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Copper in PDB 3nbj: Crystal Structure of Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast

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

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

Protein crystallography data

The structure of Crystal Structure of Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast, PDB code: 3nbj 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) 29.88 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.290, 232.470, 104.310, 90.00, 93.68, 90.00
R / Rfree (%) 21.3 / 21.7

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 3nbj

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Copper binding site 1 out of 6 in the Crystal Structure of Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast


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 Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:22.9
occ:1.00
NE2 A:HIS458 2.1 22.4 1.0
ND1 A:HIS624 2.1 19.4 1.0
NE2 A:HIS456 2.1 19.3 1.0
CD2 A:HIS458 2.9 17.6 1.0
CG A:HIS624 3.1 19.0 1.0
O5 A:TY9405 3.1 38.6 0.5
O5 A:TY9405 3.1 38.6 0.5
CE1 A:HIS456 3.1 18.3 1.0
CD2 A:HIS456 3.1 19.8 1.0
CE1 A:HIS624 3.2 18.8 1.0
CB A:HIS624 3.3 15.7 1.0
CE1 A:HIS458 3.3 20.1 1.0
C5 A:TY9405 3.8 41.8 0.5
C5 A:TY9405 3.8 41.8 0.5
O4 A:TY9405 3.9 51.7 0.5
O4 A:TY9405 3.9 51.7 0.5
CG A:HIS458 4.1 20.6 1.0
C4 A:TY9405 4.2 44.1 0.5
C4 A:TY9405 4.2 44.1 0.5
ND1 A:HIS456 4.2 16.7 1.0
CG A:HIS456 4.2 18.4 1.0
CD2 A:HIS624 4.3 18.6 1.0
ND1 A:HIS458 4.3 19.4 1.0
NE2 A:HIS624 4.3 20.3 1.0
O4A A:TY9405 4.4 48.8 0.5
O4A A:TY9405 4.4 48.8 0.5
C6 A:TY9405 4.8 38.5 0.5
C6 A:TY9405 4.8 38.5 0.5
CA A:HIS624 4.8 15.9 1.0
CD1 A:LEU425 4.8 37.3 1.0
CE A:MET634 4.9 41.3 0.5
CE A:MET634 4.9 41.3 0.5
CD1 A:ILE622 5.0 28.5 1.0

Copper binding site 2 out of 6 in 3nbj

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Copper binding site 2 out of 6 in the Crystal Structure of Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast


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 Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:22.9
occ:1.00
NE2 B:HIS458 2.1 22.4 1.0
ND1 B:HIS624 2.1 19.4 1.0
NE2 B:HIS456 2.1 19.3 1.0
CD2 B:HIS458 2.9 17.6 1.0
CG B:HIS624 3.1 19.0 1.0
O5 B:TY9405 3.1 38.6 0.5
O5 B:TY9405 3.1 38.6 0.5
CE1 B:HIS456 3.1 18.3 1.0
CD2 B:HIS456 3.1 19.8 1.0
CE1 B:HIS624 3.2 18.8 1.0
CB B:HIS624 3.3 15.7 1.0
CE1 B:HIS458 3.3 20.1 1.0
C5 B:TY9405 3.8 41.8 0.5
C5 B:TY9405 3.8 41.8 0.5
O4 B:TY9405 3.9 51.7 0.5
O4 B:TY9405 3.9 51.7 0.5
CG B:HIS458 4.1 20.6 1.0
C4 B:TY9405 4.2 44.1 0.5
C4 B:TY9405 4.2 44.1 0.5
ND1 B:HIS456 4.2 16.7 1.0
CG B:HIS456 4.2 18.4 1.0
CD2 B:HIS624 4.3 18.6 1.0
ND1 B:HIS458 4.3 19.4 1.0
NE2 B:HIS624 4.3 20.3 1.0
O4A B:TY9405 4.4 48.8 0.5
O4A B:TY9405 4.4 48.8 0.5
C6 B:TY9405 4.8 38.5 0.5
C6 B:TY9405 4.8 38.5 0.5
CA B:HIS624 4.8 15.9 1.0
CD1 B:LEU425 4.8 37.3 1.0
CE B:MET634 4.9 41.3 0.5
CE B:MET634 4.9 41.3 0.5
CD1 B:ILE622 5.0 28.5 1.0

Copper binding site 3 out of 6 in 3nbj

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Copper binding site 3 out of 6 in the Crystal Structure of Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast


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 Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu701

b:22.9
occ:1.00
NE2 C:HIS458 2.1 22.4 1.0
ND1 C:HIS624 2.1 19.4 1.0
NE2 C:HIS456 2.1 19.3 1.0
CD2 C:HIS458 2.9 17.6 1.0
CG C:HIS624 3.1 19.0 1.0
O5 C:TY9405 3.1 38.6 0.5
O5 C:TY9405 3.1 38.6 0.5
CE1 C:HIS456 3.1 18.3 1.0
CD2 C:HIS456 3.1 19.8 1.0
CE1 C:HIS624 3.2 18.8 1.0
CB C:HIS624 3.2 15.7 1.0
CE1 C:HIS458 3.3 20.1 1.0
C5 C:TY9405 3.8 41.8 0.5
C5 C:TY9405 3.8 41.8 0.5
O4 C:TY9405 4.0 51.7 0.5
O4 C:TY9405 4.0 51.7 0.5
CG C:HIS458 4.1 20.6 1.0
C4 C:TY9405 4.2 44.1 0.5
C4 C:TY9405 4.2 44.1 0.5
ND1 C:HIS456 4.2 16.7 1.0
CG C:HIS456 4.2 18.4 1.0
CD2 C:HIS624 4.3 18.6 1.0
ND1 C:HIS458 4.3 19.4 1.0
NE2 C:HIS624 4.3 20.3 1.0
O4A C:TY9405 4.4 48.8 0.5
O4A C:TY9405 4.4 48.8 0.5
C6 C:TY9405 4.8 38.5 0.5
C6 C:TY9405 4.8 38.5 0.5
CA C:HIS624 4.8 15.9 1.0
CD1 C:LEU425 4.8 37.3 1.0
CE C:MET634 4.9 41.3 0.5
CE C:MET634 4.9 41.3 0.5
CD1 C:ILE622 5.0 28.5 1.0

Copper binding site 4 out of 6 in 3nbj

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Copper binding site 4 out of 6 in the Crystal Structure of Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast


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 Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu701

b:22.9
occ:1.00
NE2 D:HIS458 2.1 22.4 1.0
ND1 D:HIS624 2.1 19.4 1.0
NE2 D:HIS456 2.1 19.3 1.0
CD2 D:HIS458 2.9 17.6 1.0
CG D:HIS624 3.1 19.0 1.0
O5 D:TY9405 3.1 38.6 0.5
O5 D:TY9405 3.1 38.6 0.5
CE1 D:HIS456 3.1 18.3 1.0
CD2 D:HIS456 3.1 19.8 1.0
CE1 D:HIS624 3.2 18.8 1.0
CB D:HIS624 3.3 15.7 1.0
CE1 D:HIS458 3.3 20.1 1.0
C5 D:TY9405 3.8 41.8 0.5
C5 D:TY9405 3.8 41.8 0.5
O4 D:TY9405 3.9 51.7 0.5
O4 D:TY9405 3.9 51.7 0.5
CG D:HIS458 4.1 20.6 1.0
C4 D:TY9405 4.2 44.1 0.5
C4 D:TY9405 4.2 44.1 0.5
ND1 D:HIS456 4.2 16.7 1.0
CG D:HIS456 4.2 18.4 1.0
CD2 D:HIS624 4.3 18.6 1.0
ND1 D:HIS458 4.3 19.4 1.0
NE2 D:HIS624 4.3 20.3 1.0
O4A D:TY9405 4.4 48.8 0.5
O4A D:TY9405 4.4 48.8 0.5
C6 D:TY9405 4.8 38.5 0.5
C6 D:TY9405 4.8 38.5 0.5
CA D:HIS624 4.8 15.9 1.0
CD1 D:LEU425 4.8 37.3 1.0
CE D:MET634 4.9 41.3 0.5
CE D:MET634 4.9 41.3 0.5
CD1 D:ILE622 5.0 28.5 1.0

Copper binding site 5 out of 6 in 3nbj

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Copper binding site 5 out of 6 in the Crystal Structure of Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast


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 Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu701

b:22.9
occ:1.00
NE2 E:HIS458 2.1 22.4 1.0
ND1 E:HIS624 2.1 19.4 1.0
NE2 E:HIS456 2.1 19.3 1.0
CD2 E:HIS458 2.9 17.6 1.0
CG E:HIS624 3.1 19.0 1.0
O5 E:TY9405 3.1 38.6 0.5
O5 E:TY9405 3.1 38.6 0.5
CE1 E:HIS456 3.1 18.3 1.0
CD2 E:HIS456 3.1 19.8 1.0
CE1 E:HIS624 3.2 18.8 1.0
CB E:HIS624 3.3 15.7 1.0
CE1 E:HIS458 3.3 20.1 1.0
C5 E:TY9405 3.8 41.8 0.5
C5 E:TY9405 3.8 41.8 0.5
O4 E:TY9405 3.9 51.7 0.5
O4 E:TY9405 3.9 51.7 0.5
CG E:HIS458 4.1 20.6 1.0
C4 E:TY9405 4.2 44.1 0.5
C4 E:TY9405 4.2 44.1 0.5
ND1 E:HIS456 4.2 16.7 1.0
CG E:HIS456 4.2 18.4 1.0
CD2 E:HIS624 4.3 18.6 1.0
ND1 E:HIS458 4.3 19.4 1.0
NE2 E:HIS624 4.3 20.3 1.0
O4A E:TY9405 4.4 48.8 0.5
O4A E:TY9405 4.4 48.8 0.5
C6 E:TY9405 4.8 38.5 0.5
C6 E:TY9405 4.8 38.5 0.5
CA E:HIS624 4.8 15.9 1.0
CD1 E:LEU425 4.8 37.3 1.0
CE E:MET634 4.9 41.3 0.5
CE E:MET634 4.9 41.3 0.5
CD1 E:ILE622 5.0 28.5 1.0

Copper binding site 6 out of 6 in 3nbj

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Copper binding site 6 out of 6 in the Crystal Structure of Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast


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 Y305F Mutant of the Copper Amine Oxidase From Hansenula Polymorpha Expressed in Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu701

b:22.9
occ:1.00
NE2 F:HIS458 2.1 22.4 1.0
ND1 F:HIS624 2.1 19.4 1.0
NE2 F:HIS456 2.1 19.3 1.0
CD2 F:HIS458 2.9 17.6 1.0
CG F:HIS624 3.1 19.0 1.0
O5 F:TY9405 3.1 38.6 0.5
O5 F:TY9405 3.1 38.6 0.5
CE1 F:HIS456 3.1 18.3 1.0
CD2 F:HIS456 3.1 19.8 1.0
CE1 F:HIS624 3.2 18.8 1.0
CB F:HIS624 3.3 15.7 1.0
CE1 F:HIS458 3.3 20.1 1.0
C5 F:TY9405 3.8 41.8 0.5
C5 F:TY9405 3.8 41.8 0.5
O4 F:TY9405 3.9 51.7 0.5
O4 F:TY9405 3.9 51.7 0.5
CG F:HIS458 4.1 20.6 1.0
C4 F:TY9405 4.2 44.1 0.5
C4 F:TY9405 4.2 44.1 0.5
ND1 F:HIS456 4.2 16.7 1.0
CG F:HIS456 4.2 18.4 1.0
CD2 F:HIS624 4.3 18.6 1.0
ND1 F:HIS458 4.3 19.4 1.0
NE2 F:HIS624 4.3 20.3 1.0
O4A F:TY9405 4.4 48.8 0.5
O4A F:TY9405 4.4 48.8 0.5
C6 F:TY9405 4.8 38.5 0.5
C6 F:TY9405 4.8 38.5 0.5
CA F:HIS624 4.8 15.9 1.0
CD1 F:LEU425 4.8 37.3 1.0
CE F:MET634 4.9 41.3 0.5
CE F:MET634 4.9 41.3 0.5
CD1 F:ILE622 5.0 28.5 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: Fri Sep 4 08:10:25 2020
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