Calcium in PDB 3una: Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nad Bound

All present enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nad Bound:
1.17.1.4; 1.17.3.2;

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

Resolution Low / High (Å)	20.00 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.028, 123.182, 147.624, 90.00, 91.02, 90.00
R / Rfree (%)	18.1 / 21.4

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nad Bound also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nad Bound (pdb code 3una). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nad Bound, PDB code: 3una:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nad Bound


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 Bovine Milk Xanthine Dehydrogenase with Nad Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1349 b:14.3 occ:1.00 O A:ALA867 2.6 12.5 1.0 O A:SER870 2.6 14.3 1.0 OG A:SER874 2.6 16.7 1.0 OG A:SER907 2.6 10.7 1.0 O A:ASN908 2.7 15.5 1.0 O A:ARG871 2.9 13.0 1.0 N A:ASN908 3.5 13.3 1.0 C A:ARG871 3.5 12.6 1.0 C A:ALA867 3.6 14.4 1.0 C A:SER870 3.7 13.7 1.0 CB A:ASP872 3.7 13.6 1.0 C A:ASN908 3.8 14.0 1.0 CB A:SER907 3.8 12.9 1.0 CB A:SER874 3.9 15.2 1.0 C A:SER907 3.9 14.6 1.0 NE2 A:HIS840 4.0 11.1 1.0 CB A:ALA867 4.0 13.3 1.0 CA A:SER907 4.0 12.7 1.0 CA A:ALA867 4.1 14.4 1.0 CA A:ASN908 4.2 14.3 1.0 CA A:ARG871 4.2 13.8 1.0 N A:ASP872 4.3 14.0 1.0 N A:ARG871 4.4 13.4 1.0 OG A:SER870 4.4 14.0 1.0 N A:SER874 4.5 14.1 1.0 CA A:ASP872 4.5 14.7 1.0 CE1 A:HIS840 4.5 13.1 1.0 N A:SER870 4.7 14.8 1.0 CA A:SER870 4.8 15.1 1.0 CA A:SER874 4.8 15.0 1.0 CB A:ASN908 4.8 13.9 1.0 N A:GLY868 4.8 15.0 1.0 O A:SER907 4.8 15.1 1.0 CG A:ASP872 4.8 13.9 1.0 N A:LEU873 4.9 13.4 1.0 N A:THR909 4.9 11.2 1.0 OD1 A:ASP872 4.9 14.6 1.0 C A:ASP872 5.0 14.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nad Bound


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 Bovine Milk Xanthine Dehydrogenase with Nad Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1346 b:15.2 occ:1.00 O B:ALA867 2.6 16.7 1.0 OG B:SER907 2.6 18.0 1.0 OG B:SER874 2.7 15.4 1.0 O B:SER870 2.7 17.5 1.0 O B:ASN908 2.7 13.6 1.0 O B:ARG871 2.9 15.8 1.0 N B:ASN908 3.5 14.8 1.0 C B:ARG871 3.5 14.7 1.0 C B:ALA867 3.6 15.2 1.0 CB B:ASP872 3.7 14.0 1.0 C B:ASN908 3.8 15.5 1.0 C B:SER870 3.8 16.4 1.0 CB B:SER907 3.8 14.4 1.0 NE2 B:HIS840 3.9 13.7 1.0 CB B:SER874 3.9 13.8 1.0 C B:SER907 4.0 14.8 1.0 CA B:SER907 4.0 14.6 1.0 CB B:ALA867 4.1 15.8 1.0 CA B:ALA867 4.1 16.3 1.0 CA B:ASN908 4.2 15.3 1.0 CA B:ARG871 4.2 16.4 1.0 N B:ASP872 4.2 15.5 1.0 N B:ARG871 4.4 16.8 1.0 OG B:SER870 4.4 14.9 1.0 CE1 B:HIS840 4.4 14.0 1.0 CA B:ASP872 4.5 14.5 1.0 N B:SER874 4.5 13.9 1.0 N B:GLY868 4.7 15.7 1.0 CA B:SER874 4.8 14.6 1.0 N B:SER870 4.8 16.0 1.0 CB B:ASN908 4.8 16.1 1.0 CG B:ASP872 4.8 15.7 1.0 O B:SER907 4.8 13.8 1.0 N B:LEU873 4.8 14.0 1.0 CA B:SER870 4.8 16.6 1.0 OD1 B:ASP872 4.9 13.6 1.0 C B:ASP872 4.9 14.4 1.0 N B:THR909 4.9 13.7 1.0

H.Ishikita, B.T.Eger, K.Okamoto, T.Nishino, E.F.Pai. Protein Conformational Gating of Enzymatic Activity in Xanthine Oxidoreductase. J.Am.Chem.Soc. V. 134 999 2012.
ISSN: ISSN 0002-7863
PubMed: 22145797
DOI: 10.1021/JA207173P