Sodium in PDB 6ph6: Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream, PDB code: 6ph6 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)	24.93 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.510, 79.675, 55.428, 90.00, 107.52, 90.00
R / Rfree (%)	18.5 / 27.6

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream (pdb code 6ph6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream, PDB code: 6ph6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:29.1 occ:1.00 O A:THR101 2.4 27.3 1.0 O A:ILE106 2.4 27.1 1.0 O A:VAL103 2.4 33.9 1.0 OP1 P:DG9 2.5 27.8 1.0 C A:ILE106 3.3 28.9 1.0 C A:VAL103 3.4 25.1 1.0 C A:THR101 3.4 26.0 1.0 N A:ILE106 3.4 26.2 1.0 P P:DG9 3.5 32.2 1.0 OP2 P:DG9 3.6 38.6 1.0 CA A:ILE106 3.9 31.4 1.0 N A:GLY105 3.9 27.9 1.0 CA A:THR101 3.9 27.1 1.0 CA A:SER104 3.9 23.1 1.0 N A:VAL103 4.0 26.5 1.0 N A:SER104 4.0 21.8 1.0 C A:SER104 4.2 28.1 1.0 N A:GLY107 4.3 27.4 1.0 O3' P:DC8 4.3 29.0 1.0 CB A:ILE106 4.3 32.7 1.0 C A:ARG102 4.3 31.7 1.0 CA A:VAL103 4.3 29.0 1.0 C A:GLY105 4.4 26.9 1.0 N A:ARG102 4.4 24.6 1.0 CB A:THR101 4.6 21.9 1.0 CA A:ARG102 4.6 30.8 1.0 CA A:GLY107 4.7 29.6 1.0 O A:LEU100 4.7 26.1 1.0 CA A:GLY105 4.7 26.4 1.0 O5' P:DG9 4.8 37.7 1.0 O A:ARG102 4.9 27.9 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:48.5 occ:1.00 CA A:PRO63 3.2 40.5 1.0 CB A:PRO63 3.5 35.1 1.0 OP1 D:DC3 3.5 39.9 1.0 N A:PRO63 3.7 42.0 1.0 O A:HOH502 3.9 34.7 1.0 O A:LEU62 4.0 40.4 1.0 O A:LYS61 4.1 44.4 1.0 C A:LEU62 4.1 40.8 1.0 O5' D:DC3 4.5 52.6 1.0 C A:PRO63 4.5 32.3 1.0 CD A:PRO63 4.6 37.4 1.0 C5' D:DC3 4.6 44.4 1.0 P D:DC3 4.6 44.3 1.0 CG A:PRO63 4.6 27.3 1.0 N A:GLY64 4.7 30.8 1.0 C A:LYS61 5.0 40.9 1.0

M.J.Howard, N.A.Cavanaugh, V.K.Batra, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Beta Nucleotide-Stabilized Template Misalignment Fidelity Depends on Local Sequence Context. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31801827
DOI: 10.1074/JBC.RA119.010594