Sodium in PDB 3s6i: Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase (MAG1) in Complex with Abasic-Dna.

All present enzymatic activity of Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase (MAG1) in Complex with Abasic-Dna.:
3.2.2.21;

The structure of Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase (MAG1) in Complex with Abasic-Dna., PDB code: 3s6i was solved by S.Adhikary, B.F.Eichman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.10 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.317, 112.298, 61.113, 90.00, 99.55, 90.00
R / Rfree (%)	18.5 / 22.5

The binding sites of Sodium atom in the Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase (MAG1) in Complex with Abasic-Dna. (pdb code 3s6i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase (MAG1) in Complex with Abasic-Dna., PDB code: 3s6i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase (MAG1) in Complex with Abasic-Dna.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase (MAG1) in Complex with Abasic-Dna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na229 b:33.5 occ:1.00 O A:THR142 2.6 28.3 1.0 OP1 B:DC10 2.6 39.6 1.0 O A:ILE147 2.6 23.3 1.0 O A:ILE144 2.7 26.8 1.0 O B:HOH39 2.8 34.8 1.0 O B:HOH15 3.0 43.8 1.0 C A:THR142 3.4 30.7 1.0 C A:ILE147 3.6 24.5 1.0 P B:DC10 3.6 38.1 1.0 C A:ILE144 3.7 32.9 1.0 OP2 B:DC10 3.7 44.8 1.0 CA A:THR142 3.8 20.9 1.0 N A:ILE147 4.0 31.1 1.0 CB A:THR142 4.2 28.7 1.0 CA A:LYS145 4.2 34.8 1.0 CA A:ILE147 4.3 23.8 1.0 N A:ILE144 4.3 33.3 1.0 N A:GLY146 4.3 28.2 1.0 C A:GLN143 4.4 33.0 1.0 N A:LYS145 4.4 38.4 1.0 N A:GLN143 4.5 28.6 1.0 N A:GLY148 4.5 30.7 1.0 O A:GLN143 4.6 39.2 1.0 CA A:ILE144 4.6 31.4 1.0 O3' B:DT9 4.7 33.6 1.0 O5' B:DC10 4.7 49.2 1.0 CB A:ILE147 4.7 20.3 1.0 CA A:GLY148 4.7 27.3 1.0 CA A:GLN143 4.8 29.4 1.0 C A:LYS145 4.8 29.4 1.0

Sodium binding site 2 out of 2 in the Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase (MAG1) in Complex with Abasic-Dna.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase (MAG1) in Complex with Abasic-Dna. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na229 b:39.9 occ:1.00 OP1 E:DC10 2.4 34.6 1.0 O D:ILE144 2.6 25.4 1.0 O D:THR142 2.6 34.9 1.0 O E:HOH38 2.7 25.1 1.0 O D:ILE147 2.7 28.9 1.0 O D:HOH251 2.8 34.0 1.0 C D:ILE144 3.4 30.2 1.0 P E:DC10 3.5 25.5 1.0 C D:THR142 3.5 25.9 1.0 C D:ILE147 3.6 25.9 1.0 OP2 E:DC10 3.7 34.8 1.0 N D:ILE147 3.8 21.0 1.0 CA D:LYS145 3.9 23.0 1.0 N D:LYS145 4.0 26.1 1.0 CA D:THR142 4.0 20.0 1.0 N D:GLY146 4.1 22.9 1.0 CA D:ILE147 4.1 24.2 1.0 N D:ILE144 4.1 22.0 1.0 C D:GLN143 4.2 31.3 1.0 O D:GLN143 4.3 30.5 1.0 C D:LYS145 4.4 26.0 1.0 CA D:ILE144 4.4 26.2 1.0 CB D:THR142 4.4 29.0 1.0 O3' E:DT9 4.5 27.9 1.0 N D:GLY148 4.5 21.0 1.0 N D:GLN143 4.5 25.6 1.0 CB D:ILE147 4.6 24.1 1.0 O5' E:DC10 4.6 29.3 1.0 CA D:GLN143 4.7 26.8 1.0 C D:GLY146 4.8 25.8 1.0 CA D:GLY148 4.8 16.8 1.0

S.Adhikary, B.F.Eichman. Analysis of Substrate Specificity of Schizosaccharomyces Pombe MAG1 Alkylpurine Dna Glycosylase. Embo Rep. V. 12 1286 2011.
ISSN: ISSN 1469-221X
PubMed: 21960007
DOI: 10.1038/EMBOR.2011.189