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Copper in PDB 4kfd: Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0

Enzymatic activity of Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0

All present enzymatic activity of Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0:
1.4.3.21;

Protein crystallography data

The structure of Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0, PDB code: 4kfd was solved by B.J.Johnson, E.T.Yukl, V.J.Klema, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.78 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.577, 222.836, 103.619, 90.00, 95.87, 90.00
R / Rfree (%) 13.4 / 16.4

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0 (pdb code 4kfd). 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 Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0, PDB code: 4kfd:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 4kfd

Go back to Copper Binding Sites List in 4kfd
Copper binding site 1 out of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0


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 Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu801

b:12.1
occ:1.00
ND1 A:HIS624 2.1 11.0 1.0
NE2 A:HIS456 2.1 8.9 1.0
NE2 A:HIS458 2.1 9.0 1.0
O2 A:PEO802 2.4 7.2 1.0
O A:HOH1428 2.5 34.1 1.0
O1 A:PEO802 2.8 10.1 1.0
CD2 A:HIS458 3.0 8.2 1.0
CD2 A:HIS456 3.0 9.2 1.0
CE1 A:HIS624 3.0 11.3 1.0
CE1 A:HIS456 3.1 10.1 1.0
CG A:HIS624 3.1 9.9 1.0
CE1 A:HIS458 3.1 8.1 1.0
CB A:HIS624 3.4 9.1 1.0
ND1 A:HIS456 4.1 8.9 1.0
NE2 A:HIS624 4.2 10.5 1.0
CG A:HIS458 4.2 7.6 1.0
ND1 A:HIS458 4.2 8.0 1.0
CG A:HIS456 4.2 8.0 1.0
CD2 A:HIS624 4.2 11.3 1.0
O A:HOH1266 4.3 33.7 1.0
O A:HOH1052 4.4 11.8 1.0
O A:HOH1192 4.6 27.1 1.0
OZ A:TYY405 4.7 12.2 1.0
CD1 A:LEU425 4.8 19.4 1.0
CA A:HIS624 4.9 8.3 1.0

Copper binding site 2 out of 6 in 4kfd

Go back to Copper Binding Sites List in 4kfd
Copper binding site 2 out of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0


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 Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu801

b:12.2
occ:1.00
ND1 B:HIS624 2.0 11.1 1.0
NE2 B:HIS456 2.1 9.1 1.0
NE2 B:HIS458 2.1 9.4 1.0
O2 B:PEO802 2.2 11.6 1.0
O1 B:PEO802 2.8 5.9 1.0
CE1 B:HIS624 3.0 11.8 1.0
CD2 B:HIS456 3.0 9.1 1.0
CD2 B:HIS458 3.0 8.4 1.0
CE1 B:HIS456 3.1 9.0 1.0
CE1 B:HIS458 3.1 8.5 1.0
CG B:HIS624 3.1 10.2 1.0
CB B:HIS624 3.4 9.2 1.0
NE2 B:HIS624 4.1 11.4 1.0
ND1 B:HIS456 4.2 8.7 1.0
CG B:HIS456 4.2 7.9 1.0
ND1 B:HIS458 4.2 8.7 1.0
CD2 B:HIS624 4.2 11.3 1.0
CG B:HIS458 4.2 8.2 1.0
O B:HOH1528 4.3 34.2 1.0
O B:HOH1096 4.4 11.0 1.0
OZ B:TYY405 4.6 13.2 1.0
O B:HOH1180 4.6 24.6 1.0
CD1 B:LEU425 4.8 22.8 1.0
CA B:HIS624 4.9 8.3 1.0
CE B:MET634 5.0 23.1 1.0
CD2 B:LEU429 5.0 10.0 1.0

Copper binding site 3 out of 6 in 4kfd

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Copper binding site 3 out of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0


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 Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu801

b:11.7
occ:1.00
ND1 C:HIS624 2.0 9.0 1.0
NE2 C:HIS458 2.1 9.6 1.0
NE2 C:HIS456 2.1 9.6 1.0
O1 C:PEO802 2.5 8.5 1.0
O C:HOH1427 2.5 39.0 1.0
O2 C:PEO802 2.7 8.1 1.0
CE1 C:HIS624 2.9 10.2 1.0
CD2 C:HIS458 3.0 9.7 1.0
CG C:HIS624 3.0 9.3 1.0
CD2 C:HIS456 3.1 9.9 1.0
CE1 C:HIS458 3.1 10.7 1.0
CE1 C:HIS456 3.1 9.1 1.0
CB C:HIS624 3.4 8.9 1.0
NE2 C:HIS624 4.1 10.0 1.0
CD2 C:HIS624 4.1 9.2 1.0
CG C:HIS458 4.1 8.8 1.0
ND1 C:HIS458 4.2 9.4 1.0
ND1 C:HIS456 4.2 8.9 1.0
CG C:HIS456 4.2 8.7 1.0
O C:HOH990 4.4 10.5 1.0
OZ C:TYY405 4.6 12.4 0.5
O C:HOH1121 4.6 27.4 1.0
OZ C:TYY405 4.8 12.0 0.5
CA C:HIS624 4.9 8.8 1.0
CD1 C:LEU425 4.9 22.5 1.0

Copper binding site 4 out of 6 in 4kfd

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Copper binding site 4 out of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0


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 Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu801

b:11.6
occ:1.00
NE2 D:HIS458 2.1 8.2 1.0
ND1 D:HIS624 2.1 10.3 1.0
NE2 D:HIS456 2.1 8.5 1.0
O2 D:PEO802 2.2 10.9 1.0
O D:HOH1473 2.7 38.6 1.0
O1 D:PEO802 2.8 6.3 1.0
CE1 D:HIS458 3.0 8.2 1.0
CD2 D:HIS458 3.0 8.5 1.0
CG D:HIS624 3.0 9.9 1.0
CE1 D:HIS624 3.0 11.1 1.0
CE1 D:HIS456 3.1 8.6 1.0
CD2 D:HIS456 3.1 8.7 1.0
CB D:HIS624 3.3 9.3 1.0
ND1 D:HIS458 4.1 8.3 1.0
NE2 D:HIS624 4.2 10.3 1.0
O D:HOH1615 4.2 35.8 1.0
CG D:HIS458 4.2 7.6 1.0
CD2 D:HIS624 4.2 10.8 1.0
ND1 D:HIS456 4.2 8.2 1.0
CG D:HIS456 4.2 7.7 1.0
O D:HOH905 4.4 10.7 1.0
O D:HOH1373 4.6 29.6 1.0
OZ D:TYY405 4.7 13.5 1.0
CA D:HIS624 4.9 8.5 1.0
CD1 D:LEU425 4.9 19.5 1.0
CE D:MET634 4.9 19.5 1.0
CD1 D:ILE622 5.0 18.3 1.0

Copper binding site 5 out of 6 in 4kfd

Go back to Copper Binding Sites List in 4kfd
Copper binding site 5 out of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0


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 Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu801

b:11.8
occ:1.00
NE2 E:HIS458 2.0 8.6 1.0
ND1 E:HIS624 2.1 11.3 1.0
NE2 E:HIS456 2.1 8.2 1.0
O2 E:PEO802 2.2 10.1 1.0
O E:HOH1439 2.5 34.2 1.0
O1 E:PEO802 2.8 6.5 1.0
CE1 E:HIS458 3.0 8.2 1.0
CD2 E:HIS458 3.0 8.4 1.0
CG E:HIS624 3.1 9.7 1.0
CE1 E:HIS624 3.1 11.9 1.0
CD2 E:HIS456 3.1 8.9 1.0
CE1 E:HIS456 3.1 9.1 1.0
CB E:HIS624 3.4 9.1 1.0
ND1 E:HIS458 4.1 8.7 1.0
NE2 E:HIS624 4.2 11.3 1.0
CG E:HIS458 4.2 7.8 1.0
CD2 E:HIS624 4.2 11.0 1.0
ND1 E:HIS456 4.2 8.8 1.0
CG E:HIS456 4.2 7.9 1.0
O E:HOH903 4.4 10.0 1.0
O E:HOH1382 4.5 29.0 1.0
OZ E:TYY405 4.7 13.5 1.0
CD1 E:LEU425 4.8 19.1 1.0
CA E:HIS624 4.9 8.4 1.0
CE E:MET634 4.9 21.5 1.0
CD1 E:ILE622 5.0 17.4 1.0
SD E:MET634 5.0 28.1 1.0

Copper binding site 6 out of 6 in 4kfd

Go back to Copper Binding Sites List in 4kfd
Copper binding site 6 out of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0


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 Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu801

b:11.9
occ:1.00
ND1 F:HIS624 2.0 9.4 1.0
NE2 F:HIS458 2.1 8.4 1.0
NE2 F:HIS456 2.1 9.8 1.0
O1 F:PEO802 2.6 9.1 1.0
O2 F:PEO802 2.6 7.8 1.0
O F:HOH1402 2.8 47.0 1.0
CE1 F:HIS624 3.0 10.1 1.0
CD2 F:HIS458 3.0 8.8 1.0
CD2 F:HIS456 3.0 9.6 1.0
CG F:HIS624 3.0 9.6 1.0
CE1 F:HIS456 3.1 9.6 1.0
CE1 F:HIS458 3.1 9.1 1.0
CB F:HIS624 3.4 8.9 1.0
NE2 F:HIS624 4.1 10.3 1.0
CD2 F:HIS624 4.1 9.3 1.0
CG F:HIS458 4.2 8.4 1.0
ND1 F:HIS456 4.2 8.9 1.0
ND1 F:HIS458 4.2 9.2 1.0
CG F:HIS456 4.2 8.4 1.0
OZ F:TYY405 4.4 12.4 0.5
O F:HOH986 4.5 11.1 1.0
O F:HOH1079 4.7 25.9 1.0
OZ F:TYY405 4.8 11.5 0.5
CD1 F:LEU425 4.9 22.4 1.0
CA F:HIS624 4.9 8.6 1.0
CD1 F:ILE622 5.0 17.8 1.0
SD F:MET634 5.0 31.6 1.0
CE F:MET634 5.0 21.7 1.0

Reference:

B.J.Johnson, E.T.Yukl, V.J.Klema, J.P.Klinman, C.M.Wilmot. Structural Evidence For the Semiquinone in A Copper Amine Oxidase From Hansenula Polymorpha: Implications For the Catalytic Mechanism J.Biol.Chem. 2013.
ISSN: ESSN 1083-351X
Page generated: Mon Jul 14 03:48:23 2025

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