Sodium in PDB 5iim: Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Da Base-Pair

All present enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Da Base-Pair:
2.7.7.7;

The structure of Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Da Base-Pair, PDB code: 5iim 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)	43.95 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.274, 63.700, 140.725, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.6

The binding sites of Sodium atom in the Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Da Base-Pair (pdb code 5iim). 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 Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Da Base-Pair, PDB code: 5iim:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Da Base-Pair


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 Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Da Base-Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:17.8 occ:1.00 O2B A:DUP601 2.0 17.6 1.0 O1A A:DUP601 2.1 18.9 1.0 OD1 A:ASP427 2.1 16.7 1.0 OD2 A:ASP429 2.1 20.5 1.0 O A:HOH763 2.2 17.3 1.0 O1G A:DUP601 2.2 19.7 1.0 CG A:ASP427 3.1 20.8 1.0 CG A:ASP429 3.1 20.1 1.0 PB A:DUP601 3.1 19.0 1.0 PA A:DUP601 3.2 19.5 1.0 OD1 A:ASP429 3.4 18.7 1.0 PG A:DUP601 3.4 21.4 1.0 OD2 A:ASP427 3.5 24.2 1.0 N3A A:DUP601 3.6 21.0 1.0 O3B A:DUP601 3.7 18.5 1.0 O A:HOH824 4.0 30.1 1.0 O A:ASP427 4.1 23.9 1.0 O2G A:DUP601 4.1 21.2 1.0 C5' A:DUP601 4.2 18.4 1.0 OG A:SER417 4.2 20.4 1.0 O5' A:DUP601 4.2 17.5 1.0 O2A A:DUP601 4.3 21.5 1.0 N A:ASP427 4.3 19.9 1.0 CB A:ASP427 4.3 19.0 1.0 N A:SER417 4.4 18.3 1.0 C A:ASP427 4.4 21.0 1.0 O A:HOH793 4.4 21.4 1.0 CA A:GLY416 4.4 15.4 1.0 O1B A:DUP601 4.4 18.7 1.0 CB A:ASP429 4.5 19.3 1.0 O3G A:DUP601 4.5 22.9 1.0 CA A:ASP427 4.6 19.3 1.0 O A:HOH778 4.6 29.2 1.0 N A:ASP429 4.9 15.7 1.0 C A:GLY416 5.0 17.0 1.0 N A:VAL428 5.0 19.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Da Base-Pair


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 Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Da Base-Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:16.7 occ:1.00 OP1 P:DA5 2.4 11.6 1.0 O A:SER339 2.4 14.4 1.0 O A:ALA344 2.4 13.8 1.0 O A:ILE341 2.4 11.2 1.0 O P:HOH127 2.5 22.5 1.0 O P:HOH104 2.6 18.9 1.0 C A:ILE341 3.3 11.7 1.0 C A:SER339 3.4 14.9 1.0 P P:DA5 3.4 13.9 1.0 C A:ALA344 3.5 13.7 1.0 OP2 P:DA5 3.6 12.2 1.0 N A:ALA344 3.7 13.8 1.0 O A:HOH865 3.8 38.6 1.0 O P:HOH125 3.9 28.7 1.0 CA A:TRP342 3.9 11.9 1.0 N A:GLY343 4.0 14.0 1.0 N A:TRP342 4.0 14.1 1.0 N A:ILE341 4.1 12.7 1.0 CA A:ALA344 4.1 13.1 1.0 CA A:SER339 4.2 16.2 1.0 C A:ASN340 4.2 14.9 1.0 C A:TRP342 4.3 13.2 1.0 N A:ASN340 4.3 15.5 1.0 O3' P:DT4 4.4 13.6 1.0 CA A:ILE341 4.4 13.2 1.0 CA A:ASN340 4.4 16.4 1.0 N A:GLY345 4.5 13.5 1.0 O P:HOH130 4.6 45.9 1.0 CB A:ALA344 4.6 13.7 1.0 O5' P:DA5 4.7 13.3 1.0 C A:GLY343 4.7 15.6 1.0 O A:HOH877 4.7 46.7 1.0 O A:HOH826 4.7 37.2 1.0 O A:ASN340 4.8 16.5 1.0 CB A:SER339 4.8 19.3 1.0 CA A:GLY345 4.8 14.8 1.0 CA A:GLY343 4.9 15.7 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