Atomistry » Calcium » PDB 3aau-3ati » 3am9
Atomistry »
  Calcium »
    PDB 3aau-3ati »
      3am9 »

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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy