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

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

Protein crystallography data

The structure of Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Dc Base-Pair, PDB code: 5iin 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) 31.36 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.471, 62.718, 140.006, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.1

Other elements in 5iin:

The structure of Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Dc Base-Pair also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

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:Dc Base-Pair (pdb code 5iin). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Dc Base-Pair, PDB code: 5iin:

Sodium binding site 1 out of 1 in 5iin

Go back to Sodium Binding Sites List in 5iin
Sodium binding site 1 out of 1 in the Crystal Structure of the Pre-Catalytic Ternary Extension Complex of Dna Polymerase Lambda with An 8-Oxo-Dg:Dc 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:Dc Base-Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:20.1
occ:1.00
 O A:ALA344 2.3 17.6 1.0
O A:SER339 2.3 21.7 1.0
OP1 P:DA5 2.3 19.9 1.0
O A:ILE341 2.4 19.0 1.0
O P:HOH127 2.4 23.6 1.0
O P:HOH110 2.6 23.8 1.0
C A:SER339 3.3 22.9 1.0
C A:ILE341 3.4 18.9 1.0
C A:ALA344 3.4 19.6 1.0
P P:DA5 3.4 19.2 1.0
OP2 P:DA5 3.6 17.8 1.0
O P:HOH126 3.7 31.4 1.0
N A:ALA344 3.7 17.7 1.0
O A:HOH787 3.7 33.5 1.0
N A:GLY343 3.9 19.6 1.0
CA A:TRP342 4.0 17.8 1.0
CA A:SER339 4.0 20.7 1.0
N A:TRP342 4.0 20.4 1.0
CA A:ALA344 4.1 18.5 1.0
N A:ILE341 4.1 17.2 1.0
N A:ASN340 4.3 21.1 1.0
C A:ASN340 4.3 17.9 1.0
C A:TRP342 4.3 21.4 1.0
O3' P:DT4 4.3 18.8 1.0
CA A:ILE341 4.4 18.7 1.0
N A:GLY345 4.4 17.3 1.0
CA A:ASN340 4.4 21.2 1.0
CB A:SER339 4.5 25.4 1.0
O P:HOH130 4.6 34.3 1.0
O5' P:DA5 4.6 20.4 1.0
CB A:ALA344 4.6 18.2 1.0
C A:GLY343 4.6 20.4 1.0
CA A:GLY345 4.7 17.0 1.0
CA A:GLY343 4.9 18.7 1.0
O A:ASN340 4.9 20.8 1.0

Reference:

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
Page generated: Mon Oct 7 21:37:22 2024

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