Calcium in PDB 1vdv: Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form

All present enzymatic activity of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form:
1.1.1.204;

The structure of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form, PDB code: 1vdv was solved by A.Fukunari, K.Okamoto, T.Nishino, B.T.Eger, E.F.Pai, M.Kamezawa, I.Yamada, N.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.817, 123.940, 148.888, 90.00, 91.16, 90.00
R / Rfree (%)	17.8 / 21.5

The structure of Bovine Milk Xanthine Dehydrogenase Y-700 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 Milk Xanthine Dehydrogenase Y-700 Bound Form (pdb code 1vdv). 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 Milk Xanthine Dehydrogenase Y-700 Bound Form, PDB code: 1vdv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Bovine Milk Xanthine Dehydrogenase Y-700 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 Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5301 b:15.1 occ:1.00 O A:ALA867 2.6 12.5 1.0 OG A:SER907 2.7 8.5 1.0 O A:SER870 2.7 12.6 1.0 O A:ASN908 2.7 14.7 1.0 OG A:SER874 2.7 14.5 1.0 O A:ARG871 3.0 16.1 1.0 N A:ASN908 3.5 12.3 1.0 C A:ARG871 3.6 14.4 1.0 C A:ALA867 3.7 14.4 1.0 CB A:ASP872 3.7 11.2 1.0 C A:SER870 3.7 13.1 1.0 C A:ASN908 3.8 15.0 1.0 CB A:SER907 3.9 10.8 1.0 CB A:SER874 3.9 14.5 1.0 C A:SER907 4.0 13.7 1.0 CB A:ALA867 4.0 15.4 1.0 NE2 A:HIS840 4.0 14.2 1.0 CA A:SER907 4.1 12.2 1.0 CA A:ALA867 4.1 15.1 1.0 CA A:ASN908 4.2 13.9 1.0 CA A:ARG871 4.2 14.6 1.0 N A:ASP872 4.3 13.3 1.0 N A:ARG871 4.4 13.8 1.0 OG A:SER870 4.4 16.1 1.0 CA A:ASP872 4.5 12.7 1.0 N A:SER874 4.5 12.0 1.0 CE1 A:HIS840 4.6 16.2 1.0 N A:GLY868 4.8 13.9 1.0 N A:SER870 4.8 13.8 1.0 CB A:ASN908 4.8 13.5 1.0 CA A:SER874 4.8 14.7 1.0 CA A:SER870 4.8 14.1 1.0 CG A:ASP872 4.8 12.4 1.0 N A:LEU873 4.9 10.5 1.0 O A:SER907 4.9 12.4 1.0 OD1 A:ASP872 4.9 11.9 1.0 N A:THR909 4.9 13.8 1.0

Calcium binding site 2 out of 4 in the Bovine Milk Xanthine Dehydrogenase Y-700 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 Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5304 b:23.5 occ:1.00 OG1 A:THR836 2.5 10.3 1.0 O A:HOH6075 2.6 43.0 1.0 O A:GLY837 2.6 8.6 1.0 O A:HOH5508 2.7 14.5 1.0 OH A:TYR743 2.8 10.8 1.0 ND1 A:HIS741 2.8 14.6 1.0 CE1 A:HIS741 3.4 11.0 1.0 CB A:THR836 3.6 11.0 1.0 CZ A:TYR743 3.8 13.3 1.0 C A:GLY837 3.8 14.2 1.0 OD2 A:ASP832 3.8 13.3 1.0 O A:THR836 3.8 14.3 1.0 C A:THR836 3.9 13.4 1.0 CG A:HIS741 4.0 14.1 1.0 N A:GLY837 4.2 14.1 1.0 CE2 A:TYR743 4.2 9.6 1.0 CA A:THR836 4.3 11.6 1.0 OD2 A:ASP740 4.4 12.7 1.0 O A:ASP832 4.4 10.8 1.0 CB A:HIS741 4.4 11.6 1.0 CA A:GLY837 4.6 10.9 1.0 NE2 A:HIS747 4.6 17.0 1.0 NE2 A:HIS741 4.7 13.1 1.0 N A:HIS741 4.7 12.7 1.0 CG2 A:THR836 4.8 10.6 1.0 CA A:GLY800 4.8 10.4 1.0 N A:GLY838 4.8 10.5 1.0 CE1 A:TYR743 4.8 6.8 1.0 CA A:GLY838 4.9 11.1 1.0 CD2 A:HIS741 4.9 13.0 1.0 CG A:ASP740 4.9 12.5 1.0 O A:GLY800 5.0 10.3 1.0

Calcium binding site 3 out of 4 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5302 b:15.4 occ:1.00 O B:ALA867 2.6 14.3 1.0 OG B:SER907 2.6 14.6 1.0 O B:ASN908 2.7 15.7 1.0 O B:SER870 2.7 15.4 1.0 OG B:SER874 2.8 19.5 1.0 O B:ARG871 3.0 17.2 1.0 N B:ASN908 3.5 16.0 1.0 C B:ARG871 3.6 16.2 1.0 C B:ALA867 3.7 14.7 1.0 CB B:ASP872 3.7 13.2 1.0 C B:SER870 3.8 14.3 1.0 C B:ASN908 3.8 16.7 1.0 CB B:SER907 3.8 14.2 1.0 C B:SER907 4.0 17.0 1.0 CB B:SER874 4.0 18.6 1.0 CA B:SER907 4.0 14.6 1.0 NE2 B:HIS840 4.1 10.6 1.0 CB B:ALA867 4.1 14.3 1.0 CA B:ALA867 4.1 15.4 1.0 CA B:ASN908 4.2 15.8 1.0 CA B:ARG871 4.2 17.1 1.0 N B:ASP872 4.3 15.4 1.0 OG B:SER870 4.4 15.6 1.0 N B:ARG871 4.4 16.7 1.0 CA B:ASP872 4.6 14.6 1.0 N B:SER874 4.6 13.4 1.0 CE1 B:HIS840 4.6 10.4 1.0 N B:SER870 4.8 13.8 1.0 N B:GLY868 4.8 16.4 1.0 CA B:SER870 4.8 14.9 1.0 CG B:ASP872 4.8 16.6 1.0 CA B:SER874 4.8 18.7 1.0 O B:SER907 4.8 12.9 1.0 CB B:ASN908 4.8 18.4 1.0 N B:LEU873 4.9 13.6 1.0 OD1 B:ASP872 4.9 12.3 1.0 N B:THR909 5.0 13.0 1.0

Calcium binding site 4 out of 4 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5303 b:22.8 occ:1.00 O B:HOH6328 2.5 27.4 1.0 O B:GLY837 2.6 9.9 1.0 OG1 B:THR836 2.6 10.5 1.0 O B:HOH5367 2.6 12.7 1.0 ND1 B:HIS741 2.7 10.9 1.0 OH B:TYR743 2.8 11.9 1.0 CE1 B:HIS741 3.2 11.3 1.0 CB B:THR836 3.6 12.8 1.0 O B:THR836 3.7 13.3 1.0 C B:GLY837 3.8 14.5 1.0 CZ B:TYR743 3.8 13.9 1.0 CG B:HIS741 3.8 11.3 1.0 C B:THR836 3.9 12.0 1.0 OD2 B:ASP832 3.9 9.0 1.0 CE2 B:TYR743 4.2 11.6 1.0 N B:GLY837 4.3 14.4 1.0 CA B:THR836 4.3 11.1 1.0 CB B:HIS741 4.4 9.9 1.0 NE2 B:HIS741 4.5 9.9 1.0 OD2 B:ASP740 4.5 18.0 1.0 NE2 B:HIS747 4.5 13.8 1.0 O B:ASP832 4.5 12.0 1.0 CA B:GLY837 4.6 12.7 1.0 N B:HIS741 4.6 14.3 1.0 CA B:GLY800 4.7 9.9 1.0 CD2 B:HIS741 4.8 6.1 1.0 N B:GLY838 4.8 11.3 1.0 CA B:GLY838 4.8 12.5 1.0 CG2 B:THR836 4.8 9.7 1.0 O B:GLY800 4.9 11.6 1.0 CE1 B:TYR743 4.9 10.7 1.0

A.Fukunari, K.Okamoto, T.Nishino, B.T.Eger, E.F.Pai, M.Kamezawa, I.Yamada, N.Kato. Y-700 [1-[3-Cyano-4-(2,2-Dimethylpropoxy)Phenyl]-1H- Pyrazole-4-Carboxylic Acid]: A Potent Xanthine Oxidoreductase Inhibitor with Hepatic Excretion J.Pharmacol.Exp.Ther. V. 311 519 2004.
ISSN: ISSN 0022-3565
PubMed: 15190124
DOI: 10.1124/JPET.104.070433