Calcium in PDB 4ysw: Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form

All present enzymatic activity of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form:
1.17.1.4; 1.17.3.2;

The structure of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form, PDB code: 4ysw was solved by T.Nishino, K.Okamoto, Y.Kawaguchi, T.Matsumura, B.T.Eger, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.41 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.460, 137.643, 222.067, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.9

The structure of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Calcium atom in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form (pdb code 4ysw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form, PDB code: 4ysw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3003 b:26.9 occ:1.00 O A:GLY867 2.6 23.8 1.0 O A:ASN908 2.6 20.2 1.0 OG A:SER874 2.7 23.9 1.0 OG A:SER907 2.8 21.1 1.0 O A:THR870 2.8 23.5 1.0 O A:GLU871 2.9 24.2 1.0 C A:GLU871 3.5 23.8 1.0 N A:ASN908 3.6 20.9 1.0 C A:GLY867 3.6 24.0 1.0 CB A:ASP872 3.6 22.7 1.0 C A:ASN908 3.7 20.6 1.0 C A:THR870 3.9 23.7 1.0 CB A:SER874 4.0 22.5 1.0 CB A:SER907 4.0 20.4 1.0 NE2 A:HIS840 4.0 22.0 1.0 CA A:GLY867 4.0 24.3 1.0 CA A:ASN908 4.1 20.9 1.0 C A:SER907 4.1 20.9 1.0 N A:ASP872 4.2 23.5 1.0 CA A:SER907 4.2 20.9 1.0 CA A:GLU871 4.3 24.1 1.0 CA A:ASP872 4.4 22.8 1.0 CE1 A:HIS840 4.5 22.2 1.0 N A:GLU871 4.5 23.8 1.0 OG1 A:THR870 4.6 24.4 1.0 N A:SER874 4.6 22.2 1.0 CB A:ASN908 4.7 20.7 1.0 CG A:ASP872 4.7 23.5 1.0 N A:LEU873 4.8 21.9 1.0 N A:GLY868 4.8 23.4 1.0 CA A:SER874 4.8 22.6 1.0 N A:THR909 4.8 20.6 1.0 OD1 A:ASP872 4.8 22.8 1.0 C A:ASP872 4.9 22.5 1.0 N A:THR870 4.9 23.3 1.0 CA A:THR870 4.9 23.4 1.0

Calcium binding site 2 out of 2 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4003 b:19.8 occ:1.00 O B:GLY867 2.6 15.9 1.0 OG B:SER874 2.6 18.4 1.0 O B:THR870 2.7 16.8 1.0 O B:ASN908 2.8 15.7 1.0 OG B:SER907 2.8 15.3 1.0 O B:GLU871 2.9 16.5 1.0 C B:GLU871 3.5 16.3 1.0 N B:ASN908 3.6 15.4 1.0 C B:GLY867 3.6 16.0 1.0 CB B:ASP872 3.7 15.6 1.0 C B:ASN908 3.8 15.6 1.0 C B:THR870 3.8 16.8 1.0 CB B:SER874 3.9 16.8 1.0 CB B:SER907 4.0 14.5 1.0 CA B:GLY867 4.0 16.3 1.0 NE2 B:HIS840 4.0 15.1 1.0 C B:SER907 4.1 15.0 1.0 CA B:SER907 4.1 14.9 1.0 CA B:ASN908 4.2 15.5 1.0 CA B:GLU871 4.2 16.7 1.0 N B:ASP872 4.2 16.1 1.0 OG1 B:THR870 4.5 17.5 1.0 CA B:ASP872 4.5 16.1 1.0 N B:GLU871 4.5 16.3 1.0 CE1 B:HIS840 4.6 15.0 1.0 N B:SER874 4.6 16.4 1.0 N B:GLY868 4.8 15.8 1.0 CB B:ASN908 4.8 15.5 1.0 CA B:SER874 4.8 16.6 1.0 N B:THR870 4.8 16.5 1.0 CG B:ASP872 4.8 16.8 1.0 N B:LEU873 4.9 16.4 1.0 OD1 B:ASP872 4.9 17.1 1.0 CA B:THR870 4.9 16.8 1.0 C B:ASP872 4.9 16.3 1.0 N B:THR909 5.0 15.0 1.0

T.Nishino, K.Okamoto, Y.Kawaguchi, T.Matsumura, B.T.Eger, E.F.Pai, T.Nishino. The C-Terminal Peptide Plays A Role in the Formation of An Intermediate Form During the Transition Between Xanthine Dehydrogenase and Xanthine Oxidase. Febs J. 2015.
ISSN: ISSN 1742-464X
PubMed: 25817260
DOI: 10.1111/FEBS.13277