Calcium in PDB 6ba1: Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis

All present enzymatic activity of Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis:
3.2.2.1;

The structure of Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis, PDB code: 6ba1 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)	80.24 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	163.270, 80.240, 223.820, 90.00, 106.50, 90.00
R / Rfree (%)	27.9 / 28.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis (pdb code 6ba1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis, PDB code: 6ba1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Purine-Preferring 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 Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:21.2 occ:1.00 OD2 A:ASP245 2.5 20.6 1.0 OD1 A:ASP14 2.5 21.8 1.0 OD1 A:ASP9 2.6 21.9 1.0 O A:THR127 2.6 20.6 1.0 OD2 A:ASP14 3.2 21.3 1.0 ND2 A:ASN38 3.2 22.9 1.0 CG A:ASP14 3.3 21.6 1.0 CG A:ASP9 3.5 22.4 1.0 OD1 A:ASP13 3.5 21.9 1.0 CG A:ASP245 3.5 20.5 1.0 OD2 A:ASP9 3.6 22.6 1.0 OD1 A:ASP245 3.7 20.6 1.0 OD1 A:ASN170 3.7 21.3 1.0 C A:THR127 3.8 20.5 1.0 ND2 A:ASN170 3.9 20.5 1.0 CG A:ASN38 4.0 23.5 1.0 OD1 A:ASN38 4.2 23.4 1.0 OG1 A:THR127 4.2 20.4 1.0 CG A:ASN170 4.3 20.9 1.0 CA A:GLY128 4.6 21.3 1.0 CG A:ASP13 4.6 22.2 1.0 N A:GLY128 4.6 20.8 1.0 CB A:THR127 4.7 20.1 1.0 O A:ASP9 4.7 23.4 1.0 CB A:ASP14 4.7 22.1 1.0 CA A:THR127 4.9 20.2 1.0 CB A:ASP245 4.9 20.5 1.0 CB A:ASP9 4.9 23.1 1.0

Calcium binding site 2 out of 18 in the Purine-Preferring 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 Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:27.0 occ:1.00 O B:THR127 2.5 26.4 1.0 OD1 B:ASP9 2.5 27.5 1.0 OD2 B:ASP245 2.5 26.5 1.0 OD1 B:ASP14 2.6 27.4 1.0 OD2 B:ASP14 3.2 26.8 1.0 CG B:ASP14 3.3 27.1 1.0 ND2 B:ASN38 3.4 28.9 1.0 CG B:ASP9 3.4 28.1 1.0 CG B:ASP245 3.5 26.6 1.0 OD2 B:ASP9 3.5 28.5 1.0 OD1 B:ASP13 3.6 28.0 1.0 OD1 B:ASN170 3.6 27.4 1.0 C B:THR127 3.7 26.3 1.0 OD1 B:ASP245 3.7 26.7 1.0 ND2 B:ASN170 3.9 26.5 1.0 CG B:ASN38 4.1 29.6 1.0 OG1 B:THR127 4.1 26.2 1.0 CG B:ASN170 4.2 26.9 1.0 OD1 B:ASN38 4.2 29.7 1.0 CA B:GLY128 4.5 27.1 1.0 N B:GLY128 4.5 26.7 1.0 CB B:THR127 4.6 26.1 1.0 CG B:ASP13 4.7 28.5 1.0 O B:ASP9 4.7 28.6 1.0 CA B:THR127 4.8 26.1 1.0 CB B:ASP14 4.8 27.4 1.0 CB B:ASP9 4.9 28.6 1.0 CB B:ASP245 4.9 26.7 1.0

Calcium binding site 3 out of 18 in the Purine-Preferring 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 Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca400 b:24.4 occ:1.00 O C:THR127 2.3 24.0 1.0 OD2 C:ASP245 2.4 24.0 1.0 OD1 C:ASP9 2.6 25.2 1.0 OD1 C:ASP14 2.6 25.1 1.0 OD2 C:ASP14 3.1 24.8 1.0 CG C:ASP14 3.2 25.0 1.0 CG C:ASP245 3.4 23.9 1.0 ND2 C:ASN38 3.5 26.1 1.0 CG C:ASP9 3.5 25.7 1.0 C C:THR127 3.6 24.0 1.0 OD1 C:ASP13 3.6 25.2 1.0 OD1 C:ASP245 3.6 23.9 1.0 OD2 C:ASP9 3.7 25.8 1.0 OD1 C:ASN170 3.7 24.4 1.0 ND2 C:ASN170 3.8 23.5 1.0 OG1 C:THR127 4.0 24.0 1.0 CG C:ASN170 4.2 23.9 1.0 CG C:ASN38 4.3 26.6 1.0 OD1 C:ASN38 4.4 26.5 1.0 N C:GLY128 4.4 24.4 1.0 CA C:GLY128 4.4 24.8 1.0 CB C:THR127 4.4 23.7 1.0 CA C:THR127 4.6 23.8 1.0 CG C:ASP13 4.7 25.5 1.0 CB C:ASP14 4.7 25.4 1.0 CB C:ASP245 4.8 24.0 1.0 O C:ASP9 4.8 26.6 1.0 CB C:ASP9 5.0 26.5 1.0

Calcium binding site 4 out of 18 in the Purine-Preferring 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 Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca400 b:30.0 occ:1.00 OD2 D:ASP245 2.5 29.1 1.0 O D:THR127 2.5 27.9 1.0 OD1 D:ASP9 2.6 30.5 1.0 OD1 D:ASP14 2.6 31.4 1.0 OD2 D:ASP14 3.3 29.6 1.0 CG D:ASP14 3.3 30.7 1.0 ND2 D:ASN38 3.4 33.8 1.0 CG D:ASP245 3.4 29.1 1.0 CG D:ASP9 3.5 31.3 1.0 OD1 D:ASP13 3.5 32.5 1.0 OD1 D:ASP245 3.6 29.4 1.0 OD1 D:ASN170 3.6 29.1 1.0 OD2 D:ASP9 3.7 31.8 1.0 C D:THR127 3.7 27.2 1.0 ND2 D:ASN170 3.8 27.9 1.0 OG1 D:THR127 4.1 27.6 1.0 CG D:ASN170 4.1 28.2 1.0 CG D:ASN38 4.2 34.6 1.0 OD1 D:ASN38 4.3 34.5 1.0 CA D:GLY128 4.5 28.0 1.0 N D:GLY128 4.5 27.2 1.0 CB D:THR127 4.6 26.9 1.0 CG D:ASP13 4.7 33.3 1.0 CA D:THR127 4.7 26.5 1.0 CB D:ASP14 4.8 31.4 1.0 O D:ASP9 4.8 33.4 1.0 CB D:ASP245 4.8 29.0 1.0 CB D:ASP9 5.0 32.0 1.0

Calcium binding site 5 out of 18 in the Purine-Preferring 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 5 of Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca400 b:32.0 occ:1.00 OD1 E:ASP14 2.5 32.9 1.0 OD2 E:ASP245 2.6 31.9 1.0 OD1 E:ASP9 2.7 32.1 1.0 O E:THR127 2.8 31.1 1.0 ND2 E:ASN38 3.1 33.6 1.0 CG E:ASP14 3.3 32.8 1.0 OD1 E:ASP13 3.3 33.5 1.0 OD2 E:ASP14 3.3 32.2 1.0 CG E:ASP245 3.5 32.1 1.0 CG E:ASP9 3.5 32.4 1.0 OD2 E:ASP9 3.6 32.4 1.0 OD1 E:ASP245 3.7 32.1 1.0 OD1 E:ASN170 3.8 31.0 1.0 CG E:ASN38 3.9 33.9 1.0 OD1 E:ASN38 4.0 33.6 1.0 ND2 E:ASN170 4.0 30.6 1.0 C E:THR127 4.1 30.9 1.0 OG1 E:THR127 4.4 31.6 1.0 CG E:ASN170 4.4 30.6 1.0 CG E:ASP13 4.4 34.1 1.0 O E:ASP9 4.7 33.6 1.0 CB E:ASP14 4.7 33.4 1.0 CA E:GLY128 4.8 31.0 1.0 N E:GLY128 4.9 30.9 1.0 CB E:THR127 4.9 31.2 1.0 OD2 E:ASP13 4.9 34.4 1.0 CB E:ASP245 4.9 32.4 1.0 CB E:ASP9 5.0 32.8 1.0

Calcium binding site 6 out of 18 in the Purine-Preferring 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 6 of Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca400 b:30.5 occ:1.00 OD2 F:ASP245 2.5 29.4 1.0 OD1 F:ASP14 2.6 30.6 1.0 O F:THR127 2.7 29.5 1.0 OD1 F:ASP9 2.8 30.9 1.0 ND2 F:ASN38 3.2 32.6 1.0 OD1 F:ASP13 3.4 31.1 1.0 CG F:ASP14 3.4 30.1 1.0 OD2 F:ASP14 3.4 29.7 1.0 CG F:ASP245 3.4 29.3 1.0 OD1 F:ASP245 3.6 29.6 1.0 CG F:ASP9 3.6 31.7 1.0 OD1 F:ASN170 3.7 31.1 1.0 OD2 F:ASP9 3.7 32.3 1.0 ND2 F:ASN170 3.8 30.0 1.0 C F:THR127 4.0 29.3 1.0 CG F:ASN38 4.0 33.5 1.0 OD1 F:ASN38 4.1 33.7 1.0 CG F:ASN170 4.2 30.6 1.0 OG1 F:THR127 4.3 28.7 1.0 CG F:ASP13 4.5 31.5 1.0 CA F:GLY128 4.7 30.4 1.0 CB F:THR127 4.8 28.5 1.0 N F:GLY128 4.8 29.7 1.0 O F:ASP9 4.8 32.1 1.0 CB F:ASP14 4.9 30.1 1.0 CB F:ASP245 4.9 29.0 1.0 OD2 F:ASP13 4.9 32.3 1.0 CA F:THR127 5.0 28.8 1.0

Calcium binding site 7 out of 18 in the Purine-Preferring 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 7 of Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca400 b:28.2 occ:1.00 OD2 G:ASP245 2.6 28.3 1.0 O G:THR127 2.7 27.3 1.0 OD1 G:ASP9 2.8 28.2 1.0 OD1 G:ASP14 2.8 29.0 1.0 ND2 G:ASN38 3.3 30.0 1.0 CG G:ASP245 3.5 28.6 1.0 OD1 G:ASP13 3.5 30.1 1.0 OD1 G:ASN170 3.5 27.5 1.0 OD1 G:ASP245 3.6 28.7 1.0 OD2 G:ASP14 3.6 28.3 1.0 CG G:ASP14 3.6 28.9 1.0 CG G:ASP9 3.7 28.6 1.0 OD2 G:ASP9 3.7 28.8 1.0 ND2 G:ASN170 3.7 27.1 1.0 C G:THR127 3.9 27.2 1.0 CG G:ASN170 4.0 27.1 1.0 CG G:ASN38 4.1 30.3 1.0 OD1 G:ASN38 4.1 30.3 1.0 OG1 G:THR127 4.4 27.9 1.0 CG G:ASP13 4.6 30.9 1.0 CA G:GLY128 4.7 27.4 1.0 N G:GLY128 4.7 27.2 1.0 CB G:THR127 4.8 27.6 1.0 CA G:THR127 4.9 27.2 1.0 CB G:ASP245 4.9 29.1 1.0 OD2 G:ASP13 5.0 31.4 1.0 O G:ASP9 5.0 29.7 1.0

Calcium binding site 8 out of 18 in the Purine-Preferring 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 8 of Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca400 b:36.2 occ:1.00 OD1 H:ASP14 2.7 36.5 1.0 OD1 H:ASP9 2.7 35.7 1.0 OD2 H:ASP245 2.7 34.9 1.0 O H:THR127 2.8 33.8 1.0 ND2 H:ASN38 3.1 38.9 1.0 OD1 H:ASP13 3.4 38.1 1.0 CG H:ASP14 3.5 35.7 1.0 CG H:ASP9 3.5 36.4 1.0 OD2 H:ASP9 3.5 37.1 1.0 OD2 H:ASP14 3.6 34.8 1.0 OD1 H:ASN170 3.6 35.5 1.0 CG H:ASP245 3.6 35.1 1.0 OD1 H:ASP245 3.7 35.6 1.0 CG H:ASN38 3.8 39.7 1.0 ND2 H:ASN170 3.9 34.5 1.0 OD1 H:ASN38 3.9 40.0 1.0 C H:THR127 4.1 33.1 1.0 CG H:ASN170 4.2 34.9 1.0 OG1 H:THR127 4.5 33.3 1.0 CG H:ASP13 4.5 39.0 1.0 CA H:GLY128 4.8 33.8 1.0 O H:ASP9 4.8 37.6 1.0 N H:GLY128 4.9 33.0 1.0 OD2 H:ASP13 5.0 40.0 1.0 CB H:THR127 5.0 32.7 1.0 CB H:ASP14 5.0 36.1 1.0

Calcium binding site 9 out of 18 in the Purine-Preferring 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 9 of Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca400 b:32.9 occ:1.00 OD2 I:ASP245 2.6 32.7 1.0 OD1 I:ASP14 2.7 35.3 1.0 OD1 I:ASP13 3.0 35.9 1.0 ND2 I:ASN38 3.1 36.1 1.0 O I:THR127 3.1 30.8 1.0 OD1 I:ASP9 3.1 33.2 1.0 CG I:ASP245 3.4 32.7 1.0 OD1 I:ASP245 3.4 32.5 1.0 CG I:ASP14 3.6 35.2 1.0 OD2 I:ASP14 3.7 34.1 1.0 OD2 I:ASP9 3.9 33.1 1.0 OD1 I:ASN170 3.9 29.8 1.0 CG I:ASP9 3.9 33.5 1.0 CG I:ASN38 3.9 36.0 1.0 OD1 I:ASN38 4.0 35.1 1.0 ND2 I:ASN170 4.0 29.1 1.0 CG I:ASP13 4.1 36.8 1.0 C I:THR127 4.3 30.2 1.0 CG I:ASN170 4.4 29.0 1.0 OD2 I:ASP13 4.5 37.0 1.0 OG1 I:THR127 4.6 32.0 1.0 CB I:ASP245 4.8 33.3 1.0 CB I:ASP14 5.0 36.9 1.0 O I:ASP9 5.0 36.9 1.0

Calcium binding site 10 out of 18 in the Purine-Preferring 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 10 of Purine-Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca400 b:31.8 occ:1.00 OD2 J:ASP245 2.5 31.2 1.0 OD1 J:ASP14 2.5 33.3 1.0 O J:THR127 2.7 29.8 1.0 OD1 J:ASP9 2.7 32.0 1.0 ND2 J:ASN38 3.2 35.0 1.0 CG J:ASP14 3.3 33.0 1.0 OD1 J:ASP13 3.3 34.5 1.0 OD2 J:ASP14 3.3 31.9 1.0 CG J:ASP245 3.4 31.3 1.0 OD1 J:ASP245 3.5 31.4 1.0 CG J:ASP9 3.6 32.6 1.0 OD2 J:ASP9 3.7 32.9 1.0 OD1 J:ASN170 3.8 30.4 1.0 ND2 J:ASN170 3.9 29.2 1.0 C J:THR127 4.0 29.2 1.0 CG J:ASN38 4.0 35.6 1.0 OD1 J:ASN38 4.2 35.3 1.0 OG1 J:THR127 4.3 30.2 1.0 CG J:ASN170 4.3 29.6 1.0 CG J:ASP13 4.4 35.5 1.0 CB J:THR127 4.7 29.3 1.0 CB J:ASP14 4.8 34.1 1.0 CA J:GLY128 4.8 29.9 1.0 N J:GLY128 4.8 29.3 1.0 O J:ASP9 4.8 34.8 1.0 CB J:ASP245 4.8 31.6 1.0 OD2 J:ASP13 4.9 36.1 1.0 CA J:THR127 5.0 28.8 1.0

N.Renner, D.A.Jacques. Inosine-Uridine Preferring Ribonucleoside Hydrolase From Gardnerella Vaginalis To Be Published.