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Calcium in PDB 3am9: Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051

Enzymatic activity of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051

All present enzymatic activity of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051, PDB code: 3am9 was solved by K.Matsumoto, K.Okamoto, N.Ashizawa, T.Matsumura, T.Kusano, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.44 / 2.17
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.916, 124.722, 146.195, 90.00, 91.04, 90.00
R / Rfree (%) 17.4 / 24.3

Other elements in 3am9:

The structure of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 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 Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 (pdb code 3am9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051, PDB code: 3am9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3am9

Go back to Calcium Binding Sites List in 3am9
Calcium binding site 1 out of 4 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

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

b:25.6
occ:1.00
OG A:SER874 2.6 26.2 1.0
O A:ASN908 2.7 22.6 1.0
O A:ALA867 2.7 22.6 1.0
OG A:SER907 2.8 20.2 1.0
O A:SER870 2.9 21.1 1.0
O A:ARG871 3.1 20.5 1.0
C A:ARG871 3.5 21.7 1.0
N A:ASN908 3.5 22.8 1.0
C A:ALA867 3.8 21.8 1.0
C A:ASN908 3.8 22.0 1.0
CB A:ASP872 3.8 23.6 1.0
C A:SER870 3.8 21.8 1.0
CB A:SER874 3.9 23.0 1.0
CB A:SER907 4.0 18.5 1.0
C A:SER907 4.0 21.7 1.0
CB A:ALA867 4.1 21.5 1.0
CA A:SER907 4.1 20.0 1.0
NE2 A:HIS840 4.2 22.3 1.0
CA A:ALA867 4.2 22.5 1.0
CA A:ARG871 4.2 23.1 1.0
CA A:ASN908 4.2 21.1 1.0
N A:ASP872 4.2 22.8 1.0
N A:ARG871 4.4 21.5 1.0
CA A:ASP872 4.5 22.8 1.0
OG A:SER870 4.5 22.5 1.0
CE1 A:HIS840 4.6 22.2 1.0
N A:SER874 4.6 21.2 1.0
N A:SER870 4.7 21.0 1.0
O A:SER907 4.8 22.8 1.0
CB A:ASN908 4.8 21.4 1.0
CA A:SER874 4.8 23.7 1.0
N A:LEU873 4.9 22.4 1.0
CG A:ASP872 4.9 24.1 1.0
CA A:SER870 4.9 22.7 1.0
OD1 A:ASP872 4.9 20.1 1.0
N A:GLY868 4.9 21.6 1.0
C A:ASP872 4.9 23.4 1.0
N A:THR909 4.9 20.7 1.0

Calcium binding site 2 out of 4 in 3am9

Go back to Calcium Binding Sites List in 3am9
Calcium binding site 2 out of 4 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1336

b:38.6
occ:1.00
O A:GLY837 2.5 17.7 1.0
O A:HOH2311 2.6 23.5 1.0
ND1 A:HIS741 2.7 12.0 1.0
OG1 A:THR836 2.7 15.5 1.0
OH A:TYR743 2.8 16.8 1.0
CE1 A:HIS741 3.3 15.1 1.0
C A:GLY837 3.7 19.4 1.0
CB A:THR836 3.8 21.1 1.0
O A:THR836 3.8 19.8 1.0
CG A:HIS741 3.8 14.4 1.0
CZ A:TYR743 3.9 21.0 1.0
C A:THR836 3.9 21.3 1.0
OD2 A:ASP832 3.9 19.4 1.0
N A:GLY837 4.1 21.2 1.0
CE2 A:TYR743 4.2 15.6 1.0
CB A:HIS741 4.3 16.6 1.0
OD2 A:ASP740 4.4 20.9 1.0
CA A:THR836 4.4 20.6 1.0
N A:HIS741 4.5 18.6 1.0
CA A:GLY837 4.5 19.5 1.0
O A:ASP832 4.5 18.8 1.0
NE2 A:HIS741 4.5 17.2 1.0
NE2 A:HIS747 4.6 19.7 1.0
N A:GLY838 4.7 18.8 1.0
CA A:GLY800 4.8 18.1 1.0
CA A:GLY838 4.8 17.1 1.0
CD2 A:HIS741 4.8 12.0 1.0
O A:GLY800 4.9 18.2 1.0
CG2 A:THR836 4.9 20.6 1.0
CE1 A:TYR743 5.0 19.3 1.0

Calcium binding site 3 out of 4 in 3am9

Go back to Calcium Binding Sites List in 3am9
Calcium binding site 3 out of 4 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4008

b:21.2
occ:1.00
OG B:SER874 2.6 22.0 1.0
O B:ALA867 2.7 18.7 1.0
O B:SER870 2.7 18.5 1.0
O B:ASN908 2.8 18.0 1.0
OG B:SER907 2.8 17.2 1.0
O B:ARG871 2.8 22.7 1.0
C B:ARG871 3.4 21.0 1.0
N B:ASN908 3.5 17.0 1.0
C B:ALA867 3.7 18.5 1.0
C B:SER870 3.7 21.1 1.0
CB B:ASP872 3.7 18.2 1.0
C B:ASN908 3.8 17.4 1.0
CB B:SER874 3.9 19.1 1.0
CB B:ALA867 3.9 19.7 1.0
CB B:SER907 4.0 17.4 1.0
N B:ASP872 4.0 20.9 1.0
NE2 B:HIS840 4.0 17.1 1.0
C B:SER907 4.1 17.4 1.0
CA B:ALA867 4.1 18.2 1.0
CA B:ARG871 4.1 22.2 1.0
CA B:SER907 4.1 17.2 1.0
CA B:ASN908 4.2 17.4 1.0
N B:ARG871 4.4 22.1 1.0
CA B:ASP872 4.4 19.9 1.0
N B:SER874 4.5 18.5 1.0
OG B:SER870 4.5 19.2 1.0
CE1 B:HIS840 4.6 18.5 1.0
CA B:SER874 4.7 19.8 1.0
N B:LEU873 4.8 19.3 1.0
N B:SER870 4.8 19.8 1.0
CB B:ASN908 4.8 16.5 1.0
N B:GLY868 4.8 18.5 1.0
C B:ASP872 4.9 20.5 1.0
CA B:SER870 4.9 20.4 1.0
O B:SER907 4.9 17.0 1.0
CG B:ASP872 4.9 18.6 1.0
N B:THR909 5.0 17.4 1.0

Calcium binding site 4 out of 4 in 3am9

Go back to Calcium Binding Sites List in 3am9
Calcium binding site 4 out of 4 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1337

b:34.2
occ:1.00
OG1 B:THR836 2.5 15.9 1.0
O B:HOH2257 2.6 16.7 1.0
O B:GLY837 2.6 17.7 1.0
OH B:TYR743 2.7 12.4 1.0
ND1 B:HIS741 2.8 17.1 1.0
CE1 B:HIS741 3.5 13.7 1.0
CB B:THR836 3.7 18.9 1.0
CZ B:TYR743 3.7 16.4 1.0
OD2 B:ASP832 3.7 17.4 1.0
O B:THR836 3.8 19.5 1.0
C B:GLY837 3.8 18.6 1.0
C B:THR836 3.9 19.2 1.0
CG B:HIS741 3.9 16.4 1.0
CE2 B:TYR743 4.1 17.6 1.0
OD2 B:ASP740 4.2 24.0 1.0
N B:GLY837 4.3 19.2 1.0
CB B:HIS741 4.3 16.6 1.0
CA B:THR836 4.4 18.8 1.0
O B:ASP832 4.4 15.7 1.0
NE2 B:HIS747 4.5 15.8 1.0
N B:HIS741 4.5 16.9 1.0
CA B:GLY837 4.6 18.2 1.0
NE2 B:HIS741 4.7 16.7 1.0
CE1 B:TYR743 4.7 12.1 1.0
N B:GLY838 4.8 15.7 1.0
CG2 B:THR836 4.8 17.2 1.0
CA B:GLY838 4.9 15.2 1.0
CA B:GLY800 4.9 13.3 1.0
CG B:ASP832 4.9 18.4 1.0
CD2 B:HIS741 4.9 14.2 1.0
CG B:ASP740 5.0 19.2 1.0
CD2 B:HIS747 5.0 12.9 1.0

Reference:

K.Matsumoto, K.Okamoto, N.Ashizawa, T.Nishino. Fyx-051: A Novel and Potent Hybrid-Type Inhibitor of Xanthine Oxidoreductase J.Pharmacol.Exp.Ther. V. 336 95 2011.
ISSN: ISSN 0022-3565
PubMed: 20952484
DOI: 10.1124/JPET.110.174540
Page generated: Sat Dec 12 04:04:41 2020

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