Sodium in PDB 3rh4: Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

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

The structure of Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh4 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)	22.59 / 1.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.170, 79.790, 55.000, 90.00, 107.95, 90.00
R / Rfree (%)	17.5 / 24

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

Manganese	(Mn)	8 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) (pdb code 3rh4). 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 Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na351 b:18.6 occ:1.00 OP1 P:DG9 2.5 16.9 1.0 O A:THR101 2.5 18.6 1.0 O A:VAL103 2.6 15.6 1.0 O A:ILE106 2.6 16.4 1.0 O P:HOH130 2.7 25.9 1.0 O A:HOH572 2.9 32.0 1.0 P P:DG9 3.5 19.9 1.0 C A:THR101 3.5 17.7 1.0 C A:VAL103 3.5 13.6 1.0 OP2 P:DG9 3.5 18.0 1.0 C A:ILE106 3.6 18.2 1.0 N A:ILE106 3.8 16.3 1.0 N A:GLY105 3.9 18.9 1.0 CA A:SER104 4.0 18.8 1.0 O A:HOH388 4.0 30.8 1.0 CA A:THR101 4.1 18.8 1.0 N A:SER104 4.1 17.2 1.0 CA A:ILE106 4.2 12.1 1.0 N A:VAL103 4.2 12.1 1.0 O A:HOH432 4.2 44.2 1.0 C A:SER104 4.3 18.4 1.0 C A:ARG102 4.4 18.1 1.0 O3' P:DC8 4.4 18.6 1.0 N A:ARG102 4.5 17.4 1.0 CA A:VAL103 4.5 14.6 1.0 N A:GLY107 4.5 16.9 1.0 CB A:ILE106 4.6 16.6 1.0 CB A:THR101 4.6 20.7 1.0 C A:GLY105 4.6 18.4 1.0 O5' P:DG9 4.7 18.5 1.0 CA A:ARG102 4.7 21.1 1.0 CA A:GLY107 4.8 19.8 1.0 O A:ARG102 4.8 17.9 1.0 CA A:GLY105 4.8 21.4 1.0 O A:HOH597 4.9 36.7 1.0 O A:LEU100 5.0 15.4 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na352 b:25.8 occ:1.00 O A:LYS60 2.5 21.0 1.0 O A:VAL65 2.5 22.6 1.0 O A:LEU62 2.6 22.7 1.0 OP1 D:DC3 2.7 21.6 1.0 O A:HOH585 2.9 32.7 1.0 O D:HOH93 2.9 29.5 1.0 C A:LYS60 3.5 30.2 1.0 C A:VAL65 3.6 25.8 1.0 C A:LEU62 3.6 24.5 1.0 P D:DC3 3.6 24.1 1.0 OP2 D:DC3 3.7 21.5 1.0 N A:VAL65 3.9 24.4 1.0 CA A:VAL65 4.1 20.1 1.0 N A:LEU62 4.1 26.9 1.0 CA A:LYS60 4.2 20.5 1.0 CA A:PRO63 4.2 29.5 1.0 C A:LYS61 4.2 34.2 1.0 N A:GLY64 4.2 26.6 1.0 N A:PRO63 4.3 33.2 1.0 CG A:LYS60 4.3 29.3 1.0 CB A:VAL65 4.4 22.5 1.0 CA A:LEU62 4.5 27.1 1.0 O A:LYS61 4.5 31.4 1.0 N A:LYS61 4.5 28.0 1.0 O3' D:DT2 4.6 22.0 1.0 N A:GLY66 4.6 19.9 1.0 C A:PRO63 4.6 23.5 1.0 CA A:LYS61 4.6 32.7 1.0 CA A:GLY66 4.9 22.6 1.0 O5' D:DC3 4.9 25.3 1.0 C A:GLY64 4.9 25.6 1.0 CB A:LYS60 4.9 23.3 1.0 O A:ALA59 4.9 22.4 1.0 NZ A:LYS60 4.9 39.9 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