Sodium in PDB 3c2k: Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site

All present enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site:
2.7.7.7;

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site, PDB code: 3c2k was solved by V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.39 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.790, 80.680, 55.060, 90.00, 108.38, 90.00
R / Rfree (%)	21 / 27.8

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site also contains other interesting chemical elements:

Manganese	(Mn)	5 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site (pdb code 3c2k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site, PDB code: 3c2k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na345 b:27.5 occ:1.00 OP1 P:DG9 2.4 25.9 1.0 O A:ILE106 2.4 17.5 1.0 O A:THR101 2.4 21.8 1.0 O A:VAL103 2.5 15.8 1.0 P P:DG9 3.4 25.2 1.0 C A:VAL103 3.4 17.3 1.0 C A:THR101 3.4 19.9 1.0 OP2 P:DG9 3.5 27.6 1.0 C A:ILE106 3.5 18.8 1.0 N A:ILE106 3.7 17.8 1.0 CA A:SER104 3.9 17.6 1.0 N A:GLY105 3.9 19.3 1.0 N A:SER104 4.0 16.8 1.0 CA A:THR101 4.0 19.6 1.0 N A:VAL103 4.1 17.9 1.0 CA A:ILE106 4.1 17.6 1.0 C A:SER104 4.2 19.4 1.0 C A:ARG102 4.3 17.0 1.0 O3' P:DC8 4.3 25.1 1.0 CA A:VAL103 4.4 17.8 1.0 O A:HOH510 4.4 30.3 1.0 N A:ARG102 4.4 17.9 1.0 CB A:ILE106 4.5 17.8 1.0 N A:GLY107 4.5 18.6 1.0 O5' P:DG9 4.6 26.2 1.0 C A:GLY105 4.6 19.6 1.0 CB A:THR101 4.7 19.7 1.0 CA A:ARG102 4.7 18.1 1.0 CA A:GLY107 4.8 18.7 1.0 O A:ARG102 4.8 15.7 1.0 CA A:GLY105 4.8 20.0 1.0 O A:LEU100 4.9 17.5 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na346 b:37.1 occ:1.00 O A:LYS60 2.2 34.7 1.0 O A:LEU62 2.4 33.0 1.0 O A:VAL65 2.5 29.0 1.0 OP1 D:DC3 2.6 33.9 1.0 O D:HOH39 3.0 24.5 1.0 C A:LYS60 3.2 34.8 1.0 C A:LEU62 3.3 32.4 1.0 C A:VAL65 3.6 29.0 1.0 N A:VAL65 3.7 28.3 1.0 P D:DC3 3.7 35.8 1.0 N A:GLY64 3.9 31.3 1.0 OP2 D:DC3 3.9 36.2 1.0 CA A:LYS60 3.9 33.2 1.0 N A:LEU62 3.9 34.3 1.0 CA A:PRO63 4.0 31.6 1.0 CG A:LYS60 4.0 35.4 1.0 N A:PRO63 4.0 32.1 1.0 CA A:VAL65 4.1 28.6 1.0 C A:LYS61 4.1 35.7 1.0 N A:LYS61 4.2 36.4 1.0 CA A:LEU62 4.3 32.4 1.0 CB A:VAL65 4.3 28.9 1.0 C A:PRO63 4.4 30.8 1.0 CA A:LYS61 4.5 36.1 1.0 O3' D:DT2 4.5 33.3 1.0 O A:LYS61 4.5 37.1 1.0 CB A:LYS60 4.6 34.6 1.0 C A:GLY64 4.6 29.9 1.0 N A:GLY66 4.7 28.2 1.0 O A:ALA59 4.7 28.5 1.0 CA A:GLY64 4.9 31.0 1.0 O5' D:DC3 5.0 35.4 1.0

V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Beta with Active-Site Mismatches Suggest A Transient Abasic Site Intermediate During Misincorporation. Mol.Cell V. 30 315 2008.
ISSN: ISSN 1097-2765
PubMed: 18471977
DOI: 10.1016/J.MOLCEL.2008.02.025