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

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 Dc:
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 Dc, PDB code: 5iik 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)	42.07 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.182, 63.475, 140.369, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.8

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 Dc (pdb code 5iik). 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 Dc, PDB code: 5iik:
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 Dc


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 Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:16.3 occ:1.00 O A:ALA344 2.3 11.8 1.0 O A:SER339 2.3 16.6 1.0 O P:HOH127 2.4 19.7 1.0 O A:ILE341 2.5 14.5 1.0 OP1 P:DA5 2.5 13.6 1.0 O P:HOH107 2.5 16.3 1.0 C A:ILE341 3.4 14.0 1.0 C A:ALA344 3.4 17.1 1.0 C A:SER339 3.4 19.1 1.0 P P:DA5 3.5 12.7 1.0 OP2 P:DA5 3.7 15.8 1.0 O A:HOH916 3.7 26.4 1.0 N A:ALA344 3.7 12.3 1.0 N A:GLY343 4.0 14.8 1.0 CA A:TRP342 4.0 12.1 1.0 N A:TRP342 4.0 15.1 1.0 N A:ILE341 4.0 11.7 1.0 CA A:ALA344 4.1 12.5 1.0 C A:ASN340 4.2 14.4 1.0 CA A:SER339 4.3 13.7 1.0 C A:TRP342 4.3 12.3 1.0 N A:ASN340 4.3 14.1 1.0 CA A:ILE341 4.4 13.2 1.0 O3' P:DT4 4.4 13.6 1.0 CA A:ASN340 4.4 15.0 1.0 O P:HOH123 4.4 30.3 1.0 N A:GLY345 4.5 15.1 1.0 OG A:SER339 4.5 27.9 1.0 CB A:ALA344 4.6 11.2 1.0 C A:GLY343 4.7 13.8 1.0 CA A:GLY345 4.7 12.6 1.0 O A:HOH883 4.8 24.9 1.0 O5' P:DA5 4.8 13.0 1.0 O A:ASN340 4.8 15.0 1.0 CA A:GLY343 4.9 15.5 1.0 O P:HOH130 4.9 32.5 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 Dc


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 Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:20.8 occ:1.00 OD1 A:ASP427 2.3 14.2 1.0 OD2 A:ASP429 2.4 17.0 1.0 O3 A:CIT601 2.4 18.1 1.0 O7 A:CIT601 2.5 20.6 1.0 O A:HOH801 2.6 19.1 1.0 OP1 P:DT7 3.0 13.9 1.0 O5 A:CIT601 3.1 19.7 1.0 C3 A:CIT601 3.3 18.7 1.0 CG A:ASP427 3.3 19.1 1.0 CG A:ASP429 3.3 19.3 1.0 C5 A:CIT601 3.4 21.2 1.0 C6 A:CIT601 3.4 21.6 1.0 OD1 A:ASP429 3.7 13.8 1.0 C4 A:CIT601 3.7 17.8 1.0 OD2 A:ASP427 3.7 14.6 1.0 P P:DT7 4.1 14.8 1.0 OG A:SER417 4.1 18.1 1.0 N A:SER417 4.1 16.1 1.0 O A:ASP427 4.1 17.6 1.0 O5' P:DT7 4.2 14.6 1.0 CA A:GLY416 4.2 16.5 1.0 C5' P:DT7 4.2 13.6 1.0 N A:ASP427 4.4 20.5 1.0 C A:ASP427 4.5 19.4 1.0 O4 A:CIT601 4.5 20.1 1.0 O6 A:CIT601 4.5 19.0 1.0 CB A:ASP427 4.6 15.9 1.0 CB A:ASP429 4.6 16.2 1.0 C2 A:CIT601 4.6 19.7 1.0 O1 A:CIT601 4.6 19.7 1.0 O A:HOH791 4.7 12.9 1.0 C A:GLY416 4.7 20.4 1.0 OP2 P:DT7 4.7 16.9 1.0 CA A:ASP427 4.8 15.6 1.0 CB A:SER417 4.8 20.1 1.0 N A:ASP429 5.0 13.9 1.0 C1 A:CIT601 5.0 21.8 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