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Calcium in PDB 1v97: Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form

Enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form

All present enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form:
1.1.1.204;

Protein crystallography data

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form, PDB code: 1v97 was solved by K.Okamoto, K.Matsumoto, R.Hille, 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) 40.00 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.987, 124.612, 146.926, 90.00, 90.99, 90.00
R / Rfree (%) 17.8 / 20.8

Other elements in 1v97:

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form (pdb code 1v97). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form, PDB code: 1v97:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1v97

Go back to Calcium Binding Sites List in 1v97
Calcium binding site 1 out of 2 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3008

b:12.0
occ:1.00
OG A:SER874 2.6 14.1 1.0
OG A:SER907 2.7 13.2 1.0
O A:ALA867 2.7 16.4 1.0
O A:SER870 2.7 12.7 1.0
O A:ASN908 2.7 13.4 1.0
O A:ARG871 2.9 13.7 1.0
C A:ARG871 3.5 12.8 1.0
N A:ASN908 3.6 14.1 1.0
C A:ALA867 3.7 14.8 1.0
C A:SER870 3.7 13.2 1.0
CB A:ASP872 3.8 14.6 1.0
C A:ASN908 3.8 13.7 1.0
CB A:SER874 3.9 12.7 1.0
CB A:SER907 3.9 11.4 1.0
C A:SER907 4.0 13.2 1.0
CB A:ALA867 4.0 14.9 1.0
CA A:SER907 4.1 12.3 1.0
NE2 A:HIS840 4.1 12.1 1.0
CA A:ALA867 4.1 14.0 1.0
CA A:ARG871 4.2 12.9 1.0
CA A:ASN908 4.2 14.2 1.0
N A:ASP872 4.2 13.9 1.0
N A:ARG871 4.4 11.9 1.0
N A:SER874 4.5 13.0 1.0
OG A:SER870 4.5 13.3 1.0
CA A:ASP872 4.5 13.2 1.0
CE1 A:HIS840 4.6 12.1 1.0
CA A:SER874 4.7 15.1 1.0
N A:SER870 4.8 14.6 1.0
O A:SER907 4.8 12.1 1.0
N A:GLY868 4.8 13.6 1.0
CB A:ASN908 4.8 12.1 1.0
CA A:SER870 4.8 14.0 1.0
N A:LEU873 4.9 13.3 1.0
CG A:ASP872 4.9 13.5 1.0
OD1 A:ASP872 5.0 13.1 1.0
N A:THR909 5.0 11.9 1.0
C A:ASP872 5.0 16.2 1.0

Calcium binding site 2 out of 2 in 1v97

Go back to Calcium Binding Sites List in 1v97
Calcium binding site 2 out of 2 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Bovine Milk Xanthine Dehydrogenase Fyx-051 Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4008

b:16.0
occ:1.00
O B:SER870 2.6 15.9 1.0
O B:ALA867 2.6 14.2 1.0
OG B:SER874 2.6 14.4 1.0
OG B:SER907 2.7 16.5 1.0
O B:ASN908 2.7 12.0 1.0
O B:ARG871 3.0 13.4 1.0
N B:ASN908 3.5 15.1 1.0
C B:ARG871 3.5 13.5 1.0
C B:ALA867 3.7 15.4 1.0
C B:SER870 3.7 15.0 1.0
CB B:ASP872 3.7 13.8 1.0
C B:ASN908 3.8 13.7 1.0
CB B:SER907 3.9 13.2 1.0
CB B:SER874 3.9 14.2 1.0
C B:SER907 4.0 15.4 1.0
CB B:ALA867 4.0 14.1 1.0
CA B:SER907 4.1 15.3 1.0
NE2 B:HIS840 4.1 12.2 1.0
CA B:ARG871 4.1 14.2 1.0
CA B:ALA867 4.1 14.6 1.0
CA B:ASN908 4.2 14.0 1.0
N B:ASP872 4.2 14.1 1.0
N B:ARG871 4.3 13.4 1.0
OG B:SER870 4.4 14.2 1.0
N B:SER874 4.5 12.3 1.0
CA B:ASP872 4.5 14.2 1.0
CE1 B:HIS840 4.5 11.3 1.0
N B:SER870 4.7 14.3 1.0
CA B:SER874 4.8 13.6 1.0
CB B:ASN908 4.8 14.1 1.0
CA B:SER870 4.8 14.1 1.0
N B:GLY868 4.8 14.4 1.0
CG B:ASP872 4.8 17.9 1.0
O B:SER907 4.9 14.6 1.0
N B:LEU873 4.9 12.9 1.0
OD1 B:ASP872 4.9 14.1 1.0
N B:THR909 4.9 12.7 1.0
C B:ASP872 5.0 13.2 1.0

Reference:

K.Okamoto, K.Matsumoto, R.Hille, B.T.Eger, E.F.Pai, T.Nishino. The Crystal Structure of Xanthine Oxidoreductase During Catalysis: Implications For Reaction Mechanism and Enzyme Inhibition. Proc.Natl.Acad.Sci.Usa V. 101 7931 2004.
ISSN: ISSN 0027-8424
PubMed: 15148401
DOI: 10.1073/PNAS.0400973101
Page generated: Sat Dec 12 03:24:44 2020

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