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Copper in PDB 4ev5: Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine

Enzymatic activity of Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine

All present enzymatic activity of Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine:
1.4.3.21;

Protein crystallography data

The structure of Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine, PDB code: 4ev5 was solved by V.J.Klema, C.J.Solheid, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.239, 233.706, 105.045, 90.00, 96.57, 90.00
R / Rfree (%) 16.9 / 23

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine (pdb code 4ev5). 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 Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine, PDB code: 4ev5:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 4ev5

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Copper binding site 1 out of 6 in the Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine


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 Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:28.8
occ:1.00
 ND1 A:HIS624 2.0 25.2 1.0
NE2 A:HIS458 2.0 25.6 1.0
NE2 A:HIS456 2.0 20.5 1.0
O2 A:PEO707 2.8 31.2 1.0
CE1 A:HIS456 2.8 24.5 1.0
CD2 A:HIS458 2.9 19.9 1.0
CE1 A:HIS624 2.9 24.2 1.0
CG A:HIS624 3.0 23.6 1.0
O1 A:PEO707 3.1 26.5 1.0
CD2 A:HIS456 3.1 21.1 1.0
CE1 A:HIS458 3.1 22.8 1.0
CB A:HIS624 3.3 20.5 1.0
ND1 A:HIS456 4.0 19.6 1.0
O A:HOH1256 4.1 47.9 1.0
NE2 A:HIS624 4.1 20.8 1.0
CG A:HIS458 4.1 23.2 1.0
CG A:HIS456 4.1 21.4 1.0
CD2 A:HIS624 4.1 22.2 1.0
ND1 A:HIS458 4.2 24.9 1.0
O A:HOH1323 4.6 24.6 1.0
OZ A:TYQ405 4.7 33.7 1.0
CA A:HIS624 4.8 20.8 1.0
CD1 A:ILE622 4.8 26.4 1.0
CD1 A:LEU425 4.8 36.1 1.0

Copper binding site 2 out of 6 in 4ev5

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Copper binding site 2 out of 6 in the Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine


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 Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:26.0
occ:1.00
 ND1 B:HIS624 2.0 23.4 1.0
NE2 B:HIS456 2.0 21.1 1.0
NE2 B:HIS458 2.1 17.8 1.0
O2 B:PEO708 2.4 26.9 1.0
CD2 B:HIS458 2.9 12.6 1.0
CD2 B:HIS456 2.9 19.6 1.0
O1 B:PEO708 2.9 24.3 1.0
CE1 B:HIS624 2.9 21.4 1.0
CG B:HIS624 3.0 19.1 1.0
CE1 B:HIS456 3.0 22.2 1.0
CE1 B:HIS458 3.3 17.5 1.0
CB B:HIS624 3.4 18.6 1.0
O B:HOH1298 3.9 46.1 1.0
CG B:HIS456 4.1 20.9 1.0
NE2 B:HIS624 4.1 20.7 1.0
ND1 B:HIS456 4.1 15.9 1.0
CG B:HIS458 4.1 17.9 1.0
CD2 B:HIS624 4.1 17.1 1.0
ND1 B:HIS458 4.3 18.8 1.0
O B:HOH837 4.6 17.8 1.0
OZ B:TYQ405 4.7 26.5 1.0
CA B:HIS624 4.9 18.5 1.0
O B:HOH1296 4.9 36.5 1.0
CD1 B:LEU425 4.9 37.3 1.0
CD1 B:ILE622 4.9 27.7 1.0
SD B:MET634 5.0 42.5 1.0

Copper binding site 3 out of 6 in 4ev5

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Copper binding site 3 out of 6 in the Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine


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 Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu701

b:33.0
occ:1.00
 ND1 C:HIS624 1.9 26.2 1.0
NE2 C:HIS456 2.0 25.6 1.0
NE2 C:HIS458 2.2 20.3 1.0
O C:HOH1235 2.6 55.5 1.0
O C:HOH1295 2.7 18.1 1.0
CE1 C:HIS624 2.8 23.3 1.0
CG C:HIS624 2.9 25.1 1.0
CD2 C:HIS456 3.0 20.0 1.0
CE1 C:HIS456 3.0 25.6 1.0
CD2 C:HIS458 3.1 18.4 1.0
CE1 C:HIS458 3.3 19.9 1.0
CB C:HIS624 3.3 25.2 1.0
NE2 C:HIS624 3.9 24.5 1.0
CD2 C:HIS624 4.0 22.7 1.0
ND1 C:HIS456 4.1 21.1 1.0
CG C:HIS456 4.1 22.5 1.0
CD2 C:LEU425 4.3 36.7 1.0
CG C:HIS458 4.3 21.9 1.0
ND1 C:HIS458 4.3 20.4 1.0
O C:HOH839 4.4 25.5 1.0
OZ C:TYQ405 4.6 37.9 1.0
CD1 C:ILE622 4.7 28.1 1.0
CA C:HIS624 4.8 26.8 1.0
CE C:MET634 5.0 18.4 0.5

Copper binding site 4 out of 6 in 4ev5

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Copper binding site 4 out of 6 in the Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine


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 Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu701

b:36.4
occ:1.00
 NE2 D:HIS458 1.9 34.5 1.0
NE2 D:HIS456 2.0 30.5 1.0
ND1 D:HIS624 2.1 30.9 1.0
O D:HOH1257 2.8 14.4 1.0
CD2 D:HIS458 2.9 28.1 1.0
CE1 D:HIS458 2.9 33.7 1.0
CD2 D:HIS456 2.9 30.3 1.0
CE1 D:HIS456 3.0 33.3 1.0
CE1 D:HIS624 3.1 29.6 1.0
CG D:HIS624 3.1 29.9 1.0
CB D:HIS624 3.4 29.6 1.0
ND1 D:HIS458 4.0 28.4 1.0
CG D:HIS458 4.0 29.1 1.0
ND1 D:HIS456 4.1 29.8 1.0
CG D:HIS456 4.1 32.1 1.0
NE2 D:HIS624 4.2 31.6 1.0
OZ D:TYQ405 4.2 47.5 1.0
CD2 D:HIS624 4.2 30.2 1.0
O D:HOH1198 4.5 33.5 1.0
CA D:HIS624 4.9 28.7 1.0
CD1 D:LEU425 4.9 44.2 1.0
CD1 D:ILE622 5.0 38.1 1.0

Copper binding site 5 out of 6 in 4ev5

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Copper binding site 5 out of 6 in the Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine


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 Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu701

b:29.0
occ:1.00
 ND1 E:HIS624 2.0 19.6 1.0
NE2 E:HIS456 2.1 17.2 1.0
NE2 E:HIS458 2.2 24.8 1.0
O2 E:PEO705 2.8 36.0 1.0
O1 E:PEO705 2.9 30.8 1.0
CE1 E:HIS456 3.0 20.8 1.0
CG E:HIS624 3.0 14.5 1.0
CE1 E:HIS624 3.0 17.6 1.0
CD2 E:HIS456 3.1 20.0 1.0
CD2 E:HIS458 3.1 21.4 1.0
CE1 E:HIS458 3.3 26.8 1.0
CB E:HIS624 3.3 18.1 1.0
O E:HOH1129 3.5 63.3 1.0
ND1 E:HIS456 4.1 19.0 1.0
NE2 E:HIS624 4.1 19.7 1.0
CD2 E:HIS624 4.1 21.8 1.0
CG E:HIS456 4.1 20.0 1.0
CG E:HIS458 4.3 25.2 1.0
ND1 E:HIS458 4.4 27.4 1.0
O E:HOH1048 4.7 19.0 1.0
OZ E:TYQ405 4.7 32.1 1.0
O E:HOH1146 4.8 52.4 1.0
CA E:HIS624 4.8 19.6 1.0
CD1 E:ILE622 5.0 26.6 1.0
CE E:MET634 5.0 34.7 0.6
CD1 E:LEU425 5.0 37.1 1.0

Copper binding site 6 out of 6 in 4ev5

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Copper binding site 6 out of 6 in the Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine


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 Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu701

b:32.0
occ:1.00
 ND1 F:HIS624 1.9 24.7 1.0
NE2 F:HIS456 2.1 25.4 1.0
NE2 F:HIS458 2.2 27.4 1.0
CE1 F:HIS624 2.8 19.6 1.0
CD2 F:HIS458 2.9 22.2 1.0
CG F:HIS624 2.9 23.3 1.0
O2 F:PEO707 3.0 36.8 1.0
O1 F:PEO707 3.0 28.9 1.0
CD2 F:HIS456 3.0 22.4 1.0
CE1 F:HIS456 3.1 23.8 1.0
CE1 F:HIS458 3.3 24.4 1.0
CB F:HIS624 3.3 24.3 1.0
NE2 F:HIS624 3.9 25.4 1.0
CD2 F:HIS624 4.0 22.8 1.0
ND1 F:HIS456 4.1 21.6 1.0
CG F:HIS458 4.1 23.5 1.0
CG F:HIS456 4.2 22.4 1.0
ND1 F:HIS458 4.3 26.8 1.0
O F:HOH1122 4.5 26.7 1.0
CD1 F:LEU425 4.6 38.3 1.0
OZ F:TYQ405 4.6 43.7 1.0
CA F:HIS624 4.9 24.6 1.0
CD1 F:ILE622 4.9 23.8 1.0
SD F:MET634 5.0 52.2 1.0

Reference:

V.J.Klema, C.J.Solheid, J.P.Klinman, C.M.Wilmot. Crystal Structure of Copper Amine Oxidase-1 From Hansenula Polymorpha in Complex with Benzylamine To Be Published.
Page generated: Sun Dec 13 11:14:22 2020

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