Atomistry » Calcium » PDB 1v3e-1vfm » 1vdv
Atomistry »
  Calcium »
    PDB 1v3e-1vfm »
      1vdv »

Calcium in PDB 1vdv: Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form

Enzymatic activity of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form

All present enzymatic activity of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form:
1.1.1.204;

Protein crystallography data

The structure of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form, PDB code: 1vdv was solved by A.Fukunari, K.Okamoto, T.Nishino, B.T.Eger, E.F.Pai, M.Kamezawa, I.Yamada, N.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.817, 123.940, 148.888, 90.00, 91.16, 90.00
R / Rfree (%) 17.8 / 21.5

Other elements in 1vdv:

The structure of Bovine Milk Xanthine Dehydrogenase Y-700 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 Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form (pdb code 1vdv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form, PDB code: 1vdv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1vdv

Go back to Calcium Binding Sites List in 1vdv
Calcium binding site 1 out of 4 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5301

b:15.1
occ:1.00
O A:ALA867 2.6 12.5 1.0
OG A:SER907 2.7 8.5 1.0
O A:SER870 2.7 12.6 1.0
O A:ASN908 2.7 14.7 1.0
OG A:SER874 2.7 14.5 1.0
O A:ARG871 3.0 16.1 1.0
N A:ASN908 3.5 12.3 1.0
C A:ARG871 3.6 14.4 1.0
C A:ALA867 3.7 14.4 1.0
CB A:ASP872 3.7 11.2 1.0
C A:SER870 3.7 13.1 1.0
C A:ASN908 3.8 15.0 1.0
CB A:SER907 3.9 10.8 1.0
CB A:SER874 3.9 14.5 1.0
C A:SER907 4.0 13.7 1.0
CB A:ALA867 4.0 15.4 1.0
NE2 A:HIS840 4.0 14.2 1.0
CA A:SER907 4.1 12.2 1.0
CA A:ALA867 4.1 15.1 1.0
CA A:ASN908 4.2 13.9 1.0
CA A:ARG871 4.2 14.6 1.0
N A:ASP872 4.3 13.3 1.0
N A:ARG871 4.4 13.8 1.0
OG A:SER870 4.4 16.1 1.0
CA A:ASP872 4.5 12.7 1.0
N A:SER874 4.5 12.0 1.0
CE1 A:HIS840 4.6 16.2 1.0
N A:GLY868 4.8 13.9 1.0
N A:SER870 4.8 13.8 1.0
CB A:ASN908 4.8 13.5 1.0
CA A:SER874 4.8 14.7 1.0
CA A:SER870 4.8 14.1 1.0
CG A:ASP872 4.8 12.4 1.0
N A:LEU873 4.9 10.5 1.0
O A:SER907 4.9 12.4 1.0
OD1 A:ASP872 4.9 11.9 1.0
N A:THR909 4.9 13.8 1.0

Calcium binding site 2 out of 4 in 1vdv

Go back to Calcium Binding Sites List in 1vdv
Calcium binding site 2 out of 4 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5304

b:23.5
occ:1.00
OG1 A:THR836 2.5 10.3 1.0
O A:HOH6075 2.6 43.0 1.0
O A:GLY837 2.6 8.6 1.0
O A:HOH5508 2.7 14.5 1.0
OH A:TYR743 2.8 10.8 1.0
ND1 A:HIS741 2.8 14.6 1.0
CE1 A:HIS741 3.4 11.0 1.0
CB A:THR836 3.6 11.0 1.0
CZ A:TYR743 3.8 13.3 1.0
C A:GLY837 3.8 14.2 1.0
OD2 A:ASP832 3.8 13.3 1.0
O A:THR836 3.8 14.3 1.0
C A:THR836 3.9 13.4 1.0
CG A:HIS741 4.0 14.1 1.0
N A:GLY837 4.2 14.1 1.0
CE2 A:TYR743 4.2 9.6 1.0
CA A:THR836 4.3 11.6 1.0
OD2 A:ASP740 4.4 12.7 1.0
O A:ASP832 4.4 10.8 1.0
CB A:HIS741 4.4 11.6 1.0
CA A:GLY837 4.6 10.9 1.0
NE2 A:HIS747 4.6 17.0 1.0
NE2 A:HIS741 4.7 13.1 1.0
N A:HIS741 4.7 12.7 1.0
CG2 A:THR836 4.8 10.6 1.0
CA A:GLY800 4.8 10.4 1.0
N A:GLY838 4.8 10.5 1.0
CE1 A:TYR743 4.8 6.8 1.0
CA A:GLY838 4.9 11.1 1.0
CD2 A:HIS741 4.9 13.0 1.0
CG A:ASP740 4.9 12.5 1.0
O A:GLY800 5.0 10.3 1.0

Calcium binding site 3 out of 4 in 1vdv

Go back to Calcium Binding Sites List in 1vdv
Calcium binding site 3 out of 4 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5302

b:15.4
occ:1.00
O B:ALA867 2.6 14.3 1.0
OG B:SER907 2.6 14.6 1.0
O B:ASN908 2.7 15.7 1.0
O B:SER870 2.7 15.4 1.0
OG B:SER874 2.8 19.5 1.0
O B:ARG871 3.0 17.2 1.0
N B:ASN908 3.5 16.0 1.0
C B:ARG871 3.6 16.2 1.0
C B:ALA867 3.7 14.7 1.0
CB B:ASP872 3.7 13.2 1.0
C B:SER870 3.8 14.3 1.0
C B:ASN908 3.8 16.7 1.0
CB B:SER907 3.8 14.2 1.0
C B:SER907 4.0 17.0 1.0
CB B:SER874 4.0 18.6 1.0
CA B:SER907 4.0 14.6 1.0
NE2 B:HIS840 4.1 10.6 1.0
CB B:ALA867 4.1 14.3 1.0
CA B:ALA867 4.1 15.4 1.0
CA B:ASN908 4.2 15.8 1.0
CA B:ARG871 4.2 17.1 1.0
N B:ASP872 4.3 15.4 1.0
OG B:SER870 4.4 15.6 1.0
N B:ARG871 4.4 16.7 1.0
CA B:ASP872 4.6 14.6 1.0
N B:SER874 4.6 13.4 1.0
CE1 B:HIS840 4.6 10.4 1.0
N B:SER870 4.8 13.8 1.0
N B:GLY868 4.8 16.4 1.0
CA B:SER870 4.8 14.9 1.0
CG B:ASP872 4.8 16.6 1.0
CA B:SER874 4.8 18.7 1.0
O B:SER907 4.8 12.9 1.0
CB B:ASN908 4.8 18.4 1.0
N B:LEU873 4.9 13.6 1.0
OD1 B:ASP872 4.9 12.3 1.0
N B:THR909 5.0 13.0 1.0

Calcium binding site 4 out of 4 in 1vdv

Go back to Calcium Binding Sites List in 1vdv
Calcium binding site 4 out of 4 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5303

b:22.8
occ:1.00
O B:HOH6328 2.5 27.4 1.0
O B:GLY837 2.6 9.9 1.0
OG1 B:THR836 2.6 10.5 1.0
O B:HOH5367 2.6 12.7 1.0
ND1 B:HIS741 2.7 10.9 1.0
OH B:TYR743 2.8 11.9 1.0
CE1 B:HIS741 3.2 11.3 1.0
CB B:THR836 3.6 12.8 1.0
O B:THR836 3.7 13.3 1.0
C B:GLY837 3.8 14.5 1.0
CZ B:TYR743 3.8 13.9 1.0
CG B:HIS741 3.8 11.3 1.0
C B:THR836 3.9 12.0 1.0
OD2 B:ASP832 3.9 9.0 1.0
CE2 B:TYR743 4.2 11.6 1.0
N B:GLY837 4.3 14.4 1.0
CA B:THR836 4.3 11.1 1.0
CB B:HIS741 4.4 9.9 1.0
NE2 B:HIS741 4.5 9.9 1.0
OD2 B:ASP740 4.5 18.0 1.0
NE2 B:HIS747 4.5 13.8 1.0
O B:ASP832 4.5 12.0 1.0
CA B:GLY837 4.6 12.7 1.0
N B:HIS741 4.6 14.3 1.0
CA B:GLY800 4.7 9.9 1.0
CD2 B:HIS741 4.8 6.1 1.0
N B:GLY838 4.8 11.3 1.0
CA B:GLY838 4.8 12.5 1.0
CG2 B:THR836 4.8 9.7 1.0
O B:GLY800 4.9 11.6 1.0
CE1 B:TYR743 4.9 10.7 1.0

Reference:

A.Fukunari, K.Okamoto, T.Nishino, B.T.Eger, E.F.Pai, M.Kamezawa, I.Yamada, N.Kato. Y-700 [1-[3-Cyano-4-(2,2-Dimethylpropoxy)Phenyl]-1H- Pyrazole-4-Carboxylic Acid]: A Potent Xanthine Oxidoreductase Inhibitor with Hepatic Excretion J.Pharmacol.Exp.Ther. V. 311 519 2004.
ISSN: ISSN 0022-3565
PubMed: 15190124
DOI: 10.1124/JPET.104.070433
Page generated: Sat Dec 12 03:24:52 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