Sodium in PDB 5ddm: Human Dna Polymerase Lambda- Apoenzyme and Complex with 6 Paired Dna

All present enzymatic activity of Human Dna Polymerase Lambda- Apoenzyme and Complex with 6 Paired Dna:
2.7.7.7;

The structure of Human Dna Polymerase Lambda- Apoenzyme and Complex with 6 Paired Dna, PDB code: 5ddm was solved by M.S.Liu, M.D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.98 / 2.80
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	83.693, 83.693, 396.326, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 23.9

The binding sites of Sodium atom in the Human Dna Polymerase Lambda- Apoenzyme and Complex with 6 Paired Dna (pdb code 5ddm). 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 Human Dna Polymerase Lambda- Apoenzyme and Complex with 6 Paired Dna, PDB code: 5ddm:

Sodium binding site 1 out of 1 in the Human Dna Polymerase Lambda- Apoenzyme and Complex with 6 Paired Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Lambda- Apoenzyme and Complex with 6 Paired Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:28.3 occ:1.00 O B:SER339 2.3 27.6 1.0 O B:ALA344 2.6 29.6 1.0 OP1 P:DT4 2.8 27.3 1.0 O B:ILE341 2.8 27.4 1.0 OP2 P:DT4 3.4 22.6 1.0 C B:SER339 3.5 24.5 1.0 P P:DT4 3.5 25.5 1.0 C B:ILE341 3.7 27.6 1.0 C B:ALA344 3.8 26.1 1.0 N B:ILE341 4.3 23.2 1.0 C B:ASN340 4.3 25.2 1.0 CA B:TRP342 4.3 25.3 1.0 N B:TRP342 4.4 25.4 1.0 CA B:ASN340 4.4 28.4 1.0 N B:ASN340 4.4 26.3 1.0 N B:ALA344 4.4 26.5 1.0 CA B:SER339 4.4 24.1 1.0 N B:GLY343 4.5 27.1 1.0 O3' P:DG3 4.5 22.8 1.0 CA B:ILE341 4.7 24.9 1.0 CA B:ALA344 4.7 24.1 1.0 N B:GLY345 4.7 20.6 1.0 CA B:GLY345 4.7 21.5 1.0 O5' P:DT4 4.8 21.6 1.0 C B:TRP342 4.8 29.1 1.0 O B:ASN340 4.9 27.7 1.0 CB B:SER339 4.9 25.1 1.0

M.S.Liu, H.Y.Tsai, X.X.Liu, M.C.Ho, W.J.Wu, M.D.Tsai. Structural Mechanism For the Fidelity Modulation of Dna Polymerase Lambda J.Am.Chem.Soc. V. 138 2389 2016.
ISSN: ESSN 1520-5126
PubMed: 26836966
DOI: 10.1021/JACS.5B13368