Sodium in PDB 6n2r: Binary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position

All present enzymatic activity of Binary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position:
2.7.7.7;

The structure of Binary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position, PDB code: 6n2r was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.84 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.485, 79.073, 55.064, 90.00, 109.20, 90.00
R / Rfree (%)	21 / 26.6

The binding sites of Sodium atom in the Binary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position (pdb code 6n2r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Binary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position, PDB code: 6n2r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Binary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:21.0 occ:1.00 O A:ILE106 2.3 26.8 1.0 OP1 P:DG9 2.4 24.0 1.0 O A:THR101 2.4 25.3 1.0 O A:VAL103 2.5 21.8 1.0 O P:HOH108 2.6 27.8 1.0 O A:HOH657 2.6 32.1 1.0 C A:ILE106 3.3 24.1 1.0 C A:VAL103 3.4 26.8 1.0 P P:DG9 3.4 26.9 1.0 C A:THR101 3.4 22.7 1.0 O A:HOH547 3.5 34.7 1.0 N A:ILE106 3.6 22.4 1.0 OP2 P:DG9 3.6 28.0 1.0 CA A:SER104 3.9 23.1 1.0 N A:SER104 3.9 28.2 1.0 CA A:THR101 3.9 23.0 1.0 CA A:ILE106 4.0 22.0 1.0 N A:GLY105 4.0 24.2 1.0 N A:VAL103 4.2 25.6 1.0 C A:SER104 4.3 26.0 1.0 N A:GLY107 4.3 22.9 1.0 C A:ARG102 4.4 25.3 1.0 CA A:VAL103 4.4 24.7 1.0 CB A:ILE106 4.4 24.7 1.0 O5' P:DG9 4.5 26.9 1.0 N A:ARG102 4.5 25.6 1.0 CB A:THR101 4.5 28.4 1.0 O3' P:DC8 4.5 22.5 1.0 C A:GLY105 4.5 25.8 1.0 CA A:GLY107 4.6 25.2 1.0 CA A:ARG102 4.7 24.7 1.0 CA A:GLY105 4.8 24.9 1.0 O A:ARG102 4.9 24.1 1.0 O A:LEU100 5.0 26.4 1.0

Sodium binding site 2 out of 2 in the Binary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:32.4 occ:1.00 O A:LEU62 2.4 34.0 1.0 O A:VAL65 2.4 31.2 1.0 O A:LYS60 2.4 33.7 1.0 O D:HOH105 2.5 25.5 1.0 O A:HOH643 2.5 32.9 1.0 OP1 D:DC3 2.7 27.8 1.0 C A:LEU62 3.4 33.2 1.0 C A:VAL65 3.5 30.1 1.0 C A:LYS60 3.6 31.4 1.0 P D:DC3 3.6 31.2 1.0 OP2 D:DC3 3.7 24.9 1.0 N A:VAL65 3.8 27.3 1.0 N A:GLY64 4.1 29.9 1.0 N A:LEU62 4.1 32.4 1.0 CA A:VAL65 4.1 27.9 1.0 CA A:PRO63 4.2 35.9 1.0 C A:LYS61 4.2 33.0 1.0 N A:PRO63 4.2 32.9 1.0 CA A:LYS60 4.3 31.0 1.0 O3' D:DT2 4.4 31.4 1.0 CA A:LEU62 4.4 33.6 1.0 O A:LYS61 4.5 38.8 1.0 CG A:LYS60 4.5 35.0 1.0 N A:GLY66 4.5 28.9 1.0 CB A:VAL65 4.5 29.7 1.0 N A:LYS61 4.5 30.1 1.0 C A:PRO63 4.6 33.9 1.0 CA A:LYS61 4.6 35.9 1.0 C A:GLY64 4.7 30.7 1.0 CA A:GLY66 4.8 26.5 1.0 O A:ALA59 4.9 26.1 1.0 O5' D:DC3 4.9 27.4 1.0 CA A:GLY64 5.0 30.2 1.0

M.J.Howard, K.G.Foley, D.D.Shock, V.K.Batra, S.H.Wilson. Molecular Basis For the Faithful Replication of 5-Methylcytosine and Its Oxidized Forms By Dna Polymerase Beta. J.Biol.Chem. V. 294 7194 2019.
ISSN: ESSN 1083-351X
PubMed: 30885943
DOI: 10.1074/JBC.RA118.006809