Sodium in PDB 3c2l: Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site:
2.7.7.7;

The structure of Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site, PDB code: 3c2l was solved by V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.14 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.470, 78.280, 54.890, 90.00, 113.18, 90.00
R / Rfree (%)	22.4 / 30.6

The structure of Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site (pdb code 3c2l). 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 of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site, PDB code: 3c2l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na354 b:25.4 occ:1.00 OP1 P:DG9 2.3 21.7 1.0 O A:HOH377 2.4 33.0 1.0 O A:THR101 2.4 23.5 1.0 O A:VAL103 2.6 19.9 1.0 O A:ILE106 2.9 20.6 1.0 P P:DG9 3.3 19.9 1.0 C A:VAL103 3.5 20.3 1.0 C A:THR101 3.5 21.9 1.0 OP2 P:DG9 3.5 15.7 1.0 C A:ILE106 3.8 18.7 1.0 CA A:SER104 3.9 21.6 1.0 N A:ILE106 4.0 19.3 1.0 N A:GLY105 4.0 21.2 1.0 N A:SER104 4.1 21.4 1.0 CA A:THR101 4.2 22.1 1.0 N A:VAL103 4.2 20.4 1.0 O5' P:DG9 4.3 25.7 1.0 CA A:ILE106 4.4 18.9 1.0 C A:SER104 4.4 22.1 1.0 O3' P:DC8 4.5 21.9 1.0 C A:ARG102 4.5 22.1 1.0 N A:ARG102 4.6 22.1 1.0 CA A:VAL103 4.6 19.0 1.0 CB A:THR101 4.7 21.0 1.0 N A:GLY107 4.7 17.4 1.0 CA A:ARG102 4.8 21.7 1.0 CB A:ILE106 4.9 17.9 1.0 C A:GLY105 4.9 20.3 1.0 C5' P:DG9 4.9 28.9 1.0 CA A:GLY107 4.9 19.4 1.0

Sodium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na355 b:39.1 occ:1.00 O A:LEU62 2.4 33.8 1.0 O A:LYS60 2.4 36.2 1.0 O A:HOH449 2.5 37.2 1.0 OP1 D:DC3 2.9 34.7 1.0 O A:VAL65 3.1 28.4 1.0 C A:LEU62 3.3 34.2 1.0 C A:LYS60 3.5 37.3 1.0 O A:LYS61 3.5 37.2 1.0 C A:LYS61 3.6 37.0 1.0 N A:LEU62 3.9 35.4 1.0 P D:DC3 4.0 35.9 1.0 N A:PRO63 4.1 33.4 1.0 C A:VAL65 4.2 28.2 1.0 CA A:LEU62 4.2 33.8 1.0 CA A:PRO63 4.2 33.5 1.0 OP2 D:DC3 4.2 30.8 1.0 CA A:LYS61 4.2 36.9 1.0 N A:LYS61 4.3 37.3 1.0 CD A:LYS60 4.4 35.0 1.0 CA A:LYS60 4.4 36.8 1.0 N A:VAL65 4.6 28.4 1.0 CE A:LYS60 4.6 32.5 1.0 N A:GLY64 4.7 32.5 1.0 CG A:LYS60 4.7 35.4 1.0 CA A:VAL65 4.8 27.2 1.0 C A:PRO63 4.9 33.1 1.0 O5' D:DC3 5.0 33.3 1.0 CB A:VAL65 5.0 28.5 1.0 O A:ALA59 5.0 34.9 1.0

V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Beta with Active-Site Mismatches Suggest A Transient Abasic Site Intermediate During Misincorporation. Mol.Cell V. 30 315 2008.
ISSN: ISSN 1097-2765
PubMed: 18471977
DOI: 10.1016/J.MOLCEL.2008.02.025