Calcium in PDB 4yrw: Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant

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

The structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, PDB code: 4yrw was solved by K.Okamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.33 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.497, 138.468, 222.213, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.9

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

Iron

(Fe)

8 atoms

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3004 b:34.0 occ:1.00 OG A:SER907 2.6 23.9 1.0 O A:ASN908 2.6 27.1 1.0 O A:GLY867 2.6 31.8 1.0 OG A:SER874 2.7 34.1 1.0 O A:THR870 2.8 23.5 1.0 O A:GLU871 3.0 27.6 1.0 C A:GLU871 3.5 29.4 1.0 N A:ASN908 3.6 23.6 1.0 CB A:ASP872 3.6 27.4 1.0 C A:GLY867 3.7 28.9 1.0 C A:ASN908 3.7 29.2 1.0 C A:THR870 3.8 25.7 1.0 CB A:SER907 3.9 20.9 1.0 CB A:SER874 3.9 25.5 1.0 C A:SER907 4.0 23.9 1.0 CA A:SER907 4.1 21.7 1.0 CA A:GLY867 4.1 29.4 1.0 NE2 A:HIS840 4.1 30.6 1.0 CA A:GLU871 4.2 27.7 1.0 N A:ASP872 4.2 29.1 1.0 CA A:ASN908 4.2 28.1 1.0 CA A:ASP872 4.4 27.7 1.0 N A:GLU871 4.4 23.9 1.0 CG2 A:THR870 4.5 25.1 1.0 N A:SER874 4.5 24.4 1.0 CE1 A:HIS840 4.6 29.6 1.0 CG A:ASP872 4.7 29.3 1.0 CA A:SER874 4.7 27.0 1.0 OD2 A:ASP872 4.7 26.8 1.0 N A:THR870 4.8 24.3 1.0 CB A:ASN908 4.8 26.9 1.0 N A:LEU873 4.8 26.1 1.0 CA A:THR870 4.8 25.5 1.0 C A:ASP872 4.8 28.7 1.0 N A:GLY868 4.8 25.4 1.0 N A:THR909 4.8 25.6 1.0 O A:SER907 5.0 20.3 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4003 b:24.6 occ:1.00 OG B:SER874 2.7 21.1 1.0 O B:GLY867 2.7 21.5 1.0 O B:ASN908 2.7 25.0 1.0 OG B:SER907 2.8 22.4 1.0 O B:THR870 2.8 19.5 1.0 O B:GLU871 3.0 18.8 1.0 C B:GLU871 3.5 20.0 1.0 N B:ASN908 3.6 20.6 1.0 C B:GLY867 3.7 20.4 1.0 CB B:ASP872 3.7 21.1 1.0 C B:ASN908 3.7 23.0 1.0 C B:THR870 3.9 22.1 1.0 CB B:SER874 3.9 21.9 1.0 CB B:SER907 4.0 22.9 1.0 CA B:GLY867 4.1 19.3 1.0 C B:SER907 4.1 20.8 1.0 CA B:SER907 4.1 21.8 1.0 NE2 B:HIS840 4.1 23.4 1.0 N B:ASP872 4.2 20.4 1.0 CA B:ASN908 4.2 20.4 1.0 CA B:GLU871 4.2 20.7 1.0 CA B:ASP872 4.4 19.2 1.0 OG1 B:THR870 4.5 22.5 1.0 N B:GLU871 4.5 20.1 1.0 CE1 B:HIS840 4.6 22.8 1.0 N B:SER874 4.6 21.8 1.0 CB B:ASN908 4.8 20.5 1.0 N B:THR870 4.8 19.7 1.0 CA B:SER874 4.8 21.6 1.0 CG B:ASP872 4.8 23.8 1.0 N B:GLY868 4.8 19.6 1.0 N B:LEU873 4.9 21.6 1.0 C B:ASP872 4.9 22.9 1.0 OD2 B:ASP872 4.9 23.9 1.0 N B:THR909 4.9 19.1 1.0 CA B:THR870 4.9 20.0 1.0 O B:SER907 5.0 19.2 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