Calcium in PDB 4yty: Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, Nadh Bound Form

All present enzymatic activity of Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, Nadh Bound Form:
1.17.1.4; 1.17.3.2;

The structure of Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, Nadh Bound Form, PDB code: 4yty 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)	49.50 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.988, 137.404, 222.705, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.1

The structure of Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form (pdb code 4yty). 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, C535A/C992R/C1324S, Nadh Bound Form, PDB code: 4yty:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3003 b:21.3 occ:1.00 O A:GLY867 2.7 16.7 1.0 O A:ASN908 2.7 15.3 1.0 OG A:SER874 2.7 16.3 1.0 OG A:SER907 2.7 16.5 1.0 O A:THR870 2.8 16.9 1.0 O A:GLU871 2.8 18.5 1.0 C A:GLU871 3.5 18.4 1.0 N A:ASN908 3.7 15.6 1.0 C A:GLY867 3.7 16.5 1.0 CB A:ASP872 3.7 18.2 1.0 C A:ASN908 3.7 15.5 1.0 C A:THR870 3.9 17.4 1.0 CB A:SER874 3.9 15.7 1.0 CB A:SER907 4.0 15.0 1.0 NE2 A:HIS840 4.1 16.4 1.0 CA A:GLY867 4.1 16.7 1.0 C A:SER907 4.1 15.3 1.0 N A:ASP872 4.1 18.2 1.0 CA A:ASN908 4.2 15.7 1.0 CA A:SER907 4.2 15.5 1.0 CA A:GLU871 4.2 18.3 1.0 CA A:ASP872 4.4 18.2 1.0 N A:GLU871 4.5 17.4 1.0 N A:SER874 4.5 15.9 1.0 OG1 A:THR870 4.6 18.1 1.0 CE1 A:HIS840 4.6 16.9 1.0 N A:LEU873 4.7 16.9 1.0 CA A:SER874 4.7 16.3 1.0 CG A:ASP872 4.8 21.3 1.0 CB A:ASN908 4.8 15.7 1.0 N A:GLY868 4.8 16.6 1.0 OD1 A:ASP872 4.8 21.2 1.0 C A:ASP872 4.8 17.5 1.0 N A:THR909 4.9 15.6 1.0 N A:THR870 4.9 17.6 1.0 CA A:THR870 4.9 17.5 1.0

Calcium binding site 2 out of 2 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4003 b:14.0 occ:1.00 O B:GLY867 2.6 12.6 1.0 O B:THR870 2.6 13.4 1.0 OG B:SER874 2.6 14.2 1.0 O B:ASN908 2.7 10.9 1.0 OG B:SER907 2.9 13.2 1.0 O B:GLU871 2.9 13.2 1.0 C B:GLU871 3.5 13.2 1.0 N B:ASN908 3.6 10.9 1.0 C B:GLY867 3.6 12.9 1.0 CB B:ASP872 3.7 13.2 1.0 C B:THR870 3.7 13.7 1.0 C B:ASN908 3.8 11.1 1.0 CB B:SER874 3.9 13.8 1.0 CB B:SER907 4.0 11.0 1.0 NE2 B:HIS840 4.1 10.9 1.0 C B:SER907 4.1 11.3 1.0 CA B:GLY867 4.1 13.4 1.0 CA B:GLU871 4.2 13.6 1.0 CA B:SER907 4.2 11.2 1.0 N B:ASP872 4.2 12.9 1.0 CA B:ASN908 4.2 11.2 1.0 N B:GLU871 4.4 13.4 1.0 CA B:ASP872 4.5 13.2 1.0 N B:SER874 4.6 13.4 1.0 CE1 B:HIS840 4.6 10.6 1.0 OG1 B:THR870 4.6 14.9 1.0 N B:GLY868 4.8 12.6 1.0 CA B:SER874 4.8 13.6 1.0 N B:THR870 4.8 14.1 1.0 CG B:ASP872 4.8 15.8 1.0 CB B:ASN908 4.8 10.9 1.0 CA B:THR870 4.8 13.8 1.0 N B:LEU873 4.9 12.8 1.0 C B:ASP872 4.9 13.2 1.0 OD1 B:ASP872 4.9 17.0 1.0 N B:THR909 4.9 11.6 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