Calcium in PDB 3hi7: Crystal Structure of Human Diamine Oxidase

All present enzymatic activity of Crystal Structure of Human Diamine Oxidase:
1.4.3.22;

The structure of Crystal Structure of Human Diamine Oxidase, PDB code: 3hi7 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)	46.57 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.506, 94.784, 196.525, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.9

The structure of Crystal Structure of Human Diamine Oxidase also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human Diamine Oxidase (pdb code 3hi7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Diamine Oxidase, PDB code: 3hi7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Diamine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Diamine Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:8.9 occ:1.00 OD1 A:ASP519 2.3 8.0 1.0 O A:LEU520 2.3 8.8 1.0 OD1 A:ASP521 2.3 12.3 1.0 O A:LEU665 2.3 7.5 1.0 OD1 A:ASP664 2.3 7.5 1.0 O A:HOH20 2.5 8.2 1.0 C A:LEU520 3.3 9.3 1.0 C A:LEU665 3.4 8.3 1.0 N A:LEU665 3.5 8.4 1.0 CG A:ASP519 3.5 8.1 1.0 CG A:ASP521 3.5 9.7 1.0 CG A:ASP664 3.6 10.6 1.0 NZ A:LYS79 3.7 9.9 1.0 C A:ASP664 4.0 9.1 1.0 N A:ASP521 4.0 8.2 1.0 CA A:LEU665 4.1 8.3 1.0 C A:ASP519 4.1 8.2 1.0 CA A:ASP521 4.1 8.5 1.0 N A:LEU520 4.1 8.7 1.0 OD2 A:ASP519 4.2 10.6 1.0 CA A:ASP664 4.3 9.8 1.0 OD2 A:ASP664 4.3 9.5 1.0 O A:ASP519 4.3 8.2 1.0 CA A:LEU520 4.4 8.9 1.0 OD2 A:ASP521 4.4 11.7 1.0 CB A:ASP521 4.4 9.0 1.0 CA A:ASP519 4.4 7.7 1.0 O A:THR525 4.4 18.3 1.0 CB A:ASP664 4.5 10.0 1.0 N A:VAL666 4.5 8.2 1.0 CB A:ASP519 4.6 7.7 1.0 OD1 A:ASN527 4.7 9.7 1.0 O A:ASP664 4.8 9.4 1.0 CB A:LEU665 4.9 8.2 1.0 CG2 A:VAL666 4.9 7.9 1.0 CA A:VAL666 4.9 7.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Diamine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Diamine Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:8.8 occ:1.00 O A:PHE653 2.3 8.5 1.0 OE1 A:GLU658 2.4 8.6 1.0 O A:HOH759 2.4 8.1 1.0 O A:HOH827 2.4 9.5 1.0 OD1 A:ASN656 2.4 9.4 1.0 OE2 A:GLU562 2.5 7.8 1.0 OE1 A:GLU562 2.5 9.9 1.0 CD A:GLU562 2.9 10.2 1.0 CG A:ASN656 3.4 10.2 1.0 CD A:GLU658 3.5 8.4 1.0 C A:PHE653 3.5 8.7 1.0 ND2 A:ASN656 3.8 10.8 1.0 CG A:GLU658 3.9 9.9 1.0 NH1 A:ARG628 4.0 10.6 1.0 O A:HOH835 4.2 12.0 1.0 CB A:GLU658 4.3 8.6 1.0 CA A:PHE653 4.4 8.5 1.0 CG A:GLU562 4.4 8.4 1.0 OE1 A:GLU631 4.5 10.4 1.0 N A:LEU654 4.5 9.3 1.0 OE2 A:GLU631 4.5 11.9 1.0 OE2 A:GLU658 4.6 9.7 1.0 CA A:LEU654 4.7 9.7 1.0 N A:GLU658 4.7 9.4 1.0 N A:LYS626 4.8 9.3 1.0 CB A:ASN656 4.8 10.2 1.0 CB A:PHE653 4.8 9.1 1.0 N A:ASN657 4.9 10.1 1.0 CB A:THR625 4.9 8.9 1.0 N A:ASN656 5.0 11.2 1.0 CD A:GLU631 5.0 13.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Diamine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Diamine Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:14.4 occ:1.00 OD1 B:ASP521 2.2 14.8 1.0 OD1 B:ASP519 2.3 13.8 1.0 OD1 B:ASP664 2.3 14.0 1.0 O B:LEU520 2.3 13.0 1.0 O B:LEU665 2.4 13.4 1.0 O B:HOH907 2.5 13.8 1.0 C B:LEU520 3.3 14.0 1.0 C B:LEU665 3.4 13.1 1.0 CG B:ASP521 3.5 13.7 1.0 N B:LEU665 3.5 15.1 1.0 CG B:ASP519 3.5 13.0 1.0 CG B:ASP664 3.5 17.0 1.0 NZ B:LYS79 3.9 15.1 1.0 CA B:LEU665 4.0 13.9 1.0 N B:ASP521 4.0 13.8 1.0 C B:ASP519 4.1 11.8 1.0 C B:ASP664 4.1 16.0 1.0 CA B:ASP521 4.1 14.4 1.0 N B:LEU520 4.1 13.3 1.0 OD2 B:ASP519 4.2 15.0 1.0 OD2 B:ASP664 4.3 14.2 1.0 CA B:ASP664 4.3 16.6 1.0 OD2 B:ASP521 4.3 15.1 1.0 O B:THR525 4.3 24.2 1.0 O B:ASP519 4.4 12.6 1.0 CB B:ASP521 4.4 14.2 1.0 CA B:LEU520 4.4 13.3 1.0 CA B:ASP519 4.4 11.5 1.0 CB B:ASP664 4.5 16.6 1.0 N B:VAL666 4.5 13.2 1.0 CB B:ASP519 4.6 11.3 1.0 OD1 B:ASN527 4.7 18.0 1.0 CG2 B:VAL666 4.8 12.9 1.0 CB B:LEU665 4.8 14.3 1.0 CA B:VAL666 4.9 13.3 1.0 O B:ASP664 4.9 16.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Diamine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Diamine Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:19.4 occ:1.00 OE1 B:GLU658 2.3 21.9 1.0 O B:HOH1048 2.3 18.3 1.0 O B:PHE653 2.3 15.7 1.0 O B:HOH5 2.4 17.4 1.0 OD1 B:ASN656 2.5 19.4 1.0 OE1 B:GLU562 2.5 18.6 1.0 OE2 B:GLU562 2.5 15.8 1.0 CD B:GLU562 2.9 15.7 1.0 CD B:GLU658 3.4 24.2 1.0 CG B:ASN656 3.4 20.5 1.0 C B:PHE653 3.6 15.7 1.0 ND2 B:ASN656 3.7 21.0 1.0 CG B:GLU658 3.8 21.7 1.0 O B:HOH1167 4.2 17.9 1.0 OE2 B:GLU631 4.4 20.3 1.0 CG B:GLU562 4.4 16.5 1.0 OE1 B:GLU631 4.4 18.0 1.0 CB B:GLU658 4.4 19.2 1.0 NE B:ARG628 4.5 31.1 1.0 N B:LEU654 4.5 15.3 1.0 OE2 B:GLU658 4.5 25.4 1.0 CA B:PHE653 4.5 15.6 1.0 CA B:LEU654 4.6 16.2 1.0 N B:GLU658 4.8 18.3 1.0 CD B:ARG628 4.8 26.9 1.0 CD B:GLU631 4.8 18.8 1.0 CB B:ASN656 4.8 18.6 1.0 N B:LYS626 4.9 15.4 1.0 N B:ASN657 4.9 18.1 1.0 CB B:PHE653 4.9 16.2 1.0 CB B:THR625 5.0 13.8 1.0 C B:LEU654 5.0 17.6 1.0 O B:LYS626 5.0 15.7 1.0

A.P.Mcgrath, K.M.Hilmer, C.A.Collyer, E.M.Shepard, B.O.Elmore, D.E.Brown, D.M.Dooley, J.M.Guss. Structure and Inhibition of Human Diamine Oxidase Biochemistry V. 48 9810 2009.
ISSN: ISSN 0006-2960
PubMed: 19764817
DOI: 10.1021/BI9014192