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Sodium in PDB 5iij: Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp

Enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp

All present enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp, PDB code: 5iij 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) 41.71 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.749, 62.850, 140.076, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.4

Other elements in 5iij:

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp 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 Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp (pdb code 5iij). 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 Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp, PDB code: 5iij:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5iij

Go back to Sodium Binding Sites List in 5iij
Sodium binding site 1 out of 2 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp


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 Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:19.1
occ:1.00
 O A:SER339 2.3 17.3 1.0
O A:ALA344 2.3 18.7 1.0
O A:HOH928 2.4 23.2 1.0
O A:ILE341 2.4 17.7 1.0
OP1 P:DA5 2.5 18.6 1.0
O P:HOH107 2.6 21.9 1.0
C A:ILE341 3.3 19.1 1.0
C A:SER339 3.4 18.1 1.0
C A:ALA344 3.5 18.2 1.0
P P:DA5 3.6 17.6 1.0
OP2 P:DA5 3.7 17.9 1.0
N A:ALA344 3.8 17.2 1.0
N A:GLY343 3.9 18.3 1.0
CA A:TRP342 3.9 19.0 1.0
N A:TRP342 4.0 18.6 1.0
O P:HOH125 4.0 32.7 1.0
N A:ILE341 4.0 18.5 1.0
CA A:ALA344 4.2 17.5 1.0
C A:ASN340 4.2 18.0 1.0
CA A:SER339 4.2 17.8 1.0
N A:ASN340 4.2 18.0 1.0
C A:TRP342 4.3 18.5 1.0
CA A:ASN340 4.3 18.2 1.0
CA A:ILE341 4.3 18.6 1.0
O3' P:DT4 4.4 17.1 1.0
N A:GLY345 4.5 15.5 1.0
CB A:ALA344 4.6 18.5 1.0
C A:GLY343 4.7 18.5 1.0
O A:ASN340 4.7 19.2 1.0
CA A:GLY345 4.8 18.3 1.0
CB A:SER339 4.8 21.8 1.0
O5' P:DA5 4.9 18.7 1.0
CA A:GLY343 4.9 16.9 1.0

Sodium binding site 2 out of 2 in 5iij

Go back to Sodium Binding Sites List in 5iij
Sodium binding site 2 out of 2 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp


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 Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:32.4
occ:1.00
 O A:SER463 2.4 22.4 1.0
O T:HOH104 2.4 33.0 1.0
O A:HOH922 2.5 35.4 1.0
O A:HOH998 2.5 41.1 1.0
O A:HOH800 2.5 39.0 1.0
O T:HOH121 2.6 30.7 1.0
C A:SER463 3.5 21.3 1.0
OP1 T:DT10 3.8 21.4 1.0
O T:HOH159 4.0 42.7 1.0
O A:HOH943 4.0 38.3 1.0
O A:HOH775 4.3 38.5 1.0
O A:HOH859 4.3 30.5 1.0
N A:GLU465 4.3 27.0 1.0
CB A:SER463 4.3 20.9 1.0
CA A:SER463 4.3 22.3 1.0
N A:GLN464 4.3 22.0 1.0
CA A:GLN464 4.4 23.7 1.0
OP2 T:DT10 4.4 20.8 1.0
O A:HOH1007 4.5 47.6 1.0
N A:SER463 4.6 19.9 1.0
P T:DT10 4.6 21.7 1.0
OE2 A:GLU465 4.8 30.5 1.0
C A:GLN464 4.9 25.4 1.0
OG A:SER463 5.0 21.5 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 21:36:47 2024

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