Sodium in PDB 5vz9: Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp, PDB code: 5vz9 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)	35.15 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.190, 68.847, 111.355, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.1

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp (pdb code 5vz9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp, PDB code: 5vz9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:5.7 occ:1.00 OD1 A:ASP332 2.0 10.2 1.0 OD1 A:ASP418 2.1 13.2 1.0 OD2 A:ASP330 2.4 36.1 1.0 OP1 P:DT5 2.4 7.5 1.0 O3' P:DA4 2.7 8.0 1.0 CG A:ASP330 2.9 25.2 1.0 OD1 A:ASP330 2.9 8.4 1.0 CG A:ASP332 3.0 6.6 1.0 P P:DT5 3.2 7.4 1.0 CG A:ASP418 3.2 11.7 1.0 OD2 A:ASP332 3.3 6.8 1.0 MG A:MG501 3.4 7.3 1.0 CB A:ASP418 3.8 7.4 1.0 C3' P:DA4 3.9 6.9 1.0 C4' P:DA4 4.0 7.3 1.0 C5' P:DA4 4.0 7.7 1.0 CB A:ASP330 4.1 9.9 1.0 OD2 A:ASP418 4.2 14.4 1.0 OP2 P:DT5 4.2 8.8 1.0 O A:HOH754 4.2 20.4 0.8 O5' P:DT5 4.3 6.1 1.0 CB A:ASP332 4.3 5.1 1.0 C5' P:DT5 4.4 6.2 1.0 NH2 A:ARG416 4.6 11.0 1.0 O2B A:TTP505 4.6 8.7 0.8 O A:VAL331 4.8 7.0 1.0 CZ3 A:TRP434 4.8 8.9 1.0 CA A:ASP332 4.8 5.4 1.0 C A:VAL331 4.9 6.0 1.0 N A:ASP418 4.9 7.4 1.0 C2' P:DA4 5.0 6.9 1.0 O5' P:DA4 5.0 8.6 1.0

Sodium binding site 2 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:12.9 occ:1.00 O A:VAL246 2.3 13.6 1.0 O A:HOH844 2.4 21.2 1.0 O A:ILE243 2.4 14.6 1.0 O A:THR241 2.4 17.1 1.0 O P:HOH217 2.4 17.8 1.0 OP1 P:DT3 2.6 13.2 1.0 C A:VAL246 3.4 13.2 1.0 C A:ILE243 3.4 17.6 1.0 C A:THR241 3.5 15.0 1.0 P P:DT3 3.6 12.0 1.0 N A:VAL246 3.7 12.9 1.0 OP2 P:DT3 3.9 10.1 1.0 O P:HOH205 3.9 30.8 1.0 O A:HOH800 4.0 46.7 1.0 CA A:VAL246 4.0 13.6 1.0 N A:ILE243 4.1 13.6 1.0 N A:GLY245 4.2 12.3 1.0 N A:PHE244 4.2 12.9 1.0 C A:GLN242 4.2 19.5 1.0 CA A:THR241 4.2 11.7 1.0 CA A:PHE244 4.2 14.7 1.0 CA A:ILE243 4.4 13.5 1.0 N A:GLY247 4.4 13.2 1.0 CB A:VAL246 4.4 13.5 1.0 N A:GLN242 4.5 14.5 1.0 O A:HOH856 4.6 55.8 1.0 O A:HOH876 4.6 33.2 1.0 CA A:GLN242 4.6 17.7 1.0 O A:GLN242 4.6 18.8 1.0 C A:PHE244 4.6 18.2 1.0 O3' P:DG2 4.6 11.9 1.0 CA A:GLY247 4.7 14.7 1.0 C A:GLY245 4.8 13.5 1.0 O A:PHE240 4.8 13.8 1.0 O5' P:DT3 4.9 9.6 1.0 CB A:THR241 4.9 15.8 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