Sodium in PDB 5vzc: Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Dttp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Dttp:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Dttp, PDB code: 5vzc 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)	32.82 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.112, 68.716, 110.993, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433S) 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 (G433S) Mutant with Incoming Dttp (pdb code 5vzc). 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 (G433S) Mutant with Incoming Dttp, PDB code: 5vzc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (G433S) 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 (G433S) Mutant with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:7.7 occ:1.00 OD1 A:ASP332 2.1 10.3 1.0 OD1 A:ASP418 2.1 13.2 1.0 OD2 A:ASP330 2.4 33.6 1.0 OP1 P:DT5 2.4 7.8 1.0 O3' P:DA4 2.6 8.7 1.0 CG A:ASP330 2.9 22.4 1.0 OD1 A:ASP330 2.9 8.5 1.0 CG A:ASP332 3.1 7.5 1.0 P P:DT5 3.1 8.6 1.0 CG A:ASP418 3.2 11.6 1.0 OD2 A:ASP332 3.4 6.9 1.0 MG A:MG501 3.4 7.6 1.0 C3' P:DA4 3.8 7.8 1.0 CB A:ASP418 3.8 7.6 1.0 C4' P:DA4 3.9 9.2 1.0 C5' P:DA4 3.9 8.9 1.0 CB A:ASP330 4.1 11.3 1.0 O A:HOH719 4.1 24.3 1.0 OD2 A:ASP418 4.1 12.1 1.0 OP2 P:DT5 4.1 10.3 1.0 O5' P:DT5 4.3 6.8 1.0 C5' P:DT5 4.4 8.6 1.0 CB A:ASP332 4.4 6.6 1.0 NH2 A:ARG416 4.5 12.3 1.0 O2B A:TTP505 4.7 9.6 0.8 CZ3 A:TRP434 4.8 11.3 1.0 O A:VAL331 4.8 8.4 1.0 O5' P:DA4 4.8 8.8 1.0 C2' P:DA4 4.9 9.8 1.0 CA A:ASP332 4.9 5.6 1.0 OP1 P:DA4 4.9 11.1 1.0 C A:VAL331 5.0 6.2 1.0

Sodium binding site 2 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (G433S) 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 (G433S) Mutant with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:13.3 occ:1.00 O A:VAL246 2.3 13.7 1.0 O P:HOH216 2.4 18.6 1.0 O A:HOH862 2.4 23.4 1.0 O A:THR241 2.4 16.5 1.0 O A:ILE243 2.4 15.4 1.0 OP1 P:DT3 2.6 13.3 1.0 C A:VAL246 3.4 13.9 1.0 C A:ILE243 3.4 18.5 1.0 C A:THR241 3.5 13.8 1.0 P P:DT3 3.6 12.6 1.0 N A:VAL246 3.7 12.9 1.0 OP2 P:DT3 3.9 11.4 1.0 O P:HOH204 4.0 36.7 1.0 CA A:VAL246 4.0 14.1 1.0 N A:ILE243 4.1 15.3 1.0 O A:HOH843 4.1 47.6 1.0 CA A:THR241 4.2 13.2 1.0 N A:GLY245 4.2 13.2 1.0 C A:GLN242 4.2 17.9 1.0 N A:PHE244 4.2 13.1 1.0 CA A:PHE244 4.3 15.4 1.0 CA A:ILE243 4.4 11.6 1.0 N A:GLY247 4.4 14.4 1.0 N A:GLN242 4.4 16.6 1.0 CB A:VAL246 4.5 14.1 1.0 O A:HOH888 4.5 19.6 0.4 O A:GLN242 4.6 20.6 1.0 CA A:GLN242 4.6 18.4 1.0 C A:PHE244 4.6 16.8 1.0 O3' P:DG2 4.6 13.2 1.0 O A:HOH890 4.6 30.5 1.0 CA A:GLY247 4.7 15.5 1.0 C A:GLY245 4.8 13.5 1.0 O A:PHE240 4.8 14.5 1.0 O5' P:DT3 4.8 9.6 1.0 CB A:THR241 4.9 15.9 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