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Calcium in PDB 3hig: Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil

Enzymatic activity of Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil

All present enzymatic activity of Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil:
1.4.3.22;

Protein crystallography data

The structure of Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil, PDB code: 3hig 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) 47.46 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.662, 94.884, 196.411, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21

Other elements in 3hig:

The structure of Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil (pdb code 3hig). 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 in Complex with the Inhibitor Berenil, PDB code: 3hig:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3hig

Go back to Calcium Binding Sites List in 3hig
Calcium binding site 1 out of 4 in the Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil


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 in Complex with the Inhibitor Berenil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:14.4
occ:1.00
 OD1 A:ASP664 2.3 11.4 1.0
O A:LEU665 2.3 12.5 1.0
OD1 A:ASP519 2.3 10.4 1.0
O A:LEU520 2.3 13.8 1.0
OD1 A:ASP521 2.3 16.9 1.0
O A:HOH20 2.5 7.8 1.0
C A:LEU520 3.3 14.3 1.0
C A:LEU665 3.4 12.1 1.0
N A:LEU665 3.4 11.7 1.0
CG A:ASP664 3.5 13.4 1.0
CG A:ASP519 3.6 11.3 1.0
CG A:ASP521 3.6 17.4 1.0
NZ A:LYS79 3.7 10.9 1.0
C A:ASP664 4.0 12.3 1.0
CA A:LEU665 4.0 12.1 1.0
N A:ASP521 4.0 14.9 1.0
N A:LEU520 4.1 12.8 1.0
C A:ASP519 4.1 11.8 1.0
CA A:ASP521 4.2 15.3 1.0
CA A:ASP664 4.2 13.1 1.0
OD2 A:ASP664 4.2 13.8 1.0
OD2 A:ASP519 4.3 13.1 1.0
CA A:LEU520 4.3 14.3 1.0
O A:THR525 4.3 22.2 1.0
O A:ASP519 4.4 12.4 1.0
OD2 A:ASP521 4.4 22.3 1.0
CA A:ASP519 4.4 11.3 1.0
CB A:ASP521 4.5 15.8 1.0
CB A:ASP664 4.5 12.6 1.0
N A:VAL666 4.5 11.3 1.0
CB A:ASP519 4.6 11.2 1.0
OD1 A:ASN527 4.7 13.0 1.0
O A:ASP664 4.8 11.8 1.0
CB A:LEU665 4.8 12.1 1.0
CG2 A:VAL666 4.8 11.1 1.0
CA A:VAL666 4.9 11.2 1.0

Calcium binding site 2 out of 4 in 3hig

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Calcium binding site 2 out of 4 in the Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil


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 in Complex with the Inhibitor Berenil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:12.4
occ:1.00
 OE1 A:GLU658 2.3 12.8 1.0
O A:PHE653 2.3 12.7 1.0
O A:HOH754 2.4 11.3 1.0
O A:HOH819 2.4 6.3 1.0
OD1 A:ASN656 2.5 13.4 1.0
OE1 A:GLU562 2.6 11.1 1.0
OE2 A:GLU562 2.6 12.7 1.0
CD A:GLU562 2.9 13.7 1.0
CD A:GLU658 3.4 13.5 1.0
CG A:ASN656 3.5 12.3 1.0
C A:PHE653 3.6 11.7 1.0
ND2 A:ASN656 3.8 13.1 1.0
CG A:GLU658 3.8 12.8 1.0
NH1 A:ARG628 3.9 14.6 1.0
O A:HOH822 4.2 16.0 1.0
CB A:GLU658 4.3 12.0 1.0
CA A:PHE653 4.4 12.1 1.0
CG A:GLU562 4.4 12.8 1.0
OE2 A:GLU631 4.4 18.1 1.0
OE2 A:GLU658 4.5 14.8 1.0
OE1 A:GLU631 4.5 17.5 1.0
N A:LEU654 4.5 12.2 1.0
N A:GLU658 4.7 11.9 1.0
CA A:LEU654 4.7 12.5 1.0
N A:LYS626 4.8 12.7 1.0
CB A:PHE653 4.8 11.7 1.0
CB A:ASN656 4.8 12.8 1.0
N A:ASN657 4.9 12.7 1.0
N A:ASN656 4.9 13.3 1.0
CD A:GLU631 4.9 17.5 1.0
CB A:THR625 5.0 12.2 1.0

Calcium binding site 3 out of 4 in 3hig

Go back to Calcium Binding Sites List in 3hig
Calcium binding site 3 out of 4 in the Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil


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 in Complex with the Inhibitor Berenil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:19.4
occ:1.00
 OD1 B:ASP521 2.2 21.6 1.0
OD1 B:ASP664 2.3 19.9 1.0
OD1 B:ASP519 2.3 18.1 1.0
O B:LEU665 2.4 17.3 1.0
O B:LEU520 2.4 16.9 1.0
O B:HOH903 2.5 17.6 1.0
C B:LEU520 3.4 17.7 1.0
C B:LEU665 3.5 16.6 1.0
CG B:ASP521 3.5 20.0 1.0
CG B:ASP664 3.5 20.9 1.0
CG B:ASP519 3.5 17.8 1.0
N B:LEU665 3.5 17.7 1.0
NZ B:LYS79 3.9 17.8 1.0
C B:ASP519 4.0 15.9 1.0
C B:ASP664 4.1 19.4 1.0
N B:LEU520 4.1 16.9 1.0
CA B:LEU665 4.1 17.5 1.0
N B:ASP521 4.1 18.0 1.0
CA B:ASP521 4.2 18.6 1.0
CA B:ASP664 4.2 20.2 1.0
OD2 B:ASP519 4.2 18.3 1.0
OD2 B:ASP664 4.3 19.8 1.0
O B:THR525 4.3 30.1 1.0
OD2 B:ASP521 4.4 18.2 1.0
O B:ASP519 4.4 16.6 1.0
CA B:ASP519 4.4 15.7 1.0
CA B:LEU520 4.4 17.7 1.0
CB B:ASP521 4.5 19.1 1.0
CB B:ASP664 4.5 20.6 1.0
CB B:ASP519 4.6 15.2 1.0
N B:VAL666 4.6 16.4 1.0
CG2 B:VAL666 4.8 14.3 1.0
OD1 B:ASN527 4.8 23.8 1.0
CA B:VAL666 4.9 15.4 1.0
CB B:LEU665 4.9 17.4 1.0
O B:ASP664 4.9 19.4 1.0

Calcium binding site 4 out of 4 in 3hig

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Calcium binding site 4 out of 4 in the Crystal Structure of Human Diamine Oxidase in Complex with the Inhibitor Berenil


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 in Complex with the Inhibitor Berenil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:29.5
occ:1.00
 O B:HOH888 2.3 23.0 1.0
OE1 B:GLU658 2.4 28.3 1.0
O B:PHE653 2.4 22.2 1.0
OE1 B:GLU562 2.4 21.1 1.0
OD1 B:ASN656 2.5 28.2 1.0
O B:HOH5 2.6 20.0 1.0
OE2 B:GLU562 2.6 19.7 1.0
CD B:GLU562 2.9 21.2 1.0
CG B:ASN656 3.4 25.1 1.0
CD B:GLU658 3.4 29.4 1.0
C B:PHE653 3.6 21.1 1.0
ND2 B:ASN656 3.6 24.9 1.0
CG B:GLU658 3.8 26.3 1.0
O B:HOH1053 4.1 18.5 1.0
OE2 B:GLU631 4.2 29.1 1.0
CG B:GLU562 4.4 21.3 1.0
NE B:ARG628 4.4 37.4 1.0
OE1 B:GLU631 4.4 29.4 1.0
N B:LEU654 4.5 20.6 1.0
CA B:PHE653 4.5 21.1 1.0
CB B:GLU658 4.5 23.6 1.0
CA B:LEU654 4.5 20.6 1.0
OE2 B:GLU658 4.6 32.4 1.0
N B:GLU658 4.7 22.9 1.0
N B:ASN657 4.8 22.4 1.0
CD B:ARG628 4.8 32.1 1.0
CD B:GLU631 4.8 27.9 1.0
CB B:ASN656 4.8 22.4 1.0
C B:LEU654 4.9 21.3 1.0
N B:ASN656 4.9 21.8 1.0
CB B:THR625 5.0 17.0 1.0

Reference:

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
Page generated: Sat Jul 13 11:00:11 2024

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