Atomistry » Calcium » PDB 4y9p-4yty » 4yty
Atomistry »
  Calcium »
    PDB 4y9p-4yty »
      4yty »

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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 4yty:

The structure of Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, Nadh Bound Form also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

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 4yty

Go back to Calcium Binding Sites List in 4yty
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 4yty

Go back to Calcium Binding Sites List in 4yty
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

Reference:

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
Page generated: Sun Jul 14 15:12:14 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy