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Sodium in PDB 3hwt: Ternary Complex of Dna Polymerase Lambda Bound to A Two Nucleotide Gapped Dna Substrate with A Scrunched Da

Enzymatic activity of Ternary Complex of Dna Polymerase Lambda Bound to A Two Nucleotide Gapped Dna Substrate with A Scrunched Da

All present enzymatic activity of Ternary Complex of Dna Polymerase Lambda Bound to A Two Nucleotide Gapped Dna Substrate with A Scrunched Da:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Lambda Bound to A Two Nucleotide Gapped Dna Substrate with A Scrunched Da, PDB code: 3hwt was solved by M.Garcia-Diaz, K.Bebenek, A.A.Larrea, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.023, 68.328, 137.850, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.1

Other elements in 3hwt:

The structure of Ternary Complex of Dna Polymerase Lambda Bound to A Two Nucleotide Gapped Dna Substrate with A Scrunched Da also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Lambda Bound to A Two Nucleotide Gapped Dna Substrate with A Scrunched Da (pdb code 3hwt). 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 Ternary Complex of Dna Polymerase Lambda Bound to A Two Nucleotide Gapped Dna Substrate with A Scrunched Da, PDB code: 3hwt:

Sodium binding site 1 out of 1 in 3hwt

Go back to Sodium Binding Sites List in 3hwt
Sodium binding site 1 out of 1 in the Ternary Complex of Dna Polymerase Lambda Bound to A Two Nucleotide Gapped Dna Substrate with A Scrunched Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Dna Polymerase Lambda Bound to A Two Nucleotide Gapped Dna Substrate with A Scrunched Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na169

b:27.3
occ:1.00
 O A:ALA344 2.3 25.9 1.0
O A:SER339 2.4 30.2 0.5
O A:SER339 2.4 25.4 0.5
O A:HOH132 2.5 28.6 1.0
O P:HOH12 2.5 36.0 1.0
OP1 P:DA5 2.5 23.7 1.0
O A:ILE341 2.6 25.5 1.0
C A:SER339 3.4 30.4 0.5
C A:ILE341 3.4 25.3 1.0
C A:ALA344 3.5 27.2 1.0
C A:SER339 3.5 25.4 0.5
P P:DA5 3.6 27.4 1.0
N A:ALA344 3.7 26.2 1.0
OP2 P:DA5 3.8 23.7 1.0
N A:ILE341 3.9 24.0 1.0
N A:GLY343 4.0 27.0 1.0
O P:HOH134 4.0 43.8 1.0
CA A:TRP342 4.0 28.6 1.0
N A:TRP342 4.1 26.6 1.0
C A:ASN340 4.2 24.4 1.0
CA A:ALA344 4.2 25.9 1.0
CA A:SER339 4.2 30.5 0.5
O A:HOH124 4.3 53.6 1.0
C A:TRP342 4.3 27.4 1.0
CA A:ASN340 4.3 25.8 1.0
N A:ASN340 4.4 24.4 1.0
CA A:ILE341 4.4 24.6 1.0
O3' P:DT4 4.4 24.6 1.0
CA A:SER339 4.4 25.9 0.5
O P:HOH267 4.5 46.8 1.0
N A:GLY345 4.6 26.0 1.0
CB A:ALA344 4.6 25.8 1.0
O P:HOH174 4.6 45.0 1.0
C A:GLY343 4.7 26.9 1.0
CB A:SER339 4.7 30.1 0.5
O A:ASN340 4.8 26.5 1.0
CA A:GLY345 4.8 26.8 1.0
O A:HOH136 4.9 39.5 1.0
O5' P:DA5 4.9 26.1 1.0
CA A:GLY343 4.9 26.5 1.0

Reference:

M.Garcia-Diaz, K.Bebenek, A.A.Larrea, J.M.Havener, L.Perera, J.M.Krahn, L.C.Pedersen, D.A.Ramsden, T.A.Kunkel. Scrunching During Dna Repair Synthesis To Be Published.
Page generated: Mon Oct 7 10:29:06 2024

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