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
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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 Sites List in 4kfd
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 Sites List in 4kfd
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
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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
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