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Calcium in PDB 3mph: The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine

Enzymatic activity of The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine

All present enzymatic activity of The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine:
1.4.3.22;

Protein crystallography data

The structure of The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine, PDB code: 3mph was solved by A.P.Mcgrath, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.13 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.685, 94.604, 196.051, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.5

Other elements in 3mph:

The structure of The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine (pdb code 3mph). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine, PDB code: 3mph:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3mph

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Calcium binding site 1 out of 4 in the The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:9.4
occ:1.00
 OD1 A:ASP664 2.3 11.9 1.0
OD1 A:ASP519 2.3 4.3 1.0
O A:LEU520 2.3 6.3 1.0
O A:LEU665 2.3 8.0 1.0
OD1 A:ASP521 2.3 8.2 1.0
O A:HOH20 2.4 3.7 1.0
C A:LEU520 3.3 7.7 1.0
C A:LEU665 3.4 8.0 1.0
N A:LEU665 3.5 8.5 1.0
CG A:ASP664 3.5 11.5 1.0
CG A:ASP519 3.5 5.8 1.0
CG A:ASP521 3.6 9.2 1.0
NZ A:LYS79 3.7 11.6 1.0
N A:ASP521 4.0 8.2 1.0
CA A:LEU665 4.0 7.9 1.0
C A:ASP664 4.1 9.4 1.0
CA A:ASP521 4.1 8.7 1.0
N A:LEU520 4.1 6.9 1.0
C A:ASP519 4.1 6.2 1.0
OD2 A:ASP664 4.2 13.2 1.0
OD2 A:ASP519 4.2 6.3 1.0
O A:THR525 4.3 16.6 1.0
CA A:ASP664 4.3 10.4 1.0
CA A:LEU520 4.4 7.4 1.0
CB A:ASP521 4.4 9.1 1.0
O A:ASP519 4.4 6.2 1.0
CA A:ASP519 4.5 5.9 1.0
OD2 A:ASP521 4.5 10.4 1.0
CB A:ASP664 4.5 10.7 1.0
N A:VAL666 4.5 7.4 1.0
CB A:ASP519 4.6 5.8 1.0
OD1 A:ASN527 4.6 10.1 1.0
CB A:LEU665 4.8 7.6 1.0
CG2 A:VAL666 4.8 6.1 1.0
O A:ASP664 4.9 9.5 1.0
CA A:VAL666 4.9 6.9 1.0

Calcium binding site 2 out of 4 in 3mph

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Calcium binding site 2 out of 4 in the The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:10.2
occ:1.00
 OE1 A:GLU658 2.3 11.3 1.0
O A:PHE653 2.3 10.7 1.0
O A:HOH758 2.3 7.1 1.0
O A:HOH814 2.4 3.1 1.0
OE2 A:GLU562 2.4 13.4 1.0
OE1 A:GLU562 2.5 14.3 1.0
OD1 A:ASN656 2.5 10.2 1.0
CD A:GLU562 2.8 12.6 1.0
CD A:GLU658 3.3 12.0 1.0
CG A:ASN656 3.5 10.2 1.0
C A:PHE653 3.5 10.6 1.0
CG A:GLU658 3.7 12.4 1.0
ND2 A:ASN656 3.8 8.7 1.0
NH1 A:ARG628 4.0 14.8 1.0
O A:HOH825 4.2 9.9 1.0
CB A:GLU658 4.3 11.2 1.0
CG A:GLU562 4.3 11.5 1.0
CA A:PHE653 4.4 10.9 1.0
OE2 A:GLU631 4.4 12.8 1.0
OE2 A:GLU658 4.5 11.0 1.0
OE1 A:GLU631 4.5 13.0 1.0
N A:LEU654 4.5 10.3 1.0
CA A:LEU654 4.6 10.5 1.0
N A:GLU658 4.7 11.0 1.0
N A:LYS626 4.8 9.2 1.0
CB A:PHE653 4.9 10.6 1.0
CB A:ASN656 4.9 9.8 1.0
CB A:THR625 4.9 8.8 1.0
N A:ASN657 4.9 10.0 1.0
CD A:GLU631 4.9 12.8 1.0
C A:LEU654 5.0 10.1 1.0

Calcium binding site 3 out of 4 in 3mph

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Calcium binding site 3 out of 4 in the The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:13.7
occ:1.00
 OD1 B:ASP521 2.1 15.3 1.0
OD1 B:ASP664 2.2 18.5 1.0
OD1 B:ASP519 2.3 12.5 1.0
O B:LEU665 2.3 12.1 1.0
O B:LEU520 2.4 11.2 1.0
O B:HOH893 2.4 11.6 1.0
C B:LEU520 3.4 11.7 1.0
CG B:ASP521 3.4 13.6 1.0
C B:LEU665 3.4 13.1 1.0
CG B:ASP664 3.5 17.4 1.0
N B:LEU665 3.5 15.2 1.0
CG B:ASP519 3.5 12.2 1.0
NZ B:LYS79 3.8 17.3 1.0
CA B:LEU665 4.0 14.0 1.0
N B:ASP521 4.0 12.7 1.0
C B:ASP664 4.1 16.6 1.0
C B:ASP519 4.1 11.0 1.0
N B:LEU520 4.1 11.4 1.0
CA B:ASP521 4.1 13.6 1.0
O B:THR525 4.2 21.6 1.0
OD2 B:ASP664 4.2 18.4 1.0
OD2 B:ASP519 4.2 12.5 1.0
OD2 B:ASP521 4.2 15.3 1.0
CA B:ASP664 4.3 17.3 1.0
CB B:ASP521 4.4 14.1 1.0
O B:ASP519 4.4 10.8 1.0
CA B:LEU520 4.4 11.5 1.0
CA B:ASP519 4.5 11.0 1.0
CB B:ASP664 4.5 17.3 1.0
N B:VAL666 4.5 12.5 1.0
CB B:ASP519 4.6 11.1 1.0
OD1 B:ASN527 4.7 15.2 1.0
CG2 B:VAL666 4.8 11.2 1.0
CB B:LEU665 4.8 14.0 1.0
CA B:VAL666 4.9 12.3 1.0
O B:ASP664 4.9 16.9 1.0

Calcium binding site 4 out of 4 in 3mph

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Calcium binding site 4 out of 4 in the The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of Human Diamine Oxidase Complexed with An Inhibitor Aminoguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:18.6
occ:1.00
 O B:HOH1022 2.3 16.4 1.0
OE1 B:GLU658 2.3 20.6 1.0
OE1 B:GLU562 2.3 16.2 1.0
O B:PHE653 2.4 17.5 1.0
OD1 B:ASN656 2.4 20.9 1.0
O B:HOH5 2.5 14.7 1.0
OE2 B:GLU562 2.6 17.6 1.0
CD B:GLU562 2.8 16.0 1.0
CD B:GLU658 3.3 20.6 1.0
CG B:ASN656 3.4 18.0 1.0
C B:PHE653 3.6 17.6 1.0
ND2 B:ASN656 3.6 17.2 1.0
CG B:GLU658 3.7 19.3 1.0
O B:HOH1071 4.1 14.5 1.0
CG B:GLU562 4.3 16.3 1.0
NE B:ARG628 4.4 27.3 1.0
OE2 B:GLU631 4.4 18.8 1.0
CB B:GLU658 4.4 18.2 1.0
CA B:PHE653 4.4 18.2 1.0
OE2 B:GLU658 4.5 23.3 1.0
OE1 B:GLU631 4.5 18.3 1.0
N B:LEU654 4.5 17.4 1.0
CA B:LEU654 4.6 17.0 1.0
N B:GLU658 4.7 17.4 1.0
CB B:ASN656 4.8 17.6 1.0
CD B:ARG628 4.8 23.2 1.0
N B:ASN657 4.9 17.0 1.0
CD B:GLU631 4.9 18.3 1.0
N B:LYS626 4.9 16.0 1.0
CB B:PHE653 4.9 17.9 1.0
C B:LEU654 5.0 17.2 1.0

Reference:

A.P.Mcgrath, T.Caradoc-Davies, C.A.Collyer, J.M.Guss. Correlation of Active Site Metal Content in Human Diamine Oxidase with Trihydroxyphenylalanine Quinone Cofactor Biogenesis Biochemistry V. 49 8316 2010.
ISSN: ISSN 0006-2960
PubMed: 20722416
DOI: 10.1021/BI1010915
Page generated: Tue Jul 8 14:39:25 2025

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