Sodium in PDB 7olb: Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi

All present enzymatic activity of Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi:
4.2.99.18;

The structure of Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi, PDB code: 7olb was solved by F.Coste, S.Goffinont, D.Flament, B.Castaing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.17 / 1.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.57, 35.92, 46.49, 95.5, 91.89, 108.41
R / Rfree (%)	14.4 / 15.7

The structure of Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi (pdb code 7olb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi, PDB code: 7olb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:27.5 occ:1.00 HA A:SER37 2.6 14.4 0.7 HA A:SER37 2.6 14.3 0.3 O A:SER32 2.8 12.6 1.0 O A:ILE35 2.9 12.5 1.0 HG A:SER37 3.0 18.6 0.7 HB2 A:SER32 3.1 13.0 1.0 OG A:SER37 3.1 15.5 0.7 HA A:SER32 3.2 12.5 1.0 HB3 A:SER37 3.3 15.9 0.3 CA A:SER37 3.3 11.9 0.3 CA A:SER37 3.3 12.0 0.7 HG12 A:VAL158 3.4 19.8 0.5 N A:SER37 3.4 12.0 1.0 C A:SER32 3.6 10.8 1.0 C A:ASP36 3.6 11.7 1.0 CA A:SER32 3.7 10.4 1.0 H A:SER37 3.7 14.4 0.7 H A:SER37 3.7 14.4 0.3 HG22 A:VAL158 3.8 18.6 0.5 HB2 A:PHE40 3.8 11.4 1.0 CB A:SER37 3.8 13.3 0.3 CB A:SER37 3.8 14.1 0.7 CB A:SER32 3.8 10.8 1.0 HG11 A:VAL158 3.9 19.8 0.5 HB3 A:PHE40 3.9 11.4 1.0 HA A:ASP36 4.0 14.9 1.0 O A:ASP36 4.0 11.2 1.0 CG1 A:VAL158 4.1 16.4 0.5 C A:ILE35 4.1 11.7 1.0 CB A:PHE40 4.2 9.5 1.0 HB2 A:SER37 4.2 15.9 0.3 HD2 A:PHE40 4.2 12.1 1.0 HB3 A:SER37 4.3 16.9 0.7 CA A:ASP36 4.3 12.4 1.0 HB3 A:SER32 4.4 13.0 1.0 CD2 A:PHE40 4.4 10.1 1.0 H A:ILE35 4.5 14.2 1.0 CG A:PHE40 4.5 9.5 1.0 HG22 A:ILE35 4.5 14.2 1.0 O A:HOH627 4.5 21.4 1.0 HB2 A:SER37 4.6 16.9 0.7 C A:SER37 4.6 11.0 1.0 HG13 A:VAL158 4.6 19.8 0.5 CG2 A:VAL158 4.6 15.5 0.5 HG23 A:ILE35 4.7 14.2 1.0 N A:ASP36 4.7 11.9 1.0 OG A:SER32 4.8 12.5 1.0 HG23 A:VAL158 4.8 18.6 0.5 O A:HOH673 4.8 57.8 1.0 HG21 A:VAL158 4.9 18.6 0.5 N A:LYS33 4.9 11.0 1.0 O A:SER37 4.9 11.4 1.0 HB A:VAL158 5.0 18.3 0.5 OG A:SER37 5.0 14.2 0.3

Sodium binding site 2 out of 2 in the Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:13.8 occ:1.00 H A:THR143 2.3 15.6 1.0 HB3 A:PRO172 2.7 25.9 1.0 HG22 A:VAL145 2.8 14.6 0.3 H A:PHE146 2.8 11.5 1.0 HB2 A:PHE146 2.9 11.8 1.0 O A:HOH557 3.1 16.6 1.0 HA A:THR143 3.1 13.9 1.0 N A:THR143 3.1 13.0 1.0 HA A:PRO172 3.4 24.0 1.0 HB A:VAL145 3.5 13.9 0.7 O4 A:CIT408 3.5 21.5 1.0 CA A:THR143 3.6 11.6 1.0 HA A:LYS142 3.6 19.0 1.0 CB A:PRO172 3.6 21.6 1.0 N A:PHE146 3.6 9.6 1.0 HD2 A:LYS142 3.6 24.3 1.0 CG2 A:VAL145 3.6 12.1 0.3 HB3 A:PHE146 3.6 11.8 1.0 CB A:PHE146 3.7 9.9 1.0 HG23 A:VAL145 3.7 14.6 0.3 H A:VAL145 3.8 12.0 0.3 H A:VAL145 3.9 12.0 0.7 O3 A:CIT408 3.9 22.4 1.0 HH22 A:ARG190 3.9 21.1 1.0 C A:THR143 4.0 10.5 1.0 CA A:PRO172 4.0 20.0 1.0 H A:GLU173 4.0 26.7 1.0 HG21 A:VAL145 4.1 14.6 0.3 HB2 A:PRO172 4.1 25.9 1.0 H A:VAL144 4.2 13.4 1.0 HH21 A:ARG190 4.2 21.1 1.0 C5 A:CIT408 4.2 20.7 1.0 C A:LYS142 4.2 14.6 1.0 CA A:PHE146 4.2 9.4 1.0 N A:VAL144 4.2 11.2 1.0 HG3 A:PRO172 4.3 25.1 1.0 N A:VAL145 4.3 10.0 1.0 CB A:VAL145 4.4 11.6 0.7 NH2 A:ARG190 4.4 17.6 1.0 CA A:LYS142 4.4 15.8 1.0 C A:VAL145 4.5 9.8 1.0 CG A:PRO172 4.6 20.9 1.0 O A:THR143 4.6 10.6 1.0 CD A:LYS142 4.6 20.3 1.0 HA A:PHE146 4.6 11.3 1.0 HG12 A:VAL145 4.6 14.1 0.7 O A:SER141 4.6 13.8 1.0 CA A:VAL145 4.6 10.1 0.7 N A:GLU173 4.6 22.3 1.0 CA A:VAL145 4.7 10.4 0.3 HZ1 A:LYS142 4.7 25.3 1.0 CB A:VAL145 4.7 11.7 0.3 C A:PRO172 4.8 22.1 1.0 CG A:PHE146 4.9 9.5 1.0 HG13 A:VAL145 4.9 14.4 0.3 HD3 A:LYS142 5.0 24.3 1.0

F.Coste, S.Goffinont, D.Flament, B.Castaing. Crystal Structure of Pab-Agog, An 8-Oxoguanine Dna Glycosylase From Pyrococcus Abyssi To Be Published.