Sodium in PDB 3n0u: Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima

All present enzymatic activity of Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima:
4.2.99.18;

The structure of Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima, PDB code: 3n0u was solved by D.R.Cooper, A.Roy, Z.S.Derewenda, Integrated Center For Structure Andfunction Innovation (Isfi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.85 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.871, 93.635, 135.895, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 19

The binding sites of Sodium atom in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima (pdb code 3n0u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima, PDB code: 3n0u:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima


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 TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:22.1 occ:1.00 O A:ALA123 2.3 21.4 1.0 O A:VAL120 2.3 20.7 1.0 O A:ILE126 2.4 18.8 1.0 O A:HOH277 2.5 34.0 1.0 O A:HOH399 2.7 42.7 1.0 O A:LEU119 3.1 19.4 1.0 HA A:VAL120 3.2 23.2 1.0 C A:VAL120 3.2 23.7 1.0 H A:ILE126 3.3 20.1 1.0 C A:ALA123 3.4 19.7 1.0 H A:ALA123 3.4 21.4 1.0 HB A:ILE126 3.5 22.3 1.0 C A:ILE126 3.5 16.4 1.0 CA A:VAL120 3.7 19.3 1.0 N A:ALA123 3.8 17.9 1.0 N A:ILE126 4.0 16.8 1.0 HA A:LYS124 4.0 22.9 1.0 HB3 A:ALA123 4.1 24.2 1.0 CA A:ILE126 4.1 16.9 1.0 CA A:ALA123 4.1 18.3 1.0 O A:HOH303 4.1 53.6 1.0 C A:LEU119 4.1 18.8 1.0 HA2 A:GLY127 4.2 25.7 1.0 CB A:ILE126 4.2 18.6 1.0 N A:ARG121 4.2 21.8 1.0 H A:ASN122 4.3 25.7 1.0 C A:ARG121 4.3 20.9 1.0 N A:ASN122 4.3 21.4 1.0 N A:LYS124 4.4 18.6 1.0 HG22 A:ILE126 4.4 24.9 1.0 N A:VAL120 4.4 18.1 1.0 O A:HOH586 4.4 57.5 1.0 HG13 A:VAL120 4.5 31.6 1.0 N A:GLY127 4.5 17.8 1.0 HA A:ARG121 4.5 25.1 1.0 CA A:LYS124 4.6 19.1 1.0 CB A:ALA123 4.6 20.2 1.0 CA A:ARG121 4.6 20.9 1.0 O A:ARG121 4.6 25.6 1.0 H A:GLY125 4.6 21.8 1.0 C A:ASN122 4.7 21.0 1.0 HG12 A:VAL120 4.7 31.6 1.0 N A:GLY125 4.8 18.1 1.0 CG2 A:ILE126 4.8 20.7 1.0 C A:LYS124 4.8 17.4 1.0 CA A:GLY127 4.9 21.4 1.0 H A:ARG121 4.9 26.1 1.0 CG1 A:VAL120 4.9 26.3 1.0 CB A:VAL120 4.9 22.4 1.0 O A:HOH213 5.0 20.7 1.0 HD3 A:LYS124 5.0 44.6 1.0 HA A:ALA123 5.0 22.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima


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 TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:20.3 occ:1.00 O B:ILE126 2.3 18.1 1.0 O B:ALA123 2.3 19.8 1.0 O B:VAL120 2.4 19.1 1.0 O B:HOH267 2.5 35.7 1.0 O B:HOH298 2.6 35.4 1.0 O B:LEU119 2.8 17.9 1.0 HA B:VAL120 2.9 20.9 1.0 C B:VAL120 3.1 19.1 1.0 H B:ALA123 3.3 20.5 1.0 H B:ILE126 3.3 19.0 1.0 C B:ALA123 3.4 17.1 1.0 HB B:ILE126 3.4 18.9 1.0 C B:ILE126 3.4 17.0 1.0 CA B:VAL120 3.5 17.4 1.0 N B:ALA123 3.7 17.1 1.0 C B:LEU119 3.8 16.4 1.0 HB3 B:ALA123 3.9 24.8 1.0 N B:ILE126 4.0 15.8 1.0 CA B:ALA123 4.0 16.8 1.0 CA B:ILE126 4.1 15.9 1.0 HA B:LYS124 4.1 19.4 1.0 HA2 B:GLY127 4.1 19.4 1.0 N B:ARG121 4.1 19.7 1.0 CB B:ILE126 4.1 15.7 1.0 N B:VAL120 4.1 16.0 1.0 H B:ASN122 4.2 23.0 1.0 N B:ASN122 4.2 19.2 1.0 O B:HOH329 4.2 43.4 1.0 C B:ARG121 4.3 18.6 1.0 HG22 B:ILE126 4.3 24.6 1.0 N B:LYS124 4.4 17.5 1.0 HG13 B:VAL120 4.4 29.3 1.0 N B:GLY127 4.5 15.8 1.0 CB B:ALA123 4.5 20.7 1.0 C B:ASN122 4.6 23.3 1.0 CA B:LYS124 4.6 16.1 1.0 CA B:ARG121 4.6 20.1 1.0 O B:ARG121 4.6 22.9 1.0 HA B:ARG121 4.6 24.1 1.0 O B:HOH265 4.7 50.1 1.0 O B:HOH209 4.7 19.9 1.0 H B:GLY125 4.8 21.1 1.0 CG2 B:ILE126 4.8 20.5 1.0 H B:ARG121 4.8 23.6 1.0 CB B:VAL120 4.8 19.8 1.0 HG12 B:VAL120 4.8 29.3 1.0 CA B:GLY127 4.8 16.2 1.0 C B:LYS124 4.9 17.2 1.0 N B:GLY125 4.9 17.6 1.0 CG1 B:VAL120 4.9 24.4 1.0 HA B:ALA123 4.9 20.1 1.0 CA B:ASN122 4.9 20.4 1.0 H B:VAL120 5.0 19.2 1.0 HA B:ILE126 5.0 19.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ C:Na208 b:23.0 occ:1.00 O C:ALA123 2.3 21.3 1.0 O C:VAL120 2.4 22.1 1.0 O C:ILE126 2.4 18.5 1.0 O C:HOH334 2.5 32.9 1.0 O C:HOH415 2.6 34.5 1.0 O C:LEU119 3.0 20.8 1.0 HA C:VAL120 3.1 23.8 1.0 C C:VAL120 3.1 20.5 1.0 H C:ILE126 3.3 19.9 1.0 C C:ALA123 3.4 18.9 1.0 HB C:ILE126 3.4 19.8 1.0 H C:ALA123 3.4 22.5 1.0 C C:ILE126 3.5 20.6 1.0 CA C:VAL120 3.6 19.8 1.0 N C:ALA123 3.8 18.7 1.0 O C:HOH628 3.9 50.7 1.0 HB3 C:ALA123 4.0 23.3 1.0 HA C:LYS124 4.0 20.0 1.0 N C:ILE126 4.0 16.6 1.0 C C:LEU119 4.0 19.6 1.0 CA C:ALA123 4.1 17.7 1.0 CA C:ILE126 4.1 16.6 1.0 HA2 C:GLY127 4.1 23.6 1.0 N C:ARG121 4.2 21.2 1.0 CB C:ILE126 4.2 16.5 1.0 H C:ASN122 4.2 28.2 1.0 N C:ASN122 4.3 23.5 1.0 C C:ARG121 4.3 21.8 1.0 HG22 C:ILE126 4.3 24.1 1.0 N C:VAL120 4.3 18.1 1.0 N C:LYS124 4.3 18.1 1.0 HG13 C:VAL120 4.5 28.6 1.0 N C:GLY127 4.5 17.6 1.0 HA C:ARG121 4.5 29.1 1.0 CA C:LYS124 4.5 16.6 1.0 CB C:ALA123 4.6 19.4 1.0 CA C:ARG121 4.6 24.3 1.0 O C:ARG121 4.6 28.1 1.0 C C:ASN122 4.6 21.3 1.0 HG12 C:VAL120 4.7 28.6 1.0 H C:GLY125 4.7 23.1 1.0 CG2 C:ILE126 4.8 20.1 1.0 CA C:GLY127 4.8 19.6 1.0 H C:ARG121 4.8 25.5 1.0 C C:LYS124 4.8 16.1 1.0 CB C:VAL120 4.8 21.0 1.0 N C:GLY125 4.9 19.3 1.0 CG1 C:VAL120 4.9 23.8 1.0 HA C:ALA123 5.0 21.2 1.0 CA C:ASN122 5.0 21.9 1.0

D.R.Cooper, A.Roy, Z.S.Derewenda. Crystal Structure of TM1821, the 8-Oxoguanine Dna Glycosylase of Thermotoga Maritima To Be Published.