Sodium in PDB 3rh5: Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)

All present enzymatic activity of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp):
2.7.7.7;

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp), PDB code: 3rh5 was solved by N.A.Cavanaugh, W.A.Beard, V.K.Batra, L.Perera, L.G.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.70 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.220, 79.920, 55.090, 90.00, 107.93, 90.00
R / Rfree (%)	20.8 / 28.1

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) also contains other interesting chemical elements:

Manganese	(Mn)	7 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) (pdb code 3rh5). 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 Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp), PDB code: 3rh5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


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 Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na346 b:22.1 occ:1.00 O A:THR101 2.5 22.0 1.0 OP1 P:DG9 2.5 21.1 1.0 O A:ILE106 2.7 19.5 1.0 O A:VAL103 2.7 23.0 1.0 O A:HOH402 3.0 25.1 1.0 OP2 P:DG9 3.3 25.0 1.0 P P:DG9 3.3 25.5 1.0 C A:ILE106 3.4 21.6 1.0 C A:THR101 3.5 20.4 1.0 C A:VAL103 3.6 24.0 1.0 N A:ILE106 3.8 21.6 1.0 CA A:THR101 4.0 20.2 1.0 CA A:ILE106 4.1 19.6 1.0 N A:GLY105 4.1 22.0 1.0 CA A:SER104 4.2 22.8 1.0 N A:VAL103 4.2 22.3 1.0 N A:SER104 4.3 21.8 1.0 N A:GLY107 4.3 24.5 1.0 O3' P:DC8 4.4 21.1 1.0 O5' P:DG9 4.5 22.1 1.0 C A:ARG102 4.5 20.3 1.0 CB A:THR101 4.5 22.0 1.0 N A:ARG102 4.5 20.6 1.0 CA A:GLY107 4.5 23.8 1.0 C A:SER104 4.5 22.6 1.0 CB A:ILE106 4.5 21.3 1.0 CA A:VAL103 4.6 20.0 1.0 C A:GLY105 4.7 22.8 1.0 CA A:ARG102 4.8 23.3 1.0 O A:HOH405 4.9 26.7 1.0 O A:ARG102 4.9 21.0 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


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 Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na347 b:30.8 occ:1.00 O A:VAL65 2.6 29.5 1.0 O A:LYS60 2.7 33.3 1.0 O A:LEU62 2.7 32.2 1.0 O A:HOH415 2.8 34.0 1.0 OP1 D:DC3 2.8 29.2 1.0 C A:LEU62 3.5 31.7 1.0 C A:LYS60 3.6 30.5 1.0 C A:VAL65 3.7 27.7 1.0 P D:DC3 3.8 30.9 1.0 OP2 D:DC3 3.8 27.2 1.0 N A:LEU62 4.0 29.6 1.0 N A:VAL65 4.1 25.8 1.0 C A:LYS61 4.1 30.8 1.0 N A:PRO63 4.1 34.4 1.0 CA A:PRO63 4.2 31.4 1.0 CA A:LYS60 4.2 25.9 1.0 CG A:LYS60 4.3 27.7 1.0 N A:GLY64 4.3 31.0 1.0 CA A:VAL65 4.3 24.6 1.0 CA A:LEU62 4.3 32.7 1.0 O A:LYS61 4.4 32.4 1.0 N A:LYS61 4.5 26.5 1.0 CB A:VAL65 4.6 28.7 1.0 CA A:LYS61 4.6 34.2 1.0 C A:PRO63 4.7 33.5 1.0 O3' D:DT2 4.7 29.8 1.0 N A:GLY66 4.8 27.9 1.0 NZ A:LYS60 4.8 30.8 1.0 CB A:LYS60 4.9 27.9 1.0 CA A:GLY66 4.9 29.0 1.0

N.A.Cavanaugh, W.A.Beard, V.K.Batra, L.Perera, L.G.Pedersen, S.H.Wilson. Molecular Insights Into Dna Polymerase Deterrents For Ribonucleotide Insertion. J.Biol.Chem. V. 286 31650 2011.
ISSN: ISSN 0021-9258
PubMed: 21733843
DOI: 10.1074/JBC.M111.253401