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Cobalt in PDB 3sxx: Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II)

Enzymatic activity of Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II)

All present enzymatic activity of Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II):
1.4.3.21;

Protein crystallography data

The structure of Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II), PDB code: 3sxx was solved by 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) 31.70 / 1.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.887, 223.364, 103.969, 90.00, 95.61, 90.00
R / Rfree (%) 10.8 / 13.8

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II) (pdb code 3sxx). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II), PDB code: 3sxx:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 3sxx

Go back to Cobalt Binding Sites List in 3sxx
Cobalt binding site 1 out of 6 in the Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co801

b:8.4
occ:0.50
 O A:HOH1736 1.3 17.3 0.5
NE2 A:HIS456 1.9 8.8 1.0
ND1 A:HIS624 2.1 9.4 0.7
OH A:TYR405 2.2 7.3 1.0
NE2 A:HIS458 2.2 7.5 1.0
O A:HOH1628 2.2 19.4 0.5
CE1 A:HIS624 2.9 9.6 0.7
CD2 A:HIS456 2.9 8.8 1.0
CE1 A:HIS456 3.0 7.5 1.0
CZ A:TYR405 3.0 6.6 1.0
CG A:HIS624 3.1 7.2 0.7
CE1 A:HIS458 3.2 7.4 1.0
CD2 A:HIS458 3.2 7.1 1.0
CB A:HIS624 3.6 9.0 0.7
CD2 A:LEU425 3.6 9.9 0.4
CE1 A:TYR405 3.7 6.9 1.0
CE2 A:TYR405 3.8 9.3 1.0
CB A:HIS624 3.8 6.9 0.3
CG A:HIS624 4.0 7.3 0.3
ND1 A:HIS456 4.1 6.4 1.0
CG A:HIS456 4.1 7.0 1.0
NE2 A:HIS624 4.1 8.6 0.7
OE2 A:GLU637 4.1 22.0 0.5
ND1 A:HIS624 4.1 11.0 0.3
CD2 A:HIS624 4.2 7.5 0.7
O A:HOH993 4.2 6.0 1.0
ND1 A:HIS458 4.3 6.4 1.0
CG A:HIS458 4.3 6.6 1.0
CD2 A:HIS624 4.7 11.9 0.3
CD2 A:LEU429 4.9 7.9 1.0
CE1 A:HIS624 4.9 5.0 0.3
CD1 A:TYR405 4.9 6.6 1.0
CG A:LEU425 4.9 6.4 0.4
CD2 A:TYR405 4.9 10.1 1.0
SD A:MET634 5.0 7.3 0.5

Cobalt binding site 2 out of 6 in 3sxx

Go back to Cobalt Binding Sites List in 3sxx
Cobalt binding site 2 out of 6 in the Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co801

b:8.4
occ:0.50
 O B:HOH1736 1.3 14.8 0.5
NE2 B:HIS456 1.9 9.5 1.0
ND1 B:HIS624 2.1 5.6 0.5
O B:HOH1629 2.1 18.7 0.5
NE2 B:HIS458 2.1 8.4 1.0
OH B:TYR405 2.2 7.4 1.0
CD2 B:HIS456 2.9 9.2 1.0
CE1 B:HIS624 2.9 6.3 0.5
CZ B:TYR405 3.0 6.8 1.0
CE1 B:HIS456 3.0 7.6 1.0
CE1 B:HIS458 3.1 7.9 1.0
CG B:HIS624 3.1 4.0 0.5
CD2 B:HIS458 3.2 7.6 1.0
CB B:HIS624 3.6 7.5 0.5
CE1 B:TYR405 3.7 7.3 1.0
CD2 B:LEU425 3.7 13.8 0.5
CE2 B:TYR405 3.7 9.7 1.0
CB B:HIS624 3.8 9.1 0.5
CG B:HIS624 3.9 9.9 0.5
CG B:HIS456 4.1 6.5 1.0
ND1 B:HIS456 4.1 6.0 1.0
NE2 B:HIS624 4.1 8.7 0.5
ND1 B:HIS624 4.1 17.1 0.5
O B:HOH979 4.2 6.2 1.0
CD2 B:HIS624 4.2 4.7 0.5
O B:HOH1919 4.2 34.8 1.0
ND1 B:HIS458 4.2 6.5 1.0
CG B:HIS458 4.3 5.4 1.0
CD2 B:HIS624 4.6 15.8 0.5
CE1 B:HIS624 4.8 7.9 0.5
CD1 B:TYR405 4.8 6.4 1.0
CD2 B:LEU429 4.9 7.3 1.0
CD2 B:TYR405 4.9 9.5 1.0
CG B:LEU425 4.9 9.1 0.5
SD B:MET634 5.0 10.0 0.7

Cobalt binding site 3 out of 6 in 3sxx

Go back to Cobalt Binding Sites List in 3sxx
Cobalt binding site 3 out of 6 in the Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co801

b:6.6
occ:0.50
 O C:HOH1731 1.2 21.4 0.5
NE2 C:HIS456 2.0 8.7 1.0
ND1 C:HIS624 2.1 6.3 0.6
O C:HOH1633 2.1 15.4 0.5
OH C:TYR405 2.1 7.6 1.0
NE2 C:HIS458 2.2 7.3 1.0
CE1 C:HIS624 2.9 6.9 0.6
CD2 C:HIS456 2.9 9.6 1.0
CE1 C:HIS456 3.0 7.3 1.0
CZ C:TYR405 3.0 6.4 1.0
CE1 C:HIS458 3.1 6.9 1.0
CG C:HIS624 3.2 5.7 0.6
CD2 C:HIS458 3.2 7.2 1.0
CB C:HIS624 3.6 7.6 0.6
CE1 C:TYR405 3.7 7.0 1.0
CD2 C:LEU425 3.7 17.7 0.5
CE2 C:TYR405 3.8 11.2 1.0
CB C:HIS624 3.8 7.9 0.4
CG C:HIS624 3.9 9.3 0.4
ND1 C:HIS456 4.1 5.6 1.0
CG C:HIS456 4.1 6.4 1.0
NE2 C:HIS624 4.1 6.7 0.6
O C:HOH952 4.1 5.9 1.0
ND1 C:HIS624 4.2 14.3 0.4
OE1 C:GLU637 4.2 18.1 0.4
CD2 C:HIS624 4.2 6.6 0.6
ND1 C:HIS458 4.3 6.2 1.0
CG C:HIS458 4.3 5.5 1.0
CD2 C:HIS624 4.5 14.3 0.4
OE2 C:GLU637 4.8 18.7 0.4
CD2 C:LEU429 4.8 8.0 1.0
CE1 C:HIS624 4.9 8.7 0.4
CE C:MET634 4.9 17.2 0.5
CD1 C:TYR405 4.9 6.7 1.0
CG C:LEU425 4.9 12.6 0.5
CD2 C:TYR405 4.9 11.4 1.0
SD C:MET634 4.9 7.2 0.5
CD C:GLU637 5.0 16.6 0.4
SD C:MET634 5.0 16.4 0.5

Cobalt binding site 4 out of 6 in 3sxx

Go back to Cobalt Binding Sites List in 3sxx
Cobalt binding site 4 out of 6 in the Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co801

b:7.5
occ:0.50
 O D:HOH1745 1.3 13.9 0.5
NE2 D:HIS456 2.0 9.5 1.0
O D:HOH1642 2.1 15.3 0.5
ND1 D:HIS624 2.1 9.0 0.7
OH D:TYR405 2.1 7.3 1.0
NE2 D:HIS458 2.2 8.0 1.0
CD2 D:HIS456 2.9 8.9 1.0
CZ D:TYR405 3.0 6.0 1.0
CE1 D:HIS456 3.0 7.8 1.0
CE1 D:HIS624 3.0 10.0 0.7
CE1 D:HIS458 3.1 6.5 1.0
CD2 D:HIS458 3.2 6.7 1.0
CG D:HIS624 3.2 7.6 0.7
CB D:HIS624 3.6 7.4 0.7
CE1 D:TYR405 3.7 6.5 1.0
CE2 D:TYR405 3.7 11.9 1.0
CD2 D:LEU425 3.7 5.6 0.2
CB D:HIS624 3.9 6.5 0.3
CG D:HIS624 4.1 7.3 0.3
CG D:HIS456 4.1 6.5 1.0
ND1 D:HIS456 4.1 5.6 1.0
ND1 D:HIS624 4.1 8.0 0.3
O D:HOH927 4.2 5.9 1.0
NE2 D:HIS624 4.2 8.7 0.7
OE2 D:GLU637 4.2 18.6 0.5
ND1 D:HIS458 4.3 6.1 1.0
CD2 D:HIS624 4.3 10.2 0.7
CG D:HIS458 4.3 5.3 1.0
OE1 D:GLU637 4.6 19.4 0.5
CD2 D:LEU429 4.8 7.0 1.0
CD2 D:HIS624 4.8 9.8 0.3
CD2 D:TYR405 4.8 10.8 1.0
CD1 D:TYR405 4.8 6.6 1.0
CD D:GLU637 4.9 16.4 0.5
CE1 D:HIS624 4.9 5.4 0.3
CG D:LEU425 4.9 3.5 0.2
SD D:MET634 5.0 6.9 0.5
SD D:MET634 5.0 15.7 0.5

Cobalt binding site 5 out of 6 in 3sxx

Go back to Cobalt Binding Sites List in 3sxx
Cobalt binding site 5 out of 6 in the Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co801

b:7.5
occ:0.50
 O E:HOH1731 1.3 19.5 0.5
NE2 E:HIS456 2.0 9.3 1.0
OH E:TYR405 2.1 7.0 1.0
ND1 E:HIS624 2.2 6.8 0.6
O E:HOH1637 2.2 18.5 0.5
NE2 E:HIS458 2.2 7.7 1.0
CD2 E:HIS456 2.9 9.2 1.0
CZ E:TYR405 3.0 6.5 1.0
CE1 E:HIS456 3.0 8.1 1.0
CE1 E:HIS624 3.0 7.7 0.6
CE1 E:HIS458 3.1 6.7 1.0
CD2 E:HIS458 3.2 6.9 1.0
CG E:HIS624 3.2 6.7 0.6
CB E:HIS624 3.6 7.4 0.6
CE1 E:TYR405 3.7 7.0 1.0
CD2 E:LEU425 3.7 14.1 0.5
CE2 E:TYR405 3.8 10.7 1.0
CB E:HIS624 3.9 8.8 0.4
CG E:HIS624 4.0 10.3 0.4
ND1 E:HIS456 4.1 5.8 1.0
CG E:HIS456 4.1 6.6 1.0
ND1 E:HIS624 4.1 11.4 0.4
O E:HOH982 4.2 5.6 1.0
NE2 E:HIS624 4.2 7.2 0.6
OE1 E:GLU637 4.2 15.3 0.4
ND1 E:HIS458 4.3 6.8 1.0
CD2 E:HIS624 4.3 7.8 0.6
CG E:HIS458 4.4 5.4 1.0
OE2 E:GLU637 4.7 19.5 0.4
CD2 E:HIS624 4.7 14.0 0.4
CD2 E:LEU429 4.8 7.3 1.0
CE1 E:HIS624 4.8 8.0 0.4
CD1 E:TYR405 4.8 7.3 1.0
CD2 E:TYR405 4.9 11.1 1.0
CD E:GLU637 4.9 16.3 0.4
SD E:MET634 4.9 9.5 0.7
CG E:LEU425 5.0 10.5 0.5

Cobalt binding site 6 out of 6 in 3sxx

Go back to Cobalt Binding Sites List in 3sxx
Cobalt binding site 6 out of 6 in the Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Hansenula Polymorpha Copper Amine Oxidase-1 in Complex with Co(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co801

b:6.6
occ:0.50
 O F:HOH1705 1.2 19.4 0.5
NE2 F:HIS456 2.0 9.7 1.0
ND1 F:HIS624 2.1 7.1 0.6
O F:HOH1599 2.2 12.9 0.5
OH F:TYR405 2.2 7.1 1.0
NE2 F:HIS458 2.2 6.9 1.0
CD2 F:HIS456 2.9 9.6 1.0
CE1 F:HIS624 3.0 8.1 0.6
CZ F:TYR405 3.0 5.9 1.0
CE1 F:HIS456 3.0 7.8 1.0
CE1 F:HIS458 3.1 6.7 1.0
CG F:HIS624 3.1 6.7 0.6
CD2 F:HIS458 3.2 6.7 1.0
CB F:HIS624 3.6 6.6 0.6
CD2 F:LEU425 3.6 17.7 0.5
CE1 F:TYR405 3.7 6.7 1.0
CE2 F:TYR405 3.8 9.6 1.0
CB F:HIS624 3.8 9.7 0.4
CG F:HIS624 3.9 8.9 0.4
CE F:MET634 4.0 24.5 0.3
CG F:HIS456 4.1 6.7 1.0
ND1 F:HIS456 4.1 5.6 1.0
NE2 F:HIS624 4.1 6.6 0.6
O F:HOH1010 4.2 5.8 1.0
OE2 F:GLU637 4.2 20.5 0.5
CD2 F:HIS624 4.2 7.8 0.6
ND1 F:HIS624 4.2 10.9 0.4
ND1 F:HIS458 4.3 6.1 1.0
CG F:HIS458 4.3 5.7 1.0
CD2 F:HIS624 4.6 14.3 0.4
CD2 F:LEU429 4.8 8.0 1.0
OE1 F:GLU637 4.8 20.7 0.5
CD2 F:TYR405 4.9 10.4 1.0
CD1 F:TYR405 4.9 7.3 1.0
CG F:LEU425 4.9 11.8 0.5
CE1 F:HIS624 4.9 6.4 0.4
SD F:MET634 5.0 10.4 0.7
CD F:GLU637 5.0 18.5 0.5

Reference:

V.J.Klema, B.J.Johnson, J.P.Klinman, C.M.Wilmot. The Precursor Form of Hansenula Polymorpha Copper Amine Oxidase 1 in Complex with Cui and Coii. Acta Crystallogr.,Sect.F V. 68 501 2012.
ISSN: ESSN 1744-3091
PubMed: 22691777
DOI: 10.1107/S1744309112012857
Page generated: Tue Jul 30 16:35:11 2024

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