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Copper in PDB 3nbb: Crystal Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha

Enzymatic activity of Crystal Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha

All present enzymatic activity of Crystal Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha:
1.4.3.21;

Protein crystallography data

The structure of Crystal Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha, PDB code: 3nbb 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) 36.13 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.523, 232.618, 104.146, 90.00, 91.51, 90.00
R / Rfree (%) 19.3 / 20

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha (pdb code 3nbb). 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 Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha, PDB code: 3nbb:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3nbb

Go back to Copper Binding Sites List in 3nbb
Copper binding site 1 out of 6 in the Crystal Structure of Mutant Y305F Expressed in E. Coli 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 Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:26.9
occ:1.00
 ND1 A:HIS624 2.1 22.4 1.0
NE2 A:HIS458 2.1 20.7 1.0
NE2 A:HIS456 2.1 19.6 1.0
CD2 A:HIS458 2.9 18.3 1.0
O5 A:TY9405 3.0 41.5 0.5
O5 A:TY9405 3.0 41.5 0.5
CG A:HIS624 3.0 24.0 1.0
CD2 A:HIS456 3.1 21.1 1.0
CE1 A:HIS456 3.1 19.6 1.0
CE1 A:HIS624 3.2 22.8 1.0
CB A:HIS624 3.3 19.8 1.0
CE1 A:HIS458 3.3 21.5 1.0
C5 A:TY9405 3.7 41.8 0.5
C5 A:TY9405 3.7 41.8 0.5
O4 A:TY9405 3.8 53.8 0.5
O4 A:TY9405 3.8 53.8 0.5
C4 A:TY9405 4.1 45.4 0.5
C4 A:TY9405 4.1 45.4 0.5
CG A:HIS458 4.2 22.8 1.0
ND1 A:HIS456 4.2 18.3 1.0
CD2 A:HIS624 4.2 25.7 1.0
CG A:HIS456 4.2 21.5 1.0
NE2 A:HIS624 4.3 25.6 1.0
ND1 A:HIS458 4.3 20.8 1.0
O4A A:TY9405 4.3 49.2 0.5
O4A A:TY9405 4.3 49.2 0.5
C6 A:TY9405 4.7 39.7 0.5
C6 A:TY9405 4.7 39.7 0.5
CA A:HIS624 4.8 21.5 1.0
CD1 A:LEU425 4.9 39.9 1.0
CE A:MET634 5.0 42.8 0.5
CE A:MET634 5.0 42.8 0.5

Copper binding site 2 out of 6 in 3nbb

Go back to Copper Binding Sites List in 3nbb
Copper binding site 2 out of 6 in the Crystal Structure of Mutant Y305F Expressed in E. Coli 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 Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:26.9
occ:1.00
 ND1 B:HIS624 2.1 22.4 1.0
NE2 B:HIS458 2.1 20.7 1.0
NE2 B:HIS456 2.1 19.6 1.0
CD2 B:HIS458 2.9 18.3 1.0
O5 B:TY9405 3.0 41.5 0.5
O5 B:TY9405 3.0 41.5 0.5
CG B:HIS624 3.0 24.0 1.0
CD2 B:HIS456 3.1 21.1 1.0
CE1 B:HIS456 3.1 19.6 1.0
CE1 B:HIS624 3.2 22.8 1.0
CB B:HIS624 3.3 19.8 1.0
CE1 B:HIS458 3.3 21.5 1.0
C5 B:TY9405 3.7 41.8 0.5
C5 B:TY9405 3.7 41.8 0.5
O4 B:TY9405 3.8 53.8 0.5
O4 B:TY9405 3.8 53.8 0.5
C4 B:TY9405 4.1 45.4 0.5
C4 B:TY9405 4.1 45.4 0.5
CG B:HIS458 4.2 22.8 1.0
ND1 B:HIS456 4.2 18.3 1.0
CD2 B:HIS624 4.2 25.7 1.0
CG B:HIS456 4.2 21.5 1.0
NE2 B:HIS624 4.3 25.6 1.0
ND1 B:HIS458 4.3 20.8 1.0
O4A B:TY9405 4.3 49.2 0.5
O4A B:TY9405 4.3 49.2 0.5
C6 B:TY9405 4.7 39.7 0.5
C6 B:TY9405 4.7 39.7 0.5
CA B:HIS624 4.8 21.5 1.0
CD1 B:LEU425 4.9 39.9 1.0
CE B:MET634 5.0 42.8 0.5
CE B:MET634 5.0 42.8 0.5

Copper binding site 3 out of 6 in 3nbb

Go back to Copper Binding Sites List in 3nbb
Copper binding site 3 out of 6 in the Crystal Structure of Mutant Y305F Expressed in E. Coli 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 Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu701

b:26.9
occ:1.00
 ND1 C:HIS624 2.1 22.4 1.0
NE2 C:HIS458 2.1 20.7 1.0
NE2 C:HIS456 2.1 19.6 1.0
CD2 C:HIS458 2.9 18.3 1.0
O5 C:TY9405 3.0 41.5 0.5
O5 C:TY9405 3.0 41.5 0.5
CG C:HIS624 3.0 24.0 1.0
CD2 C:HIS456 3.1 21.1 1.0
CE1 C:HIS456 3.1 19.6 1.0
CE1 C:HIS624 3.2 22.8 1.0
CB C:HIS624 3.3 19.8 1.0
CE1 C:HIS458 3.3 21.5 1.0
C5 C:TY9405 3.7 41.8 0.5
C5 C:TY9405 3.7 41.8 0.5
O4 C:TY9405 3.8 53.8 0.5
O4 C:TY9405 3.8 53.8 0.5
C4 C:TY9405 4.1 45.4 0.5
C4 C:TY9405 4.1 45.4 0.5
CG C:HIS458 4.2 22.8 1.0
ND1 C:HIS456 4.2 18.3 1.0
CD2 C:HIS624 4.2 25.7 1.0
CG C:HIS456 4.2 21.5 1.0
NE2 C:HIS624 4.3 25.6 1.0
ND1 C:HIS458 4.3 20.8 1.0
O4A C:TY9405 4.3 49.2 0.5
O4A C:TY9405 4.3 49.2 0.5
C6 C:TY9405 4.7 39.7 0.5
C6 C:TY9405 4.7 39.7 0.5
CA C:HIS624 4.8 21.5 1.0
CD1 C:LEU425 4.9 39.9 1.0
CE C:MET634 5.0 42.8 0.5
CE C:MET634 5.0 42.8 0.5

Copper binding site 4 out of 6 in 3nbb

Go back to Copper Binding Sites List in 3nbb
Copper binding site 4 out of 6 in the Crystal Structure of Mutant Y305F Expressed in E. Coli 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 Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu701

b:26.9
occ:1.00
 ND1 D:HIS624 2.1 22.4 1.0
NE2 D:HIS458 2.1 20.7 1.0
NE2 D:HIS456 2.1 19.6 1.0
CD2 D:HIS458 2.9 18.3 1.0
O5 D:TY9405 3.0 41.5 0.5
O5 D:TY9405 3.0 41.5 0.5
CG D:HIS624 3.0 24.0 1.0
CD2 D:HIS456 3.1 21.1 1.0
CE1 D:HIS456 3.1 19.6 1.0
CE1 D:HIS624 3.2 22.8 1.0
CB D:HIS624 3.3 19.8 1.0
CE1 D:HIS458 3.3 21.5 1.0
C5 D:TY9405 3.7 41.8 0.5
C5 D:TY9405 3.7 41.8 0.5
O4 D:TY9405 3.8 53.8 0.5
O4 D:TY9405 3.8 53.8 0.5
C4 D:TY9405 4.1 45.4 0.5
C4 D:TY9405 4.1 45.4 0.5
CG D:HIS458 4.2 22.8 1.0
ND1 D:HIS456 4.2 18.3 1.0
CD2 D:HIS624 4.2 25.7 1.0
CG D:HIS456 4.2 21.5 1.0
NE2 D:HIS624 4.3 25.6 1.0
ND1 D:HIS458 4.3 20.8 1.0
O4A D:TY9405 4.3 49.2 0.5
O4A D:TY9405 4.3 49.2 0.5
C6 D:TY9405 4.7 39.7 0.5
C6 D:TY9405 4.7 39.7 0.5
CA D:HIS624 4.8 21.5 1.0
CD1 D:LEU425 4.9 39.9 1.0
CE D:MET634 5.0 42.8 0.5
CE D:MET634 5.0 42.8 0.5

Copper binding site 5 out of 6 in 3nbb

Go back to Copper Binding Sites List in 3nbb
Copper binding site 5 out of 6 in the Crystal Structure of Mutant Y305F Expressed in E. Coli 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 Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu701

b:26.9
occ:1.00
 ND1 E:HIS624 2.1 22.4 1.0
NE2 E:HIS458 2.1 20.7 1.0
NE2 E:HIS456 2.1 19.6 1.0
CD2 E:HIS458 2.9 18.3 1.0
O5 E:TY9405 3.0 41.5 0.5
O5 E:TY9405 3.0 41.5 0.5
CG E:HIS624 3.0 24.0 1.0
CD2 E:HIS456 3.1 21.1 1.0
CE1 E:HIS456 3.1 19.6 1.0
CE1 E:HIS624 3.2 22.8 1.0
CB E:HIS624 3.3 19.8 1.0
CE1 E:HIS458 3.3 21.5 1.0
C5 E:TY9405 3.7 41.8 0.5
C5 E:TY9405 3.7 41.8 0.5
O4 E:TY9405 3.8 53.8 0.5
O4 E:TY9405 3.8 53.8 0.5
C4 E:TY9405 4.1 45.4 0.5
C4 E:TY9405 4.1 45.4 0.5
CG E:HIS458 4.2 22.8 1.0
ND1 E:HIS456 4.2 18.3 1.0
CD2 E:HIS624 4.2 25.7 1.0
CG E:HIS456 4.2 21.5 1.0
NE2 E:HIS624 4.3 25.6 1.0
ND1 E:HIS458 4.3 20.8 1.0
O4A E:TY9405 4.3 49.2 0.5
O4A E:TY9405 4.3 49.2 0.5
C6 E:TY9405 4.7 39.7 0.5
C6 E:TY9405 4.7 39.7 0.5
CA E:HIS624 4.8 21.5 1.0
CD1 E:LEU425 4.9 39.9 1.0
CE E:MET634 5.0 42.8 0.5
CE E:MET634 5.0 42.8 0.5

Copper binding site 6 out of 6 in 3nbb

Go back to Copper Binding Sites List in 3nbb
Copper binding site 6 out of 6 in the Crystal Structure of Mutant Y305F Expressed in E. Coli 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 Structure of Mutant Y305F Expressed in E. Coli in the Copper Amine Oxidase From Hansenula Polymorpha within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu701

b:26.9
occ:1.00
 ND1 F:HIS624 2.1 22.4 1.0
NE2 F:HIS458 2.1 20.7 1.0
NE2 F:HIS456 2.1 19.6 1.0
CD2 F:HIS458 2.9 18.3 1.0
O5 F:TY9405 3.0 41.5 0.5
O5 F:TY9405 3.0 41.5 0.5
CG F:HIS624 3.0 24.0 1.0
CD2 F:HIS456 3.1 21.1 1.0
CE1 F:HIS456 3.1 19.6 1.0
CE1 F:HIS624 3.2 22.8 1.0
CB F:HIS624 3.3 19.8 1.0
CE1 F:HIS458 3.3 21.5 1.0
C5 F:TY9405 3.7 41.8 0.5
C5 F:TY9405 3.7 41.8 0.5
O4 F:TY9405 3.8 53.8 0.5
O4 F:TY9405 3.8 53.8 0.5
C4 F:TY9405 4.1 45.4 0.5
C4 F:TY9405 4.1 45.4 0.5
CG F:HIS458 4.2 22.8 1.0
ND1 F:HIS456 4.2 18.3 1.0
CD2 F:HIS624 4.2 25.7 1.0
CG F:HIS456 4.2 21.5 1.0
NE2 F:HIS624 4.3 25.6 1.0
ND1 F:HIS458 4.3 20.8 1.0
O4A F:TY9405 4.3 49.2 0.5
O4A F:TY9405 4.3 49.2 0.5
C6 F:TY9405 4.7 39.7 0.5
C6 F:TY9405 4.7 39.7 0.5
CA F:HIS624 4.8 21.5 1.0
CD1 F:LEU425 4.9 39.9 1.0
CE F:MET634 5.0 42.8 0.5
CE F:MET634 5.0 42.8 0.5

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: Wed Jul 31 01:21:59 2024

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