Sodium in PDB 5twq: Post-Catalytic Nicked Complex of Human Polymerase Mu with Newly Incorporated Utp

The structure of Post-Catalytic Nicked Complex of Human Polymerase Mu with Newly Incorporated Utp, PDB code: 5twq was solved by A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.97 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.969, 68.712, 110.413, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.5

The structure of Post-Catalytic Nicked Complex of Human Polymerase Mu with Newly Incorporated Utp also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Manganese	(Mn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Post-Catalytic Nicked Complex of Human Polymerase Mu with Newly Incorporated Utp (pdb code 5twq). 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 Post-Catalytic Nicked Complex of Human Polymerase Mu with Newly Incorporated Utp, PDB code: 5twq:

Sodium binding site 1 out of 1 in the Post-Catalytic Nicked Complex of Human Polymerase Mu with Newly Incorporated Utp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Post-Catalytic Nicked Complex of Human Polymerase Mu with Newly Incorporated Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:18.3 occ:1.00 O A:VAL246 2.3 21.7 1.0 O A:ILE243 2.3 21.1 1.0 O A:THR241 2.4 22.9 1.0 O P:HOH114 2.4 26.5 1.0 O A:HOH841 2.5 29.1 1.0 OP1 P:DT3 2.5 20.1 1.0 C A:VAL246 3.4 20.5 1.0 C A:ILE243 3.4 23.1 1.0 C A:THR241 3.5 24.4 1.0 P P:DT3 3.6 19.7 1.0 N A:VAL246 3.7 19.4 1.0 OP2 P:DT3 3.8 17.1 1.0 CA A:VAL246 4.0 21.4 1.0 N A:ILE243 4.1 22.1 1.0 N A:GLY245 4.1 18.3 1.0 N A:PHE244 4.2 21.9 1.0 CA A:THR241 4.2 20.1 1.0 C A:GLN242 4.2 24.6 1.0 O A:HOH774 4.2 42.2 1.0 CA A:PHE244 4.2 21.3 1.0 CA A:ILE243 4.4 19.3 1.0 N A:GLY247 4.4 21.9 1.0 CB A:VAL246 4.4 18.8 1.0 N A:GLN242 4.4 23.0 1.0 O A:GLN242 4.5 26.3 1.0 O3' P:DG2 4.6 20.6 1.0 C A:PHE244 4.6 23.4 1.0 CA A:GLN242 4.6 24.1 1.0 CA A:GLY247 4.7 21.4 1.0 C A:GLY245 4.7 20.8 1.0 O A:PHE240 4.8 20.6 1.0 O5' P:DT3 4.8 18.3 1.0 CB A:THR241 4.8 20.0 1.0

A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Structural Accommodation of Ribonucleotide Incorporation By the Dna Repair Enzyme Polymerase Mu. Nucleic Acids Res. V. 45 9138 2017.
ISSN: ESSN 1362-4962
PubMed: 28911097
DOI: 10.1093/NAR/GKX527