Calcium in PDB 6ba0: Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis

The structure of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis, PDB code: 6ba0 was solved by N.Renner, D.A.Jacques, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.87 / 2.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.070, 79.360, 115.990, 90.00, 99.62, 90.00
R / Rfree (%)	18.6 / 21.8

The structure of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

The binding sites of Calcium atom in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis (pdb code 6ba0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis, PDB code: 6ba0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.2 occ:1.00 O A:HOH548 2.2 18.9 1.0 O A:THR124 2.4 13.9 1.0 OD1 A:ASP9 2.4 11.8 1.0 O A:HOH561 2.5 13.9 1.0 OD2 A:ASP240 2.5 17.4 1.0 OD2 A:ASP14 2.5 8.9 1.0 OD1 A:ASP14 2.5 10.1 1.0 O A:HOH604 2.6 14.5 1.0 CG A:ASP14 2.9 8.5 1.0 CG A:ASP240 3.5 13.3 1.0 C A:THR124 3.5 11.9 1.0 CG A:ASP9 3.6 13.3 1.0 OD1 A:ASP240 3.8 17.5 1.0 OD2 A:ASP9 4.1 12.7 1.0 OG1 A:THR124 4.1 14.2 1.0 CA A:GLY125 4.2 11.5 1.0 N A:GLY125 4.3 11.7 1.0 O A:ASP9 4.3 12.1 1.0 CB A:ASP14 4.3 8.6 1.0 CB A:THR124 4.4 11.2 1.0 N A:ASP9 4.4 13.0 1.0 ND2 A:ASN166 4.5 9.8 1.0 CA A:THR124 4.6 11.4 1.0 O A:HOH547 4.6 14.7 1.0 OD1 A:ASN166 4.7 12.0 1.0 C A:ASP9 4.7 11.8 1.0 N A:ASP14 4.7 12.0 1.0 CB A:ASP9 4.8 12.3 1.0 CA A:ASP9 4.9 14.2 1.0 CB A:ASP240 4.9 13.5 1.0 CA A:ASP14 4.9 11.6 1.0

Calcium binding site 2 out of 4 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:13.1 occ:1.00 O B:HOH508 2.3 19.5 1.0 O B:HOH583 2.4 13.3 1.0 O B:THR124 2.4 16.2 1.0 OD1 B:ASP9 2.4 14.9 1.0 O B:HOH558 2.4 19.7 1.0 OD2 B:ASP14 2.5 11.0 1.0 OD2 B:ASP240 2.5 16.6 1.0 OD1 B:ASP14 2.5 12.2 1.0 CG B:ASP14 2.9 13.1 1.0 C B:THR124 3.5 14.2 1.0 CG B:ASP9 3.5 13.3 1.0 CG B:ASP240 3.6 16.1 1.0 OD1 B:ASP240 3.8 18.9 1.0 OD2 B:ASP9 4.0 15.2 1.0 OG1 B:THR124 4.1 14.8 1.0 CA B:GLY125 4.2 13.8 1.0 N B:GLY125 4.2 12.3 1.0 O B:ASP9 4.3 10.4 1.0 CB B:ASP14 4.3 12.3 1.0 CB B:THR124 4.4 13.2 1.0 N B:ASP9 4.4 12.9 1.0 O B:HOH601 4.5 15.3 1.0 ND2 B:ASN166 4.5 11.1 1.0 CA B:THR124 4.5 16.5 1.0 OD1 B:ASN166 4.6 12.9 1.0 C B:ASP9 4.7 11.7 1.0 N B:ASP14 4.8 12.4 1.0 CB B:ASP9 4.8 12.3 1.0 CA B:ASP9 4.8 11.9 1.0 CB B:ASP240 4.9 15.4 1.0 CA B:ASP14 5.0 15.2 1.0

Calcium binding site 3 out of 4 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:14.8 occ:1.00 O C:HOH581 2.2 20.1 1.0 OD1 C:ASP9 2.4 14.2 1.0 O C:THR124 2.4 13.1 1.0 O C:HOH533 2.5 12.7 1.0 OD2 C:ASP240 2.5 11.5 1.0 OD2 C:ASP14 2.5 12.6 1.0 OD1 C:ASP14 2.5 15.0 1.0 O C:HOH616 2.5 22.8 1.0 CG C:ASP14 2.8 14.8 1.0 CG C:ASP240 3.5 17.5 1.0 C C:THR124 3.5 12.3 1.0 CG C:ASP9 3.6 15.4 1.0 OD1 C:ASP240 3.8 15.1 1.0 OD2 C:ASP9 4.1 12.7 1.0 OG1 C:THR124 4.1 16.8 1.0 CA C:GLY125 4.2 12.0 1.0 N C:GLY125 4.3 12.4 1.0 CB C:ASP14 4.3 17.1 1.0 O C:ASP9 4.3 11.0 1.0 CB C:THR124 4.4 16.2 1.0 N C:ASP9 4.4 11.2 1.0 ND2 C:ASN166 4.6 12.4 1.0 CA C:THR124 4.6 14.7 1.0 O C:HOH526 4.6 13.0 1.0 C C:ASP9 4.7 14.3 1.0 OD1 C:ASN166 4.7 13.4 1.0 N C:ASP14 4.7 12.0 1.0 CB C:ASP9 4.8 12.3 1.0 CA C:ASP9 4.8 13.8 1.0 CB C:ASP240 4.9 13.5 1.0 CA C:ASP14 4.9 14.3 1.0

Calcium binding site 4 out of 4 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:12.3 occ:1.00 O D:HOH563 2.3 19.6 1.0 O D:THR124 2.4 11.2 1.0 OD1 D:ASP9 2.4 15.2 1.0 O D:HOH614 2.5 15.9 1.0 O D:HOH530 2.5 13.1 1.0 OD2 D:ASP240 2.5 10.7 1.0 OD2 D:ASP14 2.5 8.8 1.0 OD1 D:ASP14 2.5 13.0 1.0 CG D:ASP14 2.9 11.0 1.0 C D:THR124 3.5 12.9 1.0 CG D:ASP240 3.5 11.5 1.0 CG D:ASP9 3.6 15.5 1.0 OD1 D:ASP240 3.8 13.3 1.0 OD2 D:ASP9 4.1 14.5 1.0 OG1 D:THR124 4.1 15.2 1.0 CA D:GLY125 4.2 10.6 1.0 N D:GLY125 4.2 10.5 1.0 CB D:ASP14 4.3 12.9 1.0 O D:ASP9 4.3 16.9 1.0 CB D:THR124 4.4 14.3 1.0 N D:ASP9 4.4 12.1 1.0 ND2 D:ASN166 4.5 11.7 1.0 CA D:THR124 4.5 13.2 1.0 O D:HOH582 4.6 9.6 1.0 OD1 D:ASN166 4.6 11.5 1.0 C D:ASP9 4.7 16.4 1.0 N D:ASP14 4.7 10.1 1.0 CB D:ASP9 4.8 13.2 1.0 CA D:ASP9 4.9 14.2 1.0 CB D:ASP240 4.9 11.9 1.0 CA D:ASP14 4.9 12.0 1.0

N.Renner, D.A.Jacques. Pyrimidine-Specific Ribonucleoside Hydrolase Rihb From Gardnerella Vaginalis To Be Published.