Sodium in PDB 5j2c: Ternary Complex Crystal Structure of Dna Polymerase Beta with C:A Mismatch at the Primer Terminus

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

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with C:A Mismatch at the Primer Terminus, PDB code: 5j2c 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)	50.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.800, 80.280, 55.490, 90.00, 107.70, 90.00
R / Rfree (%)	21.2 / 26.6

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with C:A Mismatch at the Primer Terminus also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C:A Mismatch at the Primer Terminus (pdb code 5j2c). 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 C:A Mismatch at the Primer Terminus, PDB code: 5j2c:
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 C:A 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 C:A Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:23.1 occ:1.00 O A:THR101 2.2 21.3 1.0 OP1 P:DG9 2.4 20.6 1.0 O A:VAL103 2.5 16.1 1.0 O P:HOH104 2.5 23.4 1.0 O A:HOH720 2.6 31.0 1.0 O A:ILE106 2.7 19.1 1.0 C A:THR101 3.2 21.1 1.0 C A:VAL103 3.4 18.6 1.0 P P:DG9 3.5 23.0 1.0 OP2 P:DG9 3.7 22.5 1.0 C A:ILE106 3.7 18.5 1.0 O A:HOH669 3.8 35.3 1.0 N A:ILE106 3.9 18.6 1.0 CA A:SER104 3.9 18.2 1.0 N A:GLY105 3.9 18.1 1.0 CA A:THR101 4.0 21.4 1.0 N A:SER104 4.0 16.8 1.0 N A:VAL103 4.0 18.0 1.0 C A:ARG102 4.1 19.2 1.0 N A:ARG102 4.2 19.3 1.0 C A:SER104 4.3 18.3 1.0 CA A:ILE106 4.3 18.3 1.0 CA A:VAL103 4.4 18.2 1.0 O A:ARG102 4.4 18.4 1.0 CA A:ARG102 4.5 19.7 1.0 O3' P:DC8 4.5 20.5 1.0 CB A:THR101 4.6 21.3 1.0 CB A:ILE106 4.6 18.1 1.0 O5' P:DG9 4.7 24.0 1.0 N A:GLY107 4.7 17.1 1.0 C A:GLY105 4.7 19.5 1.0 O A:LEU100 4.8 22.6 1.0 CA A:GLY105 4.9 20.5 1.0 CA A:GLY107 4.9 18.9 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C:A 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 C:A Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:29.8 occ:1.00 O A:LEU62 2.3 30.1 1.0 O A:LYS60 2.3 32.0 1.0 O A:VAL65 2.5 28.5 1.0 OP1 D:DC3 2.6 37.3 1.0 O A:HOH608 2.6 25.7 1.0 O D:HOH105 2.8 25.4 1.0 C A:LEU62 3.4 30.5 1.0 C A:LYS60 3.4 32.7 1.0 C A:VAL65 3.5 29.5 1.0 P D:DC3 3.7 34.8 1.0 O D:HOH110 3.8 45.5 1.0 N A:VAL65 3.8 29.1 1.0 OP2 D:DC3 3.9 33.4 1.0 CA A:PRO63 4.0 30.3 1.0 C A:LYS61 4.1 34.0 1.0 N A:PRO63 4.1 30.9 1.0 N A:LEU62 4.1 32.9 1.0 CA A:LYS60 4.1 31.2 1.0 N A:GLY64 4.1 29.1 1.0 CA A:VAL65 4.2 28.7 1.0 O A:LYS61 4.2 34.7 1.0 CG A:LYS60 4.3 33.6 1.0 N A:LYS61 4.3 32.8 1.0 CA A:LEU62 4.4 30.6 1.0 CB A:VAL65 4.4 29.0 1.0 C A:PRO63 4.5 30.1 1.0 CA A:LYS61 4.5 33.5 1.0 N A:GLY66 4.6 29.5 1.0 O3' D:DT2 4.7 35.6 1.0 O A:ALA59 4.8 30.1 1.0 CA A:GLY66 4.8 29.4 1.0 CB A:LYS60 4.8 32.2 1.0 C A:GLY64 4.9 28.7 1.0 O5' D:DC3 4.9 37.4 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