Calcium in PDB 8j79: Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol

All present enzymatic activity of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol:
1.17.1.4; 1.17.3.2;

The structure of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol, PDB code: 8j79 was solved by K.Okamoto, M.Sekine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.72 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.678, 123.47, 150.059, 90, 90.89, 90
R / Rfree (%)	16.3 / 19.7

The structure of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol 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 Crystallized with Oxypurinol (pdb code 8j79). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol, PDB code: 8j79:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


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 Crystallized with Oxypurinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1407 b:25.0 occ:1.00 O A:SER870 2.7 20.1 1.0 OG A:SER874 2.7 23.9 1.0 OG A:SER907 2.7 22.1 1.0 O A:ALA867 2.7 23.3 1.0 O A:ASN908 2.8 22.7 1.0 O A:ARG871 2.9 24.4 1.0 C A:ARG871 3.5 25.5 1.0 N A:ASN908 3.5 22.0 1.0 C A:SER870 3.7 22.1 1.0 C A:ALA867 3.7 26.1 1.0 CB A:ASP872 3.8 26.0 1.0 C A:ASN908 3.8 23.0 1.0 CB A:SER907 3.9 22.4 1.0 CB A:SER874 3.9 24.4 1.0 C A:SER907 4.0 23.8 1.0 CA A:SER907 4.1 21.2 1.0 CB A:ALA867 4.1 26.0 1.0 CA A:ALA867 4.1 26.6 1.0 NE2 A:HIS840 4.1 22.3 1.0 N A:ASP872 4.2 25.4 1.0 CA A:ASN908 4.2 22.2 1.0 CA A:ARG871 4.2 25.6 1.0 N A:ARG871 4.4 25.0 1.0 CA A:ASP872 4.5 25.0 1.0 OG A:SER870 4.5 23.2 1.0 N A:SER874 4.6 24.9 1.0 CE1 A:HIS840 4.7 25.7 1.0 N A:SER870 4.8 23.4 1.0 CA A:SER874 4.8 24.6 1.0 CA A:SER870 4.8 23.6 1.0 N A:LEU873 4.8 25.3 1.0 CB A:ASN908 4.9 24.6 1.0 N A:GLY868 4.9 25.5 1.0 C A:ASP872 4.9 25.0 1.0 CG A:ASP872 4.9 24.8 1.0 O A:SER907 5.0 23.8 1.0 N A:THR909 5.0 23.0 1.0

Calcium binding site 2 out of 4 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


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 Crystallized with Oxypurinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1408 b:29.8 occ:1.00 O A:GLY837 2.6 21.1 1.0 OG1 A:THR836 2.6 22.6 1.0 O A:HOH1899 2.7 31.3 1.0 OH A:TYR743 2.7 22.6 1.0 ND1 A:HIS741 2.8 24.8 1.0 CE1 A:HIS741 3.4 23.1 1.0 CZ A:TYR743 3.7 22.6 1.0 C A:GLY837 3.8 25.0 1.0 CB A:THR836 3.8 23.8 1.0 OD1 A:ASP832 3.9 25.5 1.0 C A:THR836 3.9 23.2 1.0 O A:THR836 3.9 25.0 1.0 CG A:HIS741 4.0 23.9 1.0 OD2 A:ASP740 4.0 33.7 1.0 CE2 A:TYR743 4.1 22.0 1.0 N A:GLY837 4.2 26.5 1.0 CA A:THR836 4.4 23.1 1.0 O A:ASP832 4.4 23.4 1.0 CB A:HIS741 4.4 24.2 1.0 N A:HIS741 4.6 22.4 1.0 NE2 A:HIS747 4.6 26.4 1.0 CA A:GLY837 4.6 25.7 1.0 NE2 A:HIS741 4.7 22.3 1.0 CG A:ASP740 4.7 29.8 1.0 N A:GLY838 4.8 23.9 1.0 CE1 A:TYR743 4.8 22.6 1.0 CA A:GLY800 4.8 22.7 1.0 CD2 A:HIS741 4.9 24.1 1.0 CA A:GLY838 5.0 21.1 1.0 OD1 A:ASP740 5.0 34.8 1.0

Calcium binding site 3 out of 4 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1407 b:25.3 occ:1.00 OG B:SER874 2.6 21.7 1.0 O B:ALA867 2.6 24.7 1.0 OG B:SER907 2.7 21.0 1.0 O B:ASN908 2.7 24.2 1.0 O B:SER870 2.7 24.0 1.0 O B:ARG871 2.8 22.9 1.0 C B:ARG871 3.5 23.6 1.0 N B:ASN908 3.5 23.2 1.0 C B:ALA867 3.7 23.1 1.0 CB B:ASP872 3.8 22.9 1.0 C B:ASN908 3.8 24.1 1.0 C B:SER870 3.8 27.0 1.0 CB B:SER907 3.9 22.6 1.0 CB B:SER874 3.9 21.4 1.0 NE2 B:HIS840 4.0 26.5 1.0 CB B:ALA867 4.0 26.5 1.0 C B:SER907 4.0 24.8 1.0 CA B:ALA867 4.1 23.5 1.0 CA B:SER907 4.1 23.3 1.0 N B:ASP872 4.1 22.9 1.0 CA B:ASN908 4.2 24.7 1.0 CA B:ARG871 4.2 24.3 1.0 CA B:ASP872 4.4 23.8 1.0 N B:ARG871 4.5 27.6 1.0 CE1 B:HIS840 4.6 27.1 1.0 N B:SER874 4.6 21.7 1.0 OG B:SER870 4.6 23.9 1.0 N B:SER870 4.8 23.8 1.0 CA B:SER874 4.8 23.4 1.0 N B:LEU873 4.8 23.1 1.0 CA B:SER870 4.8 26.1 1.0 CB B:ASN908 4.8 25.8 1.0 CG B:ASP872 4.9 25.4 1.0 N B:GLY868 4.9 21.3 1.0 C B:ASP872 4.9 24.9 1.0 OD2 B:ASP872 4.9 25.6 1.0 O B:SER907 4.9 25.1 1.0 N B:THR909 5.0 24.1 1.0

Calcium binding site 4 out of 4 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1408 b:29.5 occ:1.00 O B:GLY837 2.6 25.4 1.0 OG1 B:THR836 2.6 22.8 1.0 O B:HOH1659 2.7 26.4 1.0 ND1 B:HIS741 2.8 20.7 1.0 OH B:TYR743 2.9 23.4 1.0 CE1 B:HIS741 3.5 21.8 1.0 O B:THR836 3.7 23.8 1.0 CB B:THR836 3.7 24.4 1.0 OD1 B:ASP740 3.8 35.5 1.0 CZ B:TYR743 3.8 25.5 1.0 C B:THR836 3.8 22.5 1.0 C B:GLY837 3.8 27.6 1.0 OD1 B:ASP832 3.9 28.1 1.0 CG B:HIS741 4.0 23.4 1.0 CE2 B:TYR743 4.2 24.9 1.0 N B:GLY837 4.3 22.7 1.0 CA B:THR836 4.3 23.0 1.0 CB B:HIS741 4.4 21.5 1.0 O B:ASP832 4.5 22.8 1.0 N B:HIS741 4.6 21.6 1.0 NE2 B:HIS747 4.6 24.9 1.0 CA B:GLY837 4.7 24.8 1.0 NE2 B:HIS741 4.7 22.6 1.0 CG B:ASP740 4.8 30.6 1.0 CA B:GLY800 4.8 20.7 1.0 N B:GLY838 4.8 23.5 1.0 CE1 B:TYR743 4.9 23.8 1.0 CA B:GLY838 5.0 24.6 1.0 CD2 B:HIS741 5.0 22.2 1.0 CG2 B:THR836 5.0 23.9 1.0

K.Okamoto, M.Sekine. Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol To Be Published.