Sodium in PDB 8u0p: Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break

Enzymatic activity of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break

All present enzymatic activity of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break:
2.7.7.7;

Protein crystallography data

The structure of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break, PDB code: 8u0p was solved by A.M.Kaminski, L.C.Pedersen, K.Bebenek, T.A.Kunkel, K.K.Chiruvella, D.A.Ramsden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.40 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.205, 60.068, 140.729, 90, 90, 90
R / Rfree (%) 17.2 / 19.3

Other elements in 8u0p:

The structure of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break (pdb code 8u0p). 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 Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break, PDB code: 8u0p:

Sodium binding site 1 out of 1 in 8u0p

Go back to Sodium Binding Sites List in 8u0p
Sodium binding site 1 out of 1 in the Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:17.1
occ:1.00
 O A:ALA344 2.3 16.7 1.0
O A:ILE341 2.3 16.0 1.0
OP1 P:DA5 2.4 15.7 1.0
O A:SER339 2.4 15.7 1.0
O A:HOH901 2.4 22.2 1.0
O P:HOH102 2.9 26.1 1.0
C A:ILE341 3.3 15.8 1.0
C A:SER339 3.4 16.5 1.0
C A:ALA344 3.4 16.7 1.0
P P:DA5 3.4 16.8 1.0
N A:ALA344 3.7 14.5 1.0
OP2 P:DA5 3.7 16.3 1.0
N A:GLY343 3.9 17.7 1.0
CA A:TRP342 3.9 16.6 1.0
N A:TRP342 4.0 15.8 1.0
N A:ILE341 4.0 16.2 1.0
CA A:ALA344 4.1 16.6 1.0
CA A:SER339 4.1 15.8 1.0
C A:ASN340 4.2 18.4 1.0
CA A:ILE341 4.3 16.9 1.0
N A:ASN340 4.3 17.9 1.0
C A:TRP342 4.3 16.6 1.0
CA A:ASN340 4.3 18.2 1.0
O3' P:DT4 4.3 17.2 1.0
N A:GLY345 4.4 16.7 1.0
CB A:ALA344 4.6 16.3 1.0
C A:GLY343 4.6 19.9 1.0
O5' P:DA5 4.6 18.2 1.0
O A:ASN340 4.7 20.2 1.0
CB A:SER339 4.7 18.5 1.0
CA A:GLY345 4.7 17.0 1.0
O A:HOH867 4.8 31.1 1.0
CA A:GLY343 4.8 17.0 1.0
O A:HOH794 4.8 38.1 0.7
O A:PHE338 4.9 16.6 1.0

Reference:

A.M.Kaminski, K.K.Chiruvella, D.A.Ramsden, K.Bebenek, T.A.Kunkel, L.C.Pedersen. Dna Polymerase Lambda LOOP1 Variant Yields Unexpected Gain-of-Function Capabilities in Nonhomologous End-Joining. Dna Repair (Amst) V. 136 03645 2024.
ISSN: ISSN 1568-7856
PubMed: 38428373
DOI: 10.1016/J.DNAREP.2024.103645
Page generated: Wed Oct 9 13:46:31 2024

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