Sodium in PDB 3rh6: Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

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

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh6 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)	20.77 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.060, 79.810, 55.060, 90.00, 107.68, 90.00
R / Rfree (%)	19.5 / 26.6

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

Manganese	(Mn)	6 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) (pdb code 3rh6). 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 Ribonucleotide (Rctp), PDB code: 3rh6:
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 Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na345 b:27.7 occ:1.00 OP1 P:DG9 2.5 23.1 1.0 O A:VAL103 2.6 20.7 1.0 O A:THR101 2.6 19.9 1.0 O A:ILE106 2.6 16.3 1.0 O P:HOH310 2.7 30.4 1.0 O A:HOH358 2.9 24.6 1.0 P P:DG9 3.3 24.2 1.0 OP2 P:DG9 3.4 25.8 1.0 C A:VAL103 3.5 19.4 1.0 C A:THR101 3.5 18.5 1.0 C A:ILE106 3.5 17.1 1.0 N A:ILE106 3.8 17.5 1.0 CA A:SER104 3.9 21.8 1.0 N A:GLY105 4.0 24.9 1.0 O A:HOH566 4.0 34.2 1.0 CA A:THR101 4.1 20.0 1.0 N A:SER104 4.1 17.9 1.0 CA A:ILE106 4.2 16.5 1.0 N A:VAL103 4.2 18.6 1.0 C A:SER104 4.3 24.8 1.0 C A:ARG102 4.3 22.8 1.0 O3' P:DC8 4.4 19.7 1.0 CA A:VAL103 4.4 21.1 1.0 N A:ARG102 4.5 21.5 1.0 N A:GLY107 4.5 18.8 1.0 O5' P:DG9 4.5 21.4 1.0 CB A:ILE106 4.5 17.4 1.0 CB A:THR101 4.6 22.6 1.0 O A:ARG102 4.6 22.0 1.0 C A:GLY105 4.7 19.2 1.0 CA A:ARG102 4.7 23.1 1.0 CA A:GLY107 4.7 20.2 1.0 CA A:GLY105 4.9 25.7 1.0 O A:LEU100 5.0 17.8 1.0

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


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 Ribonucleotide (Rctp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na346 b:36.0 occ:1.00 O A:LEU62 2.6 29.4 1.0 O A:VAL65 2.7 33.6 1.0 O A:LYS60 2.7 35.8 1.0 OP1 D:DC3 2.8 33.9 1.0 O A:HOH544 3.0 35.5 1.0 C A:LYS60 3.6 36.3 1.0 P D:DC3 3.6 31.0 1.0 OP2 D:DC3 3.6 30.3 1.0 C A:LEU62 3.6 31.6 1.0 C A:VAL65 3.7 32.2 1.0 N A:VAL65 3.9 27.6 1.0 CA A:VAL65 4.2 30.4 1.0 C A:LYS61 4.3 35.5 1.0 N A:LEU62 4.3 31.2 1.0 CA A:LYS60 4.3 29.6 1.0 CA A:PRO63 4.3 32.8 1.0 N A:GLY64 4.3 29.2 1.0 CG A:LYS60 4.4 26.7 1.0 N A:PRO63 4.4 32.8 1.0 N A:LYS61 4.5 31.8 1.0 O A:LYS61 4.5 34.6 1.0 CB A:VAL65 4.6 31.2 1.0 O3' D:DT2 4.6 27.0 1.0 CA A:LEU62 4.6 29.5 1.0 CA A:LYS61 4.6 38.5 1.0 N A:GLY66 4.7 30.7 1.0 C A:PRO63 4.7 32.8 1.0 O5' D:DC3 4.9 36.8 1.0 CA A:GLY66 4.9 29.8 1.0 CB A:LYS60 4.9 31.0 1.0 C A:GLY64 4.9 36.1 1.0 NZ A:LYS60 5.0 46.6 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