Calcium in PDB 3amz: Bovine Xanthine Oxidoreductase Urate Bound Form

All present enzymatic activity of Bovine Xanthine Oxidoreductase Urate Bound Form:
1.17.1.4; 1.17.3.2;

The structure of Bovine Xanthine Oxidoreductase Urate Bound Form, PDB code: 3amz was solved by K.Okamoto, B.T.Eger, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.83 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.211, 124.530, 148.025, 90.00, 91.07, 90.00
R / Rfree (%)	15.1 / 20.2

The structure of Bovine Xanthine Oxidoreductase Urate Bound Form also contains other interesting chemical elements:

Molybdenum	(Mo)	2 atoms
Iron	(Fe)	8 atoms

The binding sites of Calcium atom in the Bovine Xanthine Oxidoreductase Urate Bound Form (pdb code 3amz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Bovine Xanthine Oxidoreductase Urate Bound Form, PDB code: 3amz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3008 b:20.8 occ:1.00 OG A:SER907 2.6 17.4 1.0 O A:ALA867 2.7 19.1 1.0 OG A:SER874 2.7 17.8 1.0 O A:SER870 2.7 17.9 1.0 O A:ASN908 2.8 17.4 1.0 O A:ARG871 3.0 18.0 1.0 N A:ASN908 3.4 18.4 1.0 C A:ARG871 3.5 17.1 1.0 CB A:ASP872 3.7 16.7 1.0 C A:ALA867 3.7 19.6 1.0 C A:SER870 3.8 19.5 1.0 C A:ASN908 3.8 19.4 1.0 CB A:SER907 3.8 14.7 1.0 CB A:SER874 4.0 17.0 1.0 C A:SER907 4.0 18.5 1.0 CA A:SER907 4.0 16.9 1.0 NE2 A:HIS840 4.1 15.7 1.0 CB A:ALA867 4.1 19.4 1.0 CA A:ALA867 4.1 19.0 1.0 N A:ASP872 4.2 16.6 1.0 CA A:ASN908 4.2 19.3 1.0 CA A:ARG871 4.2 18.1 1.0 CA A:ASP872 4.4 18.9 1.0 N A:ARG871 4.5 18.6 1.0 CE1 A:HIS840 4.5 15.3 1.0 N A:SER874 4.6 17.9 1.0 OG A:SER870 4.6 21.2 1.0 N A:SER870 4.7 19.1 1.0 N A:LEU873 4.8 17.7 1.0 CA A:SER874 4.8 18.3 1.0 CB A:ASN908 4.8 19.7 1.0 CA A:SER870 4.9 19.2 1.0 C A:ASP872 4.9 17.9 1.0 CG A:ASP872 4.9 22.3 1.0 N A:GLY868 4.9 17.6 1.0 O A:SER907 4.9 18.0 1.0 OD1 A:ASP872 5.0 17.9 1.0

Calcium binding site 2 out of 2 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4008 b:19.4 occ:1.00 OG B:SER874 2.6 20.2 1.0 O B:ALA867 2.7 18.9 1.0 O B:SER870 2.7 17.3 1.0 OG B:SER907 2.8 16.1 1.0 O B:ASN908 2.8 14.4 1.0 O B:ARG871 2.9 19.0 1.0 N B:ASN908 3.4 14.6 1.0 C B:ARG871 3.5 16.5 1.0 C B:ALA867 3.7 18.0 1.0 C B:SER870 3.7 17.5 1.0 CB B:ASP872 3.8 16.9 1.0 C B:ASN908 3.8 15.6 1.0 CB B:SER874 3.9 17.6 1.0 CB B:ALA867 3.9 16.4 1.0 CB B:SER907 4.0 16.8 1.0 C B:SER907 4.0 16.9 1.0 CA B:ALA867 4.0 17.6 1.0 CA B:SER907 4.1 16.5 1.0 NE2 B:HIS840 4.1 16.2 1.0 CA B:ARG871 4.1 16.6 1.0 N B:ASP872 4.2 16.2 1.0 CA B:ASN908 4.2 15.2 1.0 N B:ARG871 4.4 17.1 1.0 CA B:ASP872 4.5 17.7 1.0 N B:SER874 4.6 16.9 1.0 OG B:SER870 4.6 16.1 1.0 CE1 B:HIS840 4.6 16.1 1.0 N B:SER870 4.7 16.9 1.0 CA B:SER874 4.7 17.7 1.0 N B:LEU873 4.8 17.0 1.0 CA B:SER870 4.8 17.0 1.0 N B:GLY868 4.8 17.3 1.0 CB B:ASN908 4.8 14.1 1.0 O B:SER907 4.9 17.1 1.0 C B:ASP872 4.9 18.4 1.0 CG B:ASP872 5.0 18.4 1.0

K.Okamoto, Y.Kawaguchi, B.T.Eger, E.F.Pai, T.Nishino. Crystal Structures of Urate Bound Form of Xanthine Oxidoreductase: Substrate Orientation and Structure of the Key Reaction Intermediate J.Am.Chem.Soc. V. 132 17080 2010.
ISSN: ISSN 0002-7863
PubMed: 21077683
DOI: 10.1021/JA1077574