Copper in PDB 4kfe: Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0
Enzymatic activity of Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0
All present enzymatic activity of Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0:
1.4.3.21;
Protein crystallography data
The structure of Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0, PDB code: 4kfe
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)
|
49.03 /
2.10
|
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 (%)
|
12.9 /
18
|
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 7.0
(pdb code 4kfe). 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 7.0, PDB code: 4kfe:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 4kfe
Go back to
Copper Binding Sites List in 4kfe
Copper binding site 1 out
of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0
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 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu801
b:19.6
occ:1.00
|
ND1
|
A:HIS624
|
2.0
|
16.9
|
1.0
|
NE2
|
A:HIS456
|
2.1
|
14.5
|
1.0
|
NE2
|
A:HIS458
|
2.1
|
18.0
|
1.0
|
O1
|
A:PEO802
|
2.6
|
20.0
|
1.0
|
O2
|
A:PEO802
|
2.6
|
14.5
|
1.0
|
CE1
|
A:HIS624
|
2.9
|
18.7
|
1.0
|
CD2
|
A:HIS458
|
3.0
|
15.9
|
1.0
|
CD2
|
A:HIS456
|
3.0
|
14.6
|
1.0
|
CG
|
A:HIS624
|
3.1
|
17.5
|
1.0
|
CE1
|
A:HIS456
|
3.1
|
15.1
|
1.0
|
CE1
|
A:HIS458
|
3.2
|
16.5
|
1.0
|
CB
|
A:HIS624
|
3.4
|
15.8
|
1.0
|
NE2
|
A:HIS624
|
4.1
|
17.8
|
1.0
|
CD2
|
A:HIS624
|
4.2
|
17.3
|
1.0
|
CG
|
A:HIS456
|
4.2
|
14.4
|
1.0
|
ND1
|
A:HIS456
|
4.2
|
15.2
|
1.0
|
CG
|
A:HIS458
|
4.2
|
15.1
|
1.0
|
ND1
|
A:HIS458
|
4.2
|
15.4
|
1.0
|
O
|
A:HOH1055
|
4.4
|
22.2
|
1.0
|
OZ
|
A:TYY405
|
4.7
|
20.1
|
1.0
|
O
|
A:HOH1193
|
4.9
|
40.4
|
1.0
|
CE
|
A:MET634
|
4.9
|
29.3
|
1.0
|
CA
|
A:HIS624
|
4.9
|
14.5
|
1.0
|
CD1
|
A:ILE622
|
5.0
|
25.5
|
1.0
|
CD2
|
A:LEU429
|
5.0
|
17.1
|
1.0
|
|
Copper binding site 2 out
of 6 in 4kfe
Go back to
Copper Binding Sites List in 4kfe
Copper binding site 2 out
of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0
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 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu801
b:20.6
occ:1.00
|
ND1
|
B:HIS624
|
2.0
|
19.6
|
1.0
|
NE2
|
B:HIS456
|
2.1
|
16.8
|
1.0
|
O2
|
B:PEO802
|
2.1
|
21.2
|
1.0
|
NE2
|
B:HIS458
|
2.1
|
16.3
|
1.0
|
O1
|
B:PEO802
|
2.9
|
13.0
|
1.0
|
CE1
|
B:HIS624
|
2.9
|
20.6
|
1.0
|
CG
|
B:HIS624
|
3.0
|
19.1
|
1.0
|
CD2
|
B:HIS456
|
3.0
|
15.8
|
1.0
|
CE1
|
B:HIS456
|
3.1
|
16.6
|
1.0
|
CE1
|
B:HIS458
|
3.1
|
14.4
|
1.0
|
CD2
|
B:HIS458
|
3.1
|
14.3
|
1.0
|
CB
|
B:HIS624
|
3.4
|
16.9
|
1.0
|
NE2
|
B:HIS624
|
4.0
|
20.2
|
1.0
|
CD2
|
B:HIS624
|
4.1
|
19.4
|
1.0
|
ND1
|
B:HIS456
|
4.2
|
16.2
|
1.0
|
CG
|
B:HIS456
|
4.2
|
15.6
|
1.0
|
ND1
|
B:HIS458
|
4.2
|
15.0
|
1.0
|
CG
|
B:HIS458
|
4.3
|
14.6
|
1.0
|
O
|
B:HOH1094
|
4.4
|
21.3
|
1.0
|
O
|
B:HOH1497
|
4.5
|
56.7
|
1.0
|
OZ
|
B:TYY405
|
4.7
|
21.5
|
1.0
|
O
|
B:HOH1179
|
4.8
|
34.2
|
1.0
|
CD1
|
B:LEU425
|
4.9
|
34.4
|
1.0
|
CA
|
B:HIS624
|
5.0
|
14.7
|
1.0
|
CE
|
B:MET634
|
5.0
|
33.0
|
1.0
|
|
Copper binding site 3 out
of 6 in 4kfe
Go back to
Copper Binding Sites List in 4kfe
Copper binding site 3 out
of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0
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 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu801
b:19.4
occ:1.00
|
ND1
|
C:HIS624
|
2.1
|
16.5
|
1.0
|
NE2
|
C:HIS458
|
2.1
|
18.9
|
1.0
|
NE2
|
C:HIS456
|
2.1
|
14.0
|
1.0
|
O2
|
C:PEO802
|
2.4
|
17.7
|
1.0
|
O1
|
C:PEO802
|
2.8
|
14.2
|
1.0
|
CE1
|
C:HIS624
|
3.0
|
16.7
|
1.0
|
CD2
|
C:HIS456
|
3.0
|
13.5
|
1.0
|
O
|
C:HOH1426
|
3.0
|
50.4
|
1.0
|
CD2
|
C:HIS458
|
3.0
|
16.6
|
1.0
|
CG
|
C:HIS624
|
3.1
|
15.2
|
1.0
|
CE1
|
C:HIS458
|
3.1
|
17.8
|
1.0
|
CE1
|
C:HIS456
|
3.2
|
13.5
|
1.0
|
CB
|
C:HIS624
|
3.4
|
15.4
|
1.0
|
NE2
|
C:HIS624
|
4.1
|
15.7
|
1.0
|
CD2
|
C:HIS624
|
4.2
|
16.5
|
1.0
|
ND1
|
C:HIS458
|
4.2
|
17.4
|
1.0
|
CG
|
C:HIS458
|
4.2
|
16.2
|
1.0
|
CG
|
C:HIS456
|
4.2
|
13.6
|
1.0
|
ND1
|
C:HIS456
|
4.2
|
13.4
|
1.0
|
O
|
C:HOH990
|
4.5
|
12.2
|
1.0
|
OZ
|
C:TYY405
|
4.7
|
23.0
|
1.0
|
O
|
C:HOH1120
|
4.7
|
43.4
|
1.0
|
CD1
|
C:LEU425
|
4.8
|
38.1
|
1.0
|
CA
|
C:HIS624
|
4.9
|
14.1
|
1.0
|
|
Copper binding site 4 out
of 6 in 4kfe
Go back to
Copper Binding Sites List in 4kfe
Copper binding site 4 out
of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0
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 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu703
b:20.2
occ:1.00
|
ND1
|
D:HIS624
|
2.1
|
17.1
|
1.0
|
NE2
|
D:HIS458
|
2.1
|
16.6
|
1.0
|
NE2
|
D:HIS456
|
2.2
|
13.9
|
1.0
|
O2
|
D:PEO701
|
2.7
|
17.9
|
1.0
|
O1
|
D:PEO701
|
2.7
|
17.6
|
1.0
|
CE1
|
D:HIS624
|
3.0
|
16.9
|
1.0
|
O
|
D:HOH1351
|
3.0
|
39.1
|
1.0
|
CD2
|
D:HIS458
|
3.0
|
15.8
|
1.0
|
CD2
|
D:HIS456
|
3.1
|
14.6
|
1.0
|
CG
|
D:HIS624
|
3.1
|
16.5
|
1.0
|
CE1
|
D:HIS458
|
3.1
|
15.9
|
1.0
|
CE1
|
D:HIS456
|
3.2
|
15.5
|
1.0
|
CB
|
D:HIS624
|
3.5
|
16.6
|
1.0
|
NE2
|
D:HIS624
|
4.1
|
16.9
|
1.0
|
CD2
|
D:HIS624
|
4.2
|
16.7
|
1.0
|
ND1
|
D:HIS458
|
4.2
|
16.2
|
1.0
|
CG
|
D:HIS458
|
4.2
|
14.7
|
1.0
|
CG
|
D:HIS456
|
4.2
|
14.6
|
1.0
|
ND1
|
D:HIS456
|
4.3
|
15.0
|
1.0
|
O
|
D:HOH805
|
4.5
|
13.1
|
1.0
|
OZ
|
D:TYY405
|
4.7
|
25.0
|
1.0
|
O
|
D:HOH1268
|
4.7
|
43.5
|
1.0
|
CD1
|
D:LEU425
|
4.8
|
32.5
|
1.0
|
CE
|
D:MET634
|
5.0
|
31.9
|
1.0
|
CA
|
D:HIS624
|
5.0
|
16.0
|
1.0
|
|
Copper binding site 5 out
of 6 in 4kfe
Go back to
Copper Binding Sites List in 4kfe
Copper binding site 5 out
of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0
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 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cu801
b:20.1
occ:1.00
|
NE2
|
E:HIS458
|
2.1
|
16.5
|
1.0
|
ND1
|
E:HIS624
|
2.1
|
16.3
|
1.0
|
NE2
|
E:HIS456
|
2.2
|
14.9
|
1.0
|
O2
|
E:PEO802
|
2.6
|
14.3
|
1.0
|
O1
|
E:PEO802
|
2.9
|
20.1
|
1.0
|
O
|
E:HOH1432
|
2.9
|
40.9
|
1.0
|
CD2
|
E:HIS458
|
2.9
|
14.2
|
1.0
|
CD2
|
E:HIS456
|
3.0
|
13.6
|
1.0
|
CE1
|
E:HIS624
|
3.1
|
15.7
|
1.0
|
CG
|
E:HIS624
|
3.1
|
15.6
|
1.0
|
CE1
|
E:HIS458
|
3.1
|
14.3
|
1.0
|
CE1
|
E:HIS456
|
3.3
|
15.7
|
1.0
|
CB
|
E:HIS624
|
3.4
|
14.8
|
1.0
|
CG
|
E:HIS458
|
4.1
|
14.2
|
1.0
|
ND1
|
E:HIS458
|
4.2
|
15.1
|
1.0
|
CG
|
E:HIS456
|
4.2
|
14.2
|
1.0
|
NE2
|
E:HIS624
|
4.2
|
15.1
|
1.0
|
CD2
|
E:HIS624
|
4.3
|
15.3
|
1.0
|
ND1
|
E:HIS456
|
4.3
|
15.5
|
1.0
|
O
|
E:HOH903
|
4.5
|
11.2
|
1.0
|
OZ
|
E:TYY405
|
4.7
|
20.0
|
1.0
|
CD1
|
E:LEU425
|
4.7
|
35.0
|
1.0
|
CD1
|
E:ILE622
|
4.9
|
25.3
|
1.0
|
CA
|
E:HIS624
|
4.9
|
14.2
|
1.0
|
SD
|
E:MET634
|
5.0
|
46.4
|
1.0
|
|
Copper binding site 6 out
of 6 in 4kfe
Go back to
Copper Binding Sites List in 4kfe
Copper binding site 6 out
of 6 in the Crystal Structure of Hansenula Polymorpha Copper Amine Oxidase-1 Reduced By Methylamine at pH 7.0
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 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cu801
b:19.2
occ:1.00
|
ND1
|
F:HIS624
|
2.1
|
16.0
|
1.0
|
NE2
|
F:HIS458
|
2.1
|
16.2
|
1.0
|
NE2
|
F:HIS456
|
2.1
|
15.6
|
1.0
|
O2
|
F:PEO802
|
2.3
|
16.4
|
1.0
|
O
|
F:HOH1395
|
2.9
|
41.0
|
1.0
|
O1
|
F:PEO802
|
2.9
|
13.9
|
1.0
|
CD2
|
F:HIS456
|
3.0
|
15.0
|
1.0
|
CE1
|
F:HIS624
|
3.0
|
16.2
|
1.0
|
CD2
|
F:HIS458
|
3.0
|
15.4
|
1.0
|
CG
|
F:HIS624
|
3.1
|
14.7
|
1.0
|
CE1
|
F:HIS458
|
3.2
|
17.2
|
1.0
|
CE1
|
F:HIS456
|
3.2
|
15.6
|
1.0
|
CB
|
F:HIS624
|
3.4
|
13.9
|
1.0
|
NE2
|
F:HIS624
|
4.1
|
15.7
|
1.0
|
CD2
|
F:HIS624
|
4.2
|
15.8
|
1.0
|
CG
|
F:HIS456
|
4.2
|
15.1
|
1.0
|
CG
|
F:HIS458
|
4.2
|
16.3
|
1.0
|
ND1
|
F:HIS456
|
4.2
|
15.8
|
1.0
|
ND1
|
F:HIS458
|
4.2
|
17.2
|
1.0
|
O
|
F:HOH983
|
4.5
|
11.8
|
1.0
|
OZ
|
F:TYY405
|
4.6
|
21.8
|
1.0
|
CD1
|
F:LEU425
|
4.9
|
33.9
|
1.0
|
CD1
|
F:ILE622
|
4.9
|
26.1
|
1.0
|
CA
|
F:HIS624
|
4.9
|
13.6
|
1.0
|
O
|
F:HOH1077
|
4.9
|
36.6
|
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: Wed Jul 31 03:07:37 2024
|