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Copper in PDB 1a2v: Copper Amine Oxidase From Hansenula Polymorpha

Enzymatic activity of Copper Amine Oxidase From Hansenula Polymorpha

All present enzymatic activity of Copper Amine Oxidase From Hansenula Polymorpha:
1.4.3.6;

Protein crystallography data

The structure of Copper Amine Oxidase From Hansenula Polymorpha, PDB code: 1a2v was solved by R.Li, F.S.Mathews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 138.770, 148.220, 234.010, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.4

Copper Binding Sites:

The binding sites of Copper atom in the Copper Amine Oxidase From Hansenula Polymorpha (pdb code 1a2v). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Copper Amine Oxidase From Hansenula Polymorpha, PDB code: 1a2v:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1a2v

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Copper binding site 1 out of 6 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 Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1

b:31.1
occ:1.00
NE2 A:HIS458 1.9 9.6 1.0
ND1 A:HIS624 2.0 7.9 1.0
NE2 A:HIS456 2.1 6.6 1.0
O A:HOH753 2.6 30.9 1.0
CD2 A:HIS458 3.0 11.5 1.0
CE1 A:HIS458 3.0 10.6 1.0
CE1 A:HIS456 3.0 8.6 1.0
CE1 A:HIS624 3.0 15.3 1.0
CG A:HIS624 3.0 13.8 1.0
CD2 A:HIS456 3.1 8.7 1.0
O A:HOH1156 3.2 51.0 1.0
CB A:HIS624 3.4 16.8 1.0
ND1 A:HIS458 4.1 13.4 1.0
CG A:HIS458 4.1 11.7 1.0
NE2 A:HIS624 4.2 15.8 1.0
ND1 A:HIS456 4.2 12.9 1.0
CD2 A:HIS624 4.2 17.1 1.0
O A:HOH816 4.2 33.5 1.0
CG A:HIS456 4.3 10.0 1.0
O2 A:TPQ405 4.3 32.8 1.0
O A:HOH752 4.4 10.7 1.0
CE A:MET634 4.6 25.8 1.0
CD1 A:LEU425 4.7 22.4 1.0
CA A:HIS624 4.9 13.6 1.0
CD1 A:ILE622 4.9 14.8 1.0

Copper binding site 2 out of 6 in 1a2v

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Copper binding site 2 out of 6 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 Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1

b:26.4
occ:1.00
NE2 B:HIS458 1.9 8.6 1.0
ND1 B:HIS624 1.9 16.2 1.0
NE2 B:HIS456 2.1 15.7 1.0
O B:HOH811 2.4 17.0 1.0
CE1 B:HIS458 2.9 11.2 1.0
CG B:HIS624 2.9 17.3 1.0
CE1 B:HIS624 3.0 16.6 1.0
CD2 B:HIS458 3.0 10.5 1.0
CE1 B:HIS456 3.1 15.3 1.0
CD2 B:HIS456 3.2 12.5 1.0
CB B:HIS624 3.2 14.3 1.0
O B:HOH700 3.3 38.5 1.0
ND1 B:HIS458 4.0 8.8 1.0
CG B:HIS458 4.1 6.3 1.0
CD2 B:HIS624 4.1 19.5 1.0
NE2 B:HIS624 4.1 14.8 1.0
ND1 B:HIS456 4.3 16.2 1.0
CG B:HIS456 4.3 14.6 1.0
O B:HOH1110 4.3 42.5 1.0
O2 B:TPQ405 4.4 29.9 1.0
O B:HOH810 4.4 8.4 1.0
CE B:MET634 4.6 23.9 1.0
CD1 B:LEU425 4.7 12.9 1.0
CA B:HIS624 4.8 15.6 1.0
CD1 B:ILE622 4.9 5.7 1.0

Copper binding site 3 out of 6 in 1a2v

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Copper binding site 3 out of 6 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 Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1

b:28.2
occ:1.00
ND1 C:HIS624 2.0 7.8 1.0
NE2 C:HIS458 2.0 13.1 1.0
NE2 C:HIS456 2.1 3.5 1.0
O C:HOH807 2.8 22.3 1.0
CD2 C:HIS458 3.0 17.9 1.0
CE1 C:HIS624 3.0 6.4 1.0
CG C:HIS624 3.0 14.4 1.0
CE1 C:HIS456 3.1 5.5 1.0
CE1 C:HIS458 3.1 20.1 1.0
CD2 C:HIS456 3.2 4.1 1.0
CB C:HIS624 3.3 16.0 1.0
O C:HOH1105 3.6 36.5 1.0
NE2 C:HIS624 4.1 10.8 1.0
CD2 C:HIS624 4.1 11.4 1.0
CG C:HIS458 4.2 14.9 1.0
ND1 C:HIS458 4.2 18.2 1.0
ND1 C:HIS456 4.2 11.8 1.0
O2 C:TPQ405 4.3 37.9 1.0
CG C:HIS456 4.3 6.2 1.0
O C:HOH938 4.7 15.8 1.0
CD1 C:LEU425 4.8 24.8 1.0
CE C:MET634 4.8 10.7 1.0
CA C:HIS624 4.8 12.0 1.0
CD1 C:ILE622 4.9 14.0 1.0
CD2 C:LEU429 5.0 11.4 1.0

Copper binding site 4 out of 6 in 1a2v

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Copper binding site 4 out of 6 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 Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1

b:27.4
occ:1.00
NE2 F:HIS458 1.9 8.0 1.0
ND1 F:HIS624 2.0 18.4 1.0
NE2 F:HIS456 2.0 12.3 1.0
O F:HOH763 2.5 19.2 1.0
CE1 F:HIS458 2.9 10.0 1.0
CE1 F:HIS456 2.9 8.6 1.0
CE1 F:HIS624 3.0 20.7 1.0
CG F:HIS624 3.0 23.8 1.0
CD2 F:HIS458 3.0 12.9 1.0
CD2 F:HIS456 3.1 11.6 1.0
CB F:HIS624 3.3 20.9 1.0
ND1 F:HIS458 4.1 13.1 1.0
ND1 F:HIS456 4.1 8.9 1.0
NE2 F:HIS624 4.1 17.7 1.0
CG F:HIS458 4.1 11.3 1.0
CD2 F:HIS624 4.1 23.5 1.0
CG F:HIS456 4.2 9.8 1.0
O2 F:TPQ405 4.3 35.8 1.0
O F:HOH805 4.4 54.5 1.0
O F:HOH762 4.5 18.2 1.0
CE F:MET634 4.6 27.8 1.0
CD1 F:LEU425 4.8 25.0 1.0
CA F:HIS624 4.8 19.4 1.0
CD1 F:ILE622 4.8 28.0 1.0

Copper binding site 5 out of 6 in 1a2v

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Copper binding site 5 out of 6 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 Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu1

b:31.6
occ:1.00
NE2 E:HIS458 1.9 15.6 1.0
ND1 E:HIS624 2.0 16.9 1.0
NE2 E:HIS456 2.1 22.9 1.0
O E:HOH851 2.6 16.9 1.0
CD2 E:HIS458 2.9 17.2 1.0
CE1 E:HIS458 3.0 17.8 1.0
CE1 E:HIS624 3.0 18.1 1.0
CG E:HIS624 3.1 17.2 1.0
O E:HOH852 3.1 39.3 1.0
CD2 E:HIS456 3.1 16.2 1.0
CE1 E:HIS456 3.1 18.5 1.0
CB E:HIS624 3.4 16.5 1.0
ND1 E:HIS458 4.1 17.3 1.0
CG E:HIS458 4.1 15.8 1.0
NE2 E:HIS624 4.2 20.3 1.0
CD2 E:HIS624 4.2 16.5 1.0
O2 E:TPQ405 4.2 26.8 1.0
ND1 E:HIS456 4.3 22.5 1.0
CG E:HIS456 4.3 18.2 1.0
CE E:MET634 4.6 42.8 1.0
CD1 E:LEU425 4.6 31.0 1.0
CD1 E:ILE622 4.9 19.8 1.0
CA E:HIS624 4.9 17.6 1.0
C2 E:TPQ405 5.0 33.8 1.0

Copper binding site 6 out of 6 in 1a2v

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Copper binding site 6 out of 6 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 Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu1

b:22.8
occ:1.00
ND1 D:HIS624 1.9 13.9 1.0
NE2 D:HIS458 2.0 11.2 1.0
NE2 D:HIS456 2.1 25.3 1.0
O D:HOH1085 2.4 43.1 1.0
O D:HOH774 2.6 19.8 1.0
CG D:HIS624 2.9 16.8 1.0
CD2 D:HIS458 2.9 7.5 1.0
CE1 D:HIS456 3.0 20.2 1.0
CE1 D:HIS624 3.0 18.6 1.0
CE1 D:HIS458 3.1 8.2 1.0
CD2 D:HIS456 3.2 18.4 1.0
CB D:HIS624 3.2 18.3 1.0
CD2 D:HIS624 4.1 18.4 1.0
NE2 D:HIS624 4.1 14.1 1.0
ND1 D:HIS456 4.1 22.5 1.0
CG D:HIS458 4.2 12.2 1.0
ND1 D:HIS458 4.2 10.2 1.0
CG D:HIS456 4.3 17.6 1.0
O2 D:TPQ405 4.3 38.5 1.0
O D:HOH773 4.4 12.0 1.0
CE D:MET634 4.6 36.4 1.0
CA D:HIS624 4.7 14.8 1.0
CD1 D:ILE622 4.8 23.6 1.0
CD1 D:LEU425 4.8 35.1 1.0
O D:HOH1087 4.9 50.5 1.0
SD D:MET634 5.0 41.8 1.0
CD2 D:LEU429 5.0 19.2 1.0

Reference:

R.Li, L.Chen, D.Cai, J.P.Klinman, F.S.Mathews. Crystallographic Study of Yeast Copper Amine Oxidase. Acta Crystallogr.,Sect.D V. 53 364 1997.
ISSN: ISSN 0907-4449
PubMed: 15299901
DOI: 10.1107/S0907444997000814
Page generated: Wed Sep 2 21:31:44 2020
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