Sodium in PDB 5dmu: Structure of the Nhej Polymerase From Methanocella Paludicola

The structure of Structure of the Nhej Polymerase From Methanocella Paludicola, PDB code: 5dmu was solved by N.C.Brissett, E.J.Bartlett, A.J.Doherty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.31 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.420, 60.550, 59.410, 90.00, 101.02, 90.00
R / Rfree (%)	14.8 / 19.5

The binding sites of Sodium atom in the Structure of the Nhej Polymerase From Methanocella Paludicola (pdb code 5dmu). 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 Structure of the Nhej Polymerase From Methanocella Paludicola, PDB code: 5dmu:

Sodium binding site 1 out of 1 in the Structure of the Nhej Polymerase From Methanocella Paludicola


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Nhej Polymerase From Methanocella Paludicola within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:15.7 occ:1.00 OD1 A:ASN246 2.8 8.5 1.0 O A:ARG149 2.9 8.2 1.0 CB A:ASN246 3.3 7.8 1.0 CE1 A:PHE204 3.4 7.7 1.0 CG A:PRO147 3.4 7.9 1.0 CB A:PRO147 3.4 8.1 1.0 CG1 A:VAL207 3.5 8.0 1.0 CG A:ASN246 3.5 8.0 1.0 CA A:ASN246 3.5 7.8 1.0 CD1 A:PHE204 3.5 7.7 1.0 CD2 A:LEU138 3.8 7.4 1.0 C A:ARG149 4.0 8.0 1.0 CA A:LEU150 4.2 8.6 1.0 C A:ASN246 4.2 8.0 1.0 CB A:VAL207 4.2 8.3 1.0 CB A:LEU138 4.3 7.9 1.0 N A:LEU150 4.5 8.2 1.0 O A:ASN246 4.6 8.1 1.0 CZ A:PHE204 4.6 7.4 1.0 N A:ASN246 4.6 7.3 1.0 CG A:LEU138 4.7 8.2 1.0 CD A:PRO147 4.8 7.9 1.0 CG A:PHE204 4.8 8.1 1.0 ND2 A:ASN246 4.8 7.5 1.0 CG2 A:VAL207 4.9 7.9 1.0 CB A:LEU150 4.9 9.2 1.0 N A:ILE151 4.9 8.6 1.0 CD1 A:LEU150 5.0 10.9 1.0 N A:SER247 5.0 8.0 1.0 CA A:PRO147 5.0 7.6 1.0

E.J.Bartlett, N.C.Brissett, P.Plocinski, T.Carlberg, A.J.Doherty. Molecular Basis For Dna Strand Displacement By Nhej Repair Polymerases. Nucleic Acids Res. V. 44 2173 2016.
ISSN: ESSN 1362-4962
PubMed: 26405198
DOI: 10.1093/NAR/GKV965