Sodium in PDB 1diz: Crystal Structure of E. Coli 3-Methyladenine Dna Glycosylase (Alka) Complexed with Dna

All present enzymatic activity of Crystal Structure of E. Coli 3-Methyladenine Dna Glycosylase (Alka) Complexed with Dna:
3.2.2.21;

The structure of Crystal Structure of E. Coli 3-Methyladenine Dna Glycosylase (Alka) Complexed with Dna, PDB code: 1diz was solved by T.Hollis, Y.Ichikawa, T.E.Ellenberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.400, 82.400, 199.700, 90.00, 90.00, 120.00
R / Rfree (%)	25 / 29

The binding sites of Sodium atom in the Crystal Structure of E. Coli 3-Methyladenine Dna Glycosylase (Alka) Complexed with Dna (pdb code 1diz). 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 E. Coli 3-Methyladenine Dna Glycosylase (Alka) Complexed with Dna, PDB code: 1diz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of E. Coli 3-Methyladenine Dna Glycosylase (Alka) Complexed with Dna


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 E. Coli 3-Methyladenine Dna Glycosylase (Alka) Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na825 b:46.0 occ:1.00 OP2 E:DC11 2.5 44.5 1.0 O A:GLN210 2.5 41.9 1.0 O A:HOH850 2.6 50.1 1.0 O A:ILE215 2.7 38.1 1.0 O A:PHE212 2.8 40.2 1.0 C A:GLN210 3.5 40.7 1.0 P E:DC11 3.5 44.6 1.0 OP1 E:DC11 3.7 44.4 1.0 C A:ILE215 3.8 37.2 1.0 C A:PHE212 4.0 40.0 1.0 C A:THR211 4.0 40.6 1.0 CA A:THR211 4.2 40.5 1.0 N A:PHE212 4.2 40.7 1.0 N A:THR211 4.2 40.4 1.0 N A:ILE215 4.3 37.7 1.0 CA A:GLN210 4.3 40.8 1.0 O A:THR211 4.4 41.3 1.0 O5' E:DC11 4.5 46.5 1.0 CA A:ILE215 4.6 37.0 1.0 O A:HOH885 4.7 49.0 1.0 O E:HOH155 4.7 36.2 1.0 N A:GLY216 4.7 37.0 1.0 O3' E:DG10 4.8 44.0 1.0 CA A:PHE212 4.8 40.7 1.0 CA A:PRO213 4.8 39.2 1.0 CA A:GLY216 4.8 36.1 1.0 N A:PRO213 4.9 39.8 1.0 N A:GLY214 4.9 38.3 1.0 CB A:GLN210 4.9 40.5 1.0 C A:PRO213 5.0 38.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of E. Coli 3-Methyladenine Dna Glycosylase (Alka) Complexed with Dna


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 E. Coli 3-Methyladenine Dna Glycosylase (Alka) Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na824 b:40.0 occ:1.00 OP2 C:DC11 2.6 43.6 1.0 O B:PHE212 2.6 41.9 1.0 O B:GLN210 2.7 43.9 1.0 O B:ILE215 2.7 38.4 1.0 O B:HOH844 2.8 40.8 1.0 OP1 C:DC11 3.2 43.7 1.0 P C:DC11 3.3 43.3 1.0 C B:GLN210 3.4 43.0 1.0 C B:ILE215 3.5 38.2 1.0 C B:PHE212 3.7 41.6 1.0 N B:ILE215 3.8 38.6 1.0 C B:THR211 4.1 42.7 1.0 CA B:ILE215 4.1 38.0 1.0 N B:PHE212 4.2 42.7 1.0 CA B:GLN210 4.2 43.4 1.0 N B:THR211 4.2 42.9 1.0 CA B:THR211 4.3 42.7 1.0 O B:THR211 4.3 43.0 1.0 N B:GLY214 4.4 40.3 1.0 O5' C:DC11 4.4 46.3 1.0 CA B:PRO213 4.4 40.9 1.0 N B:GLY216 4.5 38.2 1.0 O C:HOH23 4.5 43.5 1.0 O3' C:DG10 4.5 42.9 1.0 N B:PRO213 4.5 41.1 1.0 C B:PRO213 4.6 40.8 1.0 CA B:PHE212 4.6 42.8 1.0 CB B:ILE215 4.7 37.9 1.0 CA B:GLY216 4.7 37.6 1.0 C B:GLY214 4.8 39.7 1.0 CB B:GLN210 4.8 43.6 1.0 O B:LEU209 5.0 42.0 1.0

T.Hollis, Y.Ichikawa, T.Ellenberger. Dna Bending and A Flip-Out Mechanism For Base Excision By the Helix-Hairpin-Helix Dna Glycosylase, Escherichia Coli Alka. Embo J. V. 19 758 2000.
ISSN: ISSN 0261-4189
PubMed: 10675345
DOI: 10.1093/EMBOJ/19.4.758