Calcium in PDB 3uni: Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound

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

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound, PDB code: 3uni 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 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	100.036, 146.698, 107.016, 90.00, 106.03, 90.00
R / Rfree (%)	19.8 / 24

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh 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 Nadh Bound (pdb code 3uni). 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 Nadh Bound, PDB code: 3uni:
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 Nadh 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 Nadh Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1345 b:17.9 occ:1.00 OG A:SER874 2.5 13.4 1.0 O A:ASN908 2.7 15.9 1.0 O A:ALA867 2.7 22.5 1.0 OG A:SER907 2.7 14.1 1.0 O A:SER870 2.8 16.2 1.0 O A:ARG871 2.9 15.5 1.0 N A:ASN908 3.5 18.1 1.0 C A:ARG871 3.5 17.5 1.0 C A:ALA867 3.6 18.2 1.0 CB A:ASP872 3.7 16.6 1.0 C A:ASN908 3.7 17.7 1.0 CB A:SER874 3.8 13.5 1.0 C A:SER870 3.8 15.4 1.0 CB A:SER907 3.9 14.4 1.0 CB A:ALA867 4.0 18.5 1.0 NE2 A:HIS840 4.0 22.9 1.0 C A:SER907 4.1 18.1 1.0 CA A:ALA867 4.1 18.8 1.0 CA A:ASN908 4.1 17.2 1.0 CA A:SER907 4.2 15.8 1.0 CA A:ARG871 4.2 16.2 1.0 N A:ASP872 4.2 16.7 1.0 N A:SER874 4.4 14.4 1.0 OG A:SER870 4.4 15.8 1.0 N A:ARG871 4.5 15.4 1.0 CA A:ASP872 4.5 15.1 1.0 CE1 A:HIS840 4.5 22.6 1.0 CA A:SER874 4.7 15.9 1.0 CB A:ASN908 4.7 16.5 1.0 N A:GLY868 4.7 17.4 1.0 N A:LEU873 4.8 13.1 1.0 CG A:ASP872 4.8 19.1 1.0 N A:THR909 4.9 17.2 1.0 N A:SER870 4.9 14.6 1.0 C A:ASP872 4.9 14.0 1.0 CA A:SER870 5.0 14.5 1.0 OD1 A:ASP872 5.0 18.2 1.0 O A:SER907 5.0 19.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh 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 Nadh Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1346 b:21.7 occ:1.00 O B:SER870 2.6 18.1 1.0 OG B:SER874 2.6 12.7 1.0 O B:ALA867 2.6 25.1 1.0 O B:ARG871 2.7 19.2 1.0 OG B:SER907 2.7 16.3 1.0 O B:ASN908 2.7 19.0 1.0 C B:ARG871 3.4 20.0 1.0 N B:ASN908 3.6 21.6 1.0 C B:ALA867 3.6 21.7 1.0 C B:SER870 3.7 17.3 1.0 CB B:ASP872 3.7 18.3 1.0 C B:ASN908 3.8 20.6 1.0 CB B:SER874 3.8 15.4 1.0 CB B:ALA867 3.9 21.7 1.0 CB B:SER907 4.0 18.1 1.0 CA B:ALA867 4.0 22.2 1.0 NE2 B:HIS840 4.1 25.0 1.0 CA B:ARG871 4.1 18.6 1.0 C B:SER907 4.1 21.6 1.0 CA B:SER907 4.2 20.1 1.0 N B:ASP872 4.2 19.0 1.0 CA B:ASN908 4.2 20.3 1.0 N B:ARG871 4.3 17.1 1.0 OG B:SER870 4.4 18.1 1.0 N B:SER874 4.4 16.7 1.0 CA B:ASP872 4.5 17.0 1.0 CE1 B:HIS840 4.6 23.9 1.0 CA B:SER874 4.7 17.5 1.0 N B:SER870 4.8 17.0 1.0 N B:GLY868 4.8 21.1 1.0 CA B:SER870 4.8 17.1 1.0 CB B:ASN908 4.8 22.3 1.0 N B:LEU873 4.8 14.7 1.0 CG B:ASP872 4.8 20.8 1.0 C B:ASP872 5.0 15.7 1.0 N B:THR909 5.0 17.0 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