Sodium in PDB 5iil: Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and Incorporated Da

All present enzymatic activity of Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and Incorporated Da:
2.7.7.7;

The structure of Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and Incorporated Da, PDB code: 5iil was solved by M.J.Burak, K.E.Guja, M.Garcia-Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.11 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.220, 63.554, 139.845, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.7

The binding sites of Sodium atom in the Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and Incorporated Da (pdb code 5iil). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and Incorporated Da, PDB code: 5iil:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and Incorporated Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and Incorporated Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:17.3 occ:1.00 O A:ALA344 2.3 15.4 1.0 O A:SER339 2.3 18.7 1.0 O A:HOH917 2.3 22.0 1.0 O A:ILE341 2.4 17.1 1.0 OP1 P:DA5 2.5 17.7 1.0 O P:HOH113 2.5 16.9 1.0 C A:ILE341 3.4 14.3 1.0 C A:SER339 3.4 18.2 1.0 C A:ALA344 3.4 18.3 1.0 P P:DA5 3.5 18.3 1.0 OP2 P:DA5 3.7 16.6 1.0 N A:ALA344 3.7 14.2 1.0 O A:HOH919 3.8 34.8 1.0 N A:GLY343 3.9 17.0 1.0 CA A:TRP342 3.9 14.9 1.0 N A:TRP342 4.0 18.0 1.0 N A:ILE341 4.0 15.2 1.0 CA A:ALA344 4.1 15.8 1.0 O P:HOH130 4.1 26.8 1.0 C A:ASN340 4.2 17.1 1.0 CA A:SER339 4.3 19.9 0.5 CA A:SER339 4.3 19.9 0.5 C A:TRP342 4.3 17.6 1.0 N A:ASN340 4.3 14.2 1.0 O3' P:DT4 4.3 17.4 1.0 CA A:ILE341 4.3 13.9 1.0 CA A:ASN340 4.4 16.4 1.0 OG A:SER339 4.4 23.8 0.5 N A:GLY345 4.5 16.2 1.0 CB A:ALA344 4.6 13.8 1.0 C A:GLY343 4.7 18.1 1.0 CA A:GLY345 4.8 16.4 1.0 O5' P:DA5 4.8 14.7 1.0 O A:ASN340 4.9 18.4 1.0 CA A:GLY343 4.9 18.6 1.0 CB A:SER339 5.0 20.2 0.5 CB A:SER339 5.0 20.2 0.5 O A:PHE338 5.0 16.6 1.0 O A:HOH892 5.0 28.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and Incorporated Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and Incorporated Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:23.8 occ:1.00 O3 A:CIT601 2.2 21.2 1.0 OD1 A:ASP427 2.3 18.6 1.0 OD2 A:ASP429 2.3 18.7 1.0 O7 A:CIT601 2.5 21.2 1.0 O A:HOH851 2.6 23.3 1.0 OP1 P:DT7 2.8 16.3 1.0 C5 A:CIT601 3.2 20.7 1.0 O5 A:CIT601 3.2 21.2 1.0 CG A:ASP429 3.2 20.7 1.0 CG A:ASP427 3.3 19.5 1.0 C3 A:CIT601 3.3 23.1 1.0 OD1 A:ASP429 3.6 16.2 1.0 C6 A:CIT601 3.6 21.2 1.0 OD2 A:ASP427 3.6 19.1 1.0 C4 A:CIT601 3.7 20.5 1.0 P P:DT7 3.9 17.8 1.0 C5' P:DT7 4.0 18.1 1.0 O5' P:DT7 4.1 19.6 1.0 N A:SER417 4.2 17.7 1.0 CA A:GLY416 4.2 14.4 1.0 O4 A:CIT601 4.3 20.3 1.0 O A:ASP427 4.3 20.3 1.0 OG A:SER417 4.3 19.7 1.0 N A:ASP427 4.5 20.8 1.0 C A:ASP427 4.6 18.8 1.0 CB A:ASP429 4.6 21.6 1.0 CB A:ASP427 4.6 15.7 1.0 OP2 P:DT7 4.7 18.9 1.0 O A:HOH828 4.7 17.6 1.0 O1 A:CIT601 4.7 26.5 1.0 C2 A:CIT601 4.7 21.6 1.0 O6 A:CIT601 4.7 23.0 1.0 C A:GLY416 4.8 23.3 1.0 CA A:ASP427 4.8 17.4 1.0 N A:ASP429 4.9 16.2 1.0 CB A:SER417 5.0 17.5 1.0

M.J.Burak, K.E.Guja, E.Hambardjieva, B.Derkunt, M.Garcia-Diaz. A Fidelity Mechanism in Dna Polymerase Lambda Promotes Error-Free Bypass of 8-Oxo-Dg. Embo J. V. 35 2045 2016.
ISSN: ESSN 1460-2075
PubMed: 27481934
DOI: 10.15252/EMBJ.201694332