Sodium in PDB 5j2i: Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus, PDB code: 5j2i 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)	25.11 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.630, 80.150, 55.460, 90.00, 107.51, 90.00
R / Rfree (%)	18.2 / 26.9

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus 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 T:C Mismatch at the Primer Terminus (pdb code 5j2i). 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 T:C Mismatch at the Primer Terminus, PDB code: 5j2i:
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 T:C Mismatch at the Primer Terminus


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 T:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:36.1 occ:1.00 OP1 P:DG9 2.4 35.9 1.0 O P:HOH106 2.4 33.0 1.0 O A:THR101 2.6 35.1 1.0 O A:ILE106 2.6 27.5 1.0 O A:VAL103 2.7 31.8 1.0 O A:HOH661 2.9 38.1 1.0 P P:DG9 3.4 35.7 1.0 C A:VAL103 3.5 30.8 1.0 C A:THR101 3.5 34.5 1.0 C A:ILE106 3.6 32.2 1.0 OP2 P:DG9 3.6 42.8 1.0 N A:ILE106 3.9 31.8 1.0 N A:GLY105 3.9 33.6 1.0 CA A:SER104 3.9 28.9 1.0 N A:SER104 4.0 29.3 1.0 N A:VAL103 4.1 35.5 1.0 CA A:THR101 4.1 33.8 1.0 C A:ARG102 4.3 34.7 1.0 CA A:ILE106 4.3 23.3 1.0 C A:SER104 4.3 32.4 1.0 N A:ARG102 4.4 34.6 1.0 O3' P:DC8 4.5 38.0 1.0 CA A:VAL103 4.5 34.6 1.0 CA A:ARG102 4.6 33.3 1.0 N A:GLY107 4.6 30.8 1.0 O5' P:DG9 4.6 37.9 1.0 CB A:ILE106 4.7 32.2 1.0 C A:GLY105 4.7 31.0 1.0 O A:ARG102 4.7 36.4 1.0 O A:HOH623 4.8 45.3 1.0 CB A:THR101 4.8 33.1 1.0 CA A:GLY105 4.8 30.5 1.0 O A:LEU100 4.9 32.9 1.0 CA A:GLY107 4.9 31.2 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus


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 T:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:41.3 occ:1.00 O A:LEU62 2.4 42.2 1.0 O A:VAL65 2.4 44.2 1.0 O A:LYS60 2.5 37.2 1.0 OP1 D:DC3 2.6 44.4 1.0 C A:VAL65 3.3 40.1 1.0 C A:LEU62 3.4 38.9 1.0 P D:DC3 3.5 42.8 1.0 OP2 D:DC3 3.6 45.3 1.0 C A:LYS60 3.6 41.5 1.0 N A:VAL65 3.7 33.0 1.0 CA A:PRO63 3.9 36.2 1.0 N A:GLY64 3.9 42.5 1.0 CA A:VAL65 4.0 35.0 1.0 N A:PRO63 4.1 35.8 1.0 N A:LEU62 4.2 39.7 1.0 N A:GLY66 4.2 36.9 1.0 C A:PRO63 4.3 43.3 1.0 C A:LYS61 4.3 41.3 1.0 CA A:LYS60 4.4 40.3 1.0 O3' D:DT2 4.4 44.2 1.0 CB A:VAL65 4.4 38.7 1.0 CA A:LEU62 4.5 38.4 1.0 CG A:LYS60 4.5 41.3 1.0 CA A:GLY66 4.6 38.0 1.0 C A:GLY64 4.6 38.4 1.0 O A:LYS61 4.6 41.2 1.0 N A:LYS61 4.6 40.3 1.0 CA A:LYS61 4.7 42.5 1.0 CA A:GLY64 4.8 40.2 1.0 O5' D:DC3 4.9 51.1 1.0

V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Mispaired Dna Termini Transitioning to Pre-Catalytic Complexes Support An Induced-Fit Fidelity Mechanism. Structure V. 24 1863 2016.
ISSN: ISSN 0969-2126
PubMed: 27642161
DOI: 10.1016/J.STR.2016.08.006