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Calcium in PDB 4ytz: Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol

Enzymatic activity of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol

All present enzymatic activity of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol, PDB code: 4ytz was solved by T.Nishino, K.Okamoto, Y.Kawaguchi, T.Matsumura, B.T.Eger, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.172, 139.123, 223.273, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 26.5

Other elements in 4ytz:

The structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol (pdb code 4ytz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol, PDB code: 4ytz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4ytz

Go back to Calcium Binding Sites List in 4ytz
Calcium binding site 1 out of 4 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1406

b:31.5
occ:1.00
 O A:GLY867 2.6 32.8 1.0
O A:GLU871 2.6 32.9 1.0
OG A:SER874 2.7 33.5 1.0
OG A:SER907 2.7 31.5 1.0
O A:THR870 2.8 32.3 1.0
O A:ASN908 2.8 30.4 1.0
C A:GLU871 3.4 33.4 1.0
N A:ASN908 3.6 29.6 1.0
C A:GLY867 3.7 32.5 1.0
CB A:ASP872 3.8 33.1 1.0
C A:ASN908 3.8 30.6 1.0
C A:THR870 3.9 33.4 1.0
CB A:SER874 3.9 31.4 1.0
CB A:SER907 4.0 26.7 1.0
CA A:GLY867 4.1 31.6 1.0
C A:SER907 4.1 28.9 1.0
CA A:SER907 4.1 27.7 1.0
NE2 A:HIS840 4.1 32.5 1.0
N A:ASP872 4.1 32.6 1.0
CA A:ASN908 4.2 30.7 1.0
CA A:GLU871 4.3 33.5 1.0
CA A:ASP872 4.4 33.1 1.0
N A:GLU871 4.5 33.6 1.0
OG1 A:THR870 4.6 34.6 1.0
N A:SER874 4.6 31.6 1.0
CE1 A:HIS840 4.6 34.5 1.0
OD2 A:ASP872 4.7 33.2 1.0
N A:LEU873 4.7 32.9 1.0
N A:THR870 4.8 33.8 1.0
CG A:ASP872 4.8 34.4 1.0
C A:ASP872 4.8 33.9 1.0
CA A:SER874 4.8 32.1 1.0
N A:GLY868 4.8 32.7 1.0
CB A:ASN908 4.9 30.8 1.0
CA A:THR870 4.9 34.0 1.0
O A:SER907 5.0 28.2 1.0

Calcium binding site 2 out of 4 in 4ytz

Go back to Calcium Binding Sites List in 4ytz
Calcium binding site 2 out of 4 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1407

b:33.0
occ:1.00
 OG1 A:THR836 2.7 26.8 1.0
O A:GLY837 2.8 31.0 1.0
ND1 A:HIS741 2.8 24.0 1.0
OE2 A:GLU740 2.9 34.1 1.0
OH A:TYR743 2.9 22.7 1.0
OE1 A:GLU740 3.3 32.6 1.0
CD A:GLU740 3.5 34.3 1.0
CE1 A:HIS741 3.5 22.9 1.0
CZ A:TYR743 3.8 28.7 1.0
CB A:THR836 3.9 27.9 1.0
OD1 A:ASP832 3.9 19.4 1.0
CG A:HIS741 4.0 27.5 1.0
C A:GLY837 4.0 30.9 1.0
CE2 A:TYR743 4.1 27.3 1.0
C A:THR836 4.1 28.9 1.0
O A:THR836 4.2 29.1 1.0
N A:HIS741 4.3 28.2 1.0
N A:GLY837 4.4 29.3 1.0
CB A:HIS741 4.4 27.1 1.0
O A:ASP832 4.5 30.5 1.0
CA A:THR836 4.6 28.0 1.0
O A:HOH1502 4.6 19.9 1.0
NE2 A:HIS741 4.7 22.5 1.0
CE1 A:TYR743 4.8 26.2 1.0
CA A:GLY837 4.9 29.4 1.0
CA A:GLY800 4.9 25.6 1.0
CG A:GLU740 4.9 30.2 1.0
N A:GLY838 4.9 30.6 1.0
CD2 A:HIS741 4.9 27.9 1.0
CA A:HIS741 5.0 27.3 1.0
CA A:GLY838 5.0 30.0 1.0

Calcium binding site 3 out of 4 in 4ytz

Go back to Calcium Binding Sites List in 4ytz
Calcium binding site 3 out of 4 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1406

b:27.6
occ:1.00
 OG B:SER874 2.5 26.1 1.0
O B:THR870 2.7 26.0 1.0
O B:ASN908 2.8 22.1 1.0
O B:GLY867 2.8 21.3 1.0
OG B:SER907 2.8 26.5 1.0
O B:GLU871 3.0 22.9 1.0
N B:ASN908 3.4 23.5 1.0
C B:GLU871 3.5 23.9 1.0
C B:GLY867 3.7 21.3 1.0
CB B:ASP872 3.8 24.0 1.0
C B:THR870 3.8 25.5 1.0
C B:ASN908 3.8 22.5 1.0
CB B:SER874 3.9 25.4 1.0
CB B:SER907 4.0 22.8 1.0
C B:SER907 4.1 23.5 1.0
CA B:GLU871 4.1 24.9 1.0
N B:ASP872 4.1 23.9 1.0
CA B:GLY867 4.2 21.2 1.0
CA B:ASN908 4.2 22.5 1.0
CA B:SER907 4.2 23.7 1.0
NE2 B:HIS840 4.2 20.0 1.0
N B:GLU871 4.4 24.6 1.0
CA B:ASP872 4.5 24.2 1.0
OG1 B:THR870 4.5 24.3 1.0
N B:SER874 4.6 23.1 1.0
CA B:SER874 4.8 24.9 1.0
CE1 B:HIS840 4.8 22.8 1.0
CB B:ASN908 4.8 22.3 1.0
N B:THR870 4.9 25.1 1.0
N B:GLY868 4.9 21.8 1.0
CA B:THR870 4.9 25.3 1.0
N B:LEU873 4.9 23.2 1.0
CG B:ASP872 4.9 28.7 1.0
C B:ASP872 4.9 24.8 1.0
N B:THR909 4.9 23.3 1.0
OD2 B:ASP872 5.0 26.0 1.0

Calcium binding site 4 out of 4 in 4ytz

Go back to Calcium Binding Sites List in 4ytz
Calcium binding site 4 out of 4 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1407

b:29.6
occ:1.00
 O B:GLY837 2.7 24.2 1.0
OG1 B:THR836 2.8 21.9 1.0
ND1 B:HIS741 2.8 23.3 1.0
OE2 B:GLU740 2.8 22.3 1.0
OH B:TYR743 2.9 25.6 1.0
OE1 B:GLU740 3.1 24.2 1.0
CD B:GLU740 3.4 25.3 1.0
CE1 B:HIS741 3.4 23.9 1.0
CZ B:TYR743 3.8 24.4 1.0
CB B:THR836 3.8 21.9 1.0
C B:GLY837 3.9 23.5 1.0
CG B:HIS741 4.0 20.8 1.0
OD1 B:ASP832 4.0 22.7 1.0
C B:THR836 4.0 21.7 1.0
O B:THR836 4.1 23.4 1.0
CE2 B:TYR743 4.1 22.2 1.0
N B:GLY837 4.3 21.2 1.0
N B:HIS741 4.3 22.2 1.0
CB B:HIS741 4.5 22.5 1.0
CA B:THR836 4.5 21.5 1.0
NE2 B:HIS741 4.6 21.6 1.0
CA B:GLY837 4.7 22.7 1.0
O B:ASP832 4.7 24.6 1.0
CE1 B:TYR743 4.8 26.1 1.0
N B:GLY838 4.8 24.7 1.0
CA B:GLY838 4.9 24.6 1.0
CG B:GLU740 4.9 24.5 1.0
CD2 B:HIS741 4.9 16.1 1.0
CA B:GLY800 5.0 20.9 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 15:16:14 2024

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