Sodium in PDB 7un7: Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate

All present enzymatic activity of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate:
2.7.7.7;

The structure of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate, PDB code: 7un7 was solved by J.A.Jamsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.76 / 2.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.135, 62.774, 140.193, 90, 90, 90
R / Rfree (%)	22 / 24.7

The structure of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate (pdb code 7un7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate, PDB code: 7un7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:19.2 occ:1.00 O A:ALA344 2.2 18.4 1.0 OP1 P:DA5 2.3 26.2 0.9 O A:SER339 2.3 19.1 1.0 O A:ILE341 2.4 22.6 1.0 OP1 P:DA5 2.4 24.6 0.1 O P:HOH114 2.5 25.7 1.0 O P:HOH105 2.8 26.4 1.0 C A:ALA344 3.3 23.2 1.0 C A:ILE341 3.3 22.5 1.0 C A:SER339 3.4 20.9 1.0 P P:DA5 3.4 23.4 0.9 P P:DA5 3.5 22.1 0.1 N A:ALA344 3.6 20.5 1.0 OP2 P:DA5 3.7 17.8 0.9 OP2 P:DA5 3.7 17.8 0.1 O A:HOH765 3.8 31.2 1.0 N A:ILE341 4.0 17.1 1.0 CA A:ALA344 4.0 23.2 1.0 CA A:TRP342 4.0 18.6 1.0 N A:TRP342 4.0 22.5 1.0 N A:GLY343 4.1 19.8 1.0 CA A:SER339 4.1 23.3 1.0 C A:ASN340 4.3 16.8 1.0 CA A:ILE341 4.3 18.0 1.0 N A:ASN340 4.3 22.8 1.0 N A:GLY345 4.4 20.1 1.0 O3' P:DT4 4.4 18.4 1.0 C A:TRP342 4.4 20.5 1.0 CB A:ALA344 4.4 20.7 1.0 O P:HOH117 4.4 30.1 1.0 CA A:ASN340 4.4 20.5 1.0 O5' P:DA5 4.6 19.5 0.9 C A:GLY343 4.6 21.9 1.0 CA A:GLY345 4.7 19.9 1.0 O5' P:DA5 4.8 20.1 0.1 CB A:SER339 4.8 19.2 1.0 O A:PHE338 4.9 21.4 1.0 O A:ASN340 4.9 20.9 1.0 CA A:GLY343 4.9 19.8 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:57.9 occ:1.00 NE2 A:GLN366 2.4 60.1 1.0 O A:HOH758 3.4 51.8 1.0 CD A:GLN366 3.6 53.2 1.0 O A:HOH728 3.8 50.7 1.0 OD1 A:ASP362 3.9 29.1 1.0 OE1 A:GLN366 4.1 58.5 1.0 CG A:ASP362 4.3 28.8 1.0 OD2 A:ASP362 4.7 32.5 1.0 CG A:GLN366 4.8 48.4 1.0 CB A:ASP362 4.9 26.9 1.0 CD1 A:PHE357 4.9 40.3 1.0

G.Chandramouly, J.Jamsen, N.Borisonnik, M.Tyagi, M.L.Calbert, T.Tredinnick, A.Y.Ozdemir, T.Kent, E.V.Demidova, S.Arora, S.H.Wilson, R.T.Pomerantz. Pol Lambda Promotes Microhomology-Mediated End-Joining. Nat.Struct.Mol.Biol. V. 30 107 2023.
ISSN: ESSN 1545-9985
PubMed: 36536104
DOI: 10.1038/S41594-022-00895-4