Atomistry » Cobalt » PDB 3r86-3ura » 3sxx
Atomistry »
  Cobalt »
    PDB 3r86-3ura »
      3sxx »

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: Sun Jul 13 19:22:04 2025

Last articles

Mg in 9F28
Mg in 9F2R
Mg in 9F12
Mg in 9F11
Mg in 9F10
Mg in 9F0Z
Mg in 9F0Y
Mg in 9F07
Mg in 9F0H
Mg in 9EZY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy