1.0
CE D:MET634 4.7 41.8 1.0
CD1 D:ILE622 4.7 24.1 1.0
C3 D:TPQ405 4.8 52.1 1.0
CA D:HIS624 4.9 20.2 1.0
C2 D:TPQ405 4.9 49.3 1.0
SD D:MET634 4.9 46.8 1.0

Copper binding site 5 out of 6 in 3n9h

Go back to Copper Binding Sites List in 3n9h
Copper binding site 5 out of 6 in the Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu701

b:31.2
occ:1.00
 NE2 E:HIS456 2.2 27.3 1.0
ND1 E:HIS624 2.2 23.2 1.0
NE2 E:HIS458 2.2 23.9 1.0
O E:HOH1497 2.8 30.2 1.0
CD2 E:HIS458 2.9 23.1 1.0
CG E:HIS624 3.1 22.6 1.0
CE1 E:HIS456 3.1 26.6 1.0
CD2 E:HIS456 3.1 26.3 1.0
CE1 E:HIS624 3.2 23.2 1.0
CE1 E:HIS458 3.3 24.6 1.0
CB E:HIS624 3.3 20.4 1.0
O2 E:TPQ405 4.2 47.9 1.0
CG E:HIS458 4.2 23.9 1.0
ND1 E:HIS456 4.2 27.0 1.0
CD2 E:HIS624 4.2 24.1 1.0
NE2 E:HIS624 4.3 24.4 1.0
CG E:HIS456 4.3 25.0 1.0
ND1 E:HIS458 4.3 26.5 1.0
O E:HOH1499 4.4 30.2 1.0
CD1 E:LEU425 4.4 35.4 1.0
O E:HOH1053 4.5 45.1 1.0
CE E:MET634 4.7 41.8 1.0
CD1 E:ILE622 4.7 24.1 1.0
C3 E:TPQ405 4.8 52.1 1.0
CA E:HIS624 4.9 20.2 1.0
C2 E:TPQ405 4.9 49.3 1.0
SD E:MET634 4.9 46.8 1.0

Copper binding site 6 out of 6 in 3n9h

Go back to Copper Binding Sites List in 3n9h
Copper binding site 6 out of 6 in the Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structural of Mutant Y305A in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu701

b:31.2
occ:1.00
 NE2 F:HIS456 2.2 27.3 1.0
ND1 F:HIS624 2.2 23.2 1.0
NE2 F:HIS458 2.2 23.9 1.0
O F:HOH1497 2.8 30.2 1.0
CD2 F:HIS458 2.9 23.1 1.0
CG F:HIS624 3.1 22.6 1.0
CE1 F:HIS456 3.1 26.6 1.0
CD2 F:HIS456 3.1 26.3 1.0
CE1 F:HIS624 3.2 23.2 1.0
CB F:HIS624 3.3 20.4 1.0
CE1 F:HIS458 3.3 24.6 1.0
O2 F:TPQ405 4.2 47.9 1.0
CG F:HIS458 4.2 23.9 1.0
ND1 F:HIS456 4.2 27.0 1.0
CD2 F:HIS624 4.2 24.1 1.0
NE2 F:HIS624 4.3 24.4 1.0
CG F:HIS456 4.3 25.0 1.0
ND1 F:HIS458 4.3 26.5 1.0
O F:HOH1499 4.4 30.2 1.0
CD1 F:LEU425 4.4 35.4 1.0
O F:HOH1053 4.5 45.1 1.0
CE F:MET634 4.7 41.8 1.0
CD1 F:ILE622 4.7 24.1 1.0
C3 F:TPQ405 4.8 52.1 1.0
CA F:HIS624 4.9 20.2 1.0
C2 F:TPQ405 4.9 49.3 1.0
SD F:MET634 4.9 46.8 1.0

Reference:

Z.W.Chen, S.Datta, J.L.Dubois, J.P.Klinman, F.S.Mathews. Mutation at A Strictly Conserved, Active Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity. Biochemistry V. 49 7393 2010.
ISSN: ISSN 0006-2960
PubMed: 20684524
DOI: 10.1021/BI100643Y
Page generated: Sun Dec 13 11:10:54 2020

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