Calcium in PDB 6adj: Rat Xanthine Oxidoreductase, D428E Variant

Enzymatic activity of Rat Xanthine Oxidoreductase, D428E Variant

All present enzymatic activity of Rat Xanthine Oxidoreductase, D428E Variant:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Rat Xanthine Oxidoreductase, D428E Variant, PDB code: 6adj was solved by K.Okamoto, Y.Kawaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.40 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.836, 138.665, 222.463, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21

Other elements in 6adj:

The structure of Rat Xanthine Oxidoreductase, D428E Variant also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Rat Xanthine Oxidoreductase, D428E Variant (pdb code 6adj). 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, D428E Variant, PDB code: 6adj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6adj

Go back to Calcium Binding Sites List in 6adj
Calcium binding site 1 out of 2 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3003

b:22.6
occ:1.00
OG A:SER907 2.6 20.6 1.0
OG A:SER874 2.7 20.1 1.0
O A:ASN908 2.7 21.7 1.0
O A:GLY867 2.7 22.5 1.0
O A:THR870 2.7 20.0 1.0
O A:GLU871 3.0 22.0 1.0
C A:GLU871 3.5 23.8 1.0
N A:ASN908 3.5 21.7 1.0
C A:GLY867 3.7 21.9 1.0
CB A:ASP872 3.7 23.1 1.0
C A:ASN908 3.7 21.3 1.0
C A:THR870 3.8 22.7 1.0
CB A:SER907 3.9 19.6 1.0
CB A:SER874 3.9 19.1 1.0
CA A:GLY867 4.0 20.7 1.0
C A:SER907 4.1 19.8 1.0
NE2 A:HIS840 4.1 21.6 1.0
CA A:SER907 4.1 19.2 1.0
CA A:GLU871 4.2 23.6 1.0
CA A:ASN908 4.2 21.6 1.0
N A:ASP872 4.2 22.3 1.0
N A:GLU871 4.4 21.1 1.0
CA A:ASP872 4.5 21.8 1.0
CG2 A:THR870 4.6 21.4 1.0
N A:SER874 4.6 19.2 1.0
CE1 A:HIS840 4.6 22.7 1.0
CA A:SER874 4.8 19.8 1.0
CB A:ASN908 4.8 21.4 1.0
N A:THR870 4.8 24.1 1.0
N A:LEU873 4.8 18.5 1.0
N A:GLY868 4.8 20.8 1.0
CA A:THR870 4.8 23.0 1.0
CG A:ASP872 4.8 24.6 1.0
C A:ASP872 4.9 20.6 1.0
OD2 A:ASP872 4.9 21.4 1.0
N A:THR909 4.9 20.0 1.0

Calcium binding site 2 out of 2 in 6adj

Go back to Calcium Binding Sites List in 6adj
Calcium binding site 2 out of 2 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4003

b:19.6
occ:1.00
OG B:SER874 2.7 15.6 1.0
O B:ASN908 2.7 17.0 1.0
O B:GLY867 2.7 17.5 1.0
O B:THR870 2.7 13.8 1.0
OG B:SER907 2.8 16.5 1.0
O B:GLU871 3.1 17.0 1.0
C B:GLU871 3.5 16.7 1.0
N B:ASN908 3.6 15.3 1.0
C B:GLY867 3.7 16.9 1.0
CB B:ASP872 3.7 18.4 1.0
C B:ASN908 3.8 16.6 1.0
C B:THR870 3.8 16.4 1.0
CB B:SER874 3.9 15.5 1.0
CB B:SER907 3.9 15.4 1.0
CA B:GLY867 4.1 17.1 1.0
C B:SER907 4.1 15.8 1.0
CA B:SER907 4.1 15.9 1.0
N B:ASP872 4.2 16.1 1.0
NE2 B:HIS840 4.2 16.0 1.0
CA B:GLU871 4.2 17.8 1.0
CA B:ASN908 4.2 16.5 1.0
N B:GLU871 4.4 15.6 1.0
CA B:ASP872 4.4 17.2 1.0
CG2 B:THR870 4.5 16.2 1.0
N B:SER874 4.6 17.0 1.0
CE1 B:HIS840 4.7 16.6 1.0
CA B:SER874 4.7 16.0 1.0
N B:THR870 4.8 15.9 1.0
CA B:THR870 4.8 17.3 1.0
N B:GLY868 4.8 15.8 1.0
CG B:ASP872 4.8 20.3 1.0
OD2 B:ASP872 4.9 19.3 1.0
CB B:ASN908 4.9 16.4 1.0
C B:ASP872 4.9 17.3 1.0
N B:LEU873 4.9 16.7 1.0
N B:THR909 4.9 15.6 1.0
O B:SER907 5.0 15.3 1.0

Reference:

K.Okamoto, Y.Kawaguchi. Rat Xanthine Oxidoreductase, D428A Variant, Nad Bound Form To Be Published.
Page generated: Sat Dec 12 05:56:48 2020

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