Sodium in PDB 5vzf: Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp, PDB code: 5vzf 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)	32.79 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.866, 68.690, 110.224, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.5

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Dttp (pdb code 5vzf). 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 (W434A) Mutant with Incoming Dttp, PDB code: 5vzf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (W434A) 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 (W434A) Mutant with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:9.8 occ:1.00 O A:HOH1029 2.2 13.9 0.6 O P:HOH821 2.3 21.2 1.0 OP1 P:DT5 2.3 21.4 0.4 O A:VAL246 2.3 14.7 1.0 O A:THR241 2.3 16.0 1.0 O A:ILE243 2.5 15.8 1.0 OP1 P:DT3 2.5 14.2 1.0 C A:VAL246 3.4 16.3 1.0 C A:THR241 3.5 17.0 1.0 C A:ILE243 3.5 20.6 1.0 P P:DT3 3.6 13.2 1.0 P P:DT5 3.8 18.7 0.4 N A:VAL246 3.8 14.7 1.0 OP2 P:DT3 3.9 10.8 1.0 C5' P:DT5 4.1 17.3 0.4 CA A:VAL246 4.1 15.3 1.0 N A:ILE243 4.1 16.2 1.0 N A:GLY245 4.2 14.3 1.0 CA A:THR241 4.2 13.3 1.0 C A:GLN242 4.2 20.2 1.0 N A:PHE244 4.3 14.8 1.0 CA A:PHE244 4.3 15.2 1.0 O5' P:DT5 4.4 21.6 0.4 N A:GLY247 4.5 15.0 1.0 CA A:ILE243 4.5 12.9 1.0 N A:GLN242 4.5 17.7 1.0 OP2 P:DA4 4.5 11.8 0.4 CB A:VAL246 4.6 15.1 1.0 CA A:GLN242 4.6 20.3 1.0 O3' P:DG2 4.6 13.6 1.0 O A:GLN242 4.6 21.8 1.0 OP2 P:DT5 4.6 19.2 0.4 C A:PHE244 4.7 19.2 1.0 C3' P:DA4 4.7 16.9 0.4 O3' P:DA4 4.7 15.9 0.4 CA A:GLY247 4.7 18.2 1.0 O5' P:DT3 4.8 12.1 1.0 C A:GLY245 4.8 15.2 1.0 O A:PHE240 4.9 14.7 1.0 CB A:THR241 4.9 16.1 1.0 O P:HOH816 5.0 15.2 0.6

Sodium binding site 2 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (W434A) 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 (W434A) Mutant with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:22.0 occ:0.56 MG A:MG703 0.0 2.3 0.4 OD2 A:ASP330 2.0 23.0 1.0 OD1 A:ASP332 2.1 9.2 1.0 OD2 A:ASP418 2.1 14.5 1.0 O P:HOH818 2.2 9.7 0.4 O A:HOH864 2.3 13.4 0.4 OP1 P:DT5 2.3 6.4 0.6 O3' P:DA4 2.3 6.9 0.6 O2A P:TTP701 2.3 3.6 0.4 CG A:ASP330 2.8 17.8 1.0 P P:DT5 2.9 6.0 0.6 OD1 A:ASP330 3.1 8.6 1.0 CG A:ASP332 3.1 7.8 1.0 CG A:ASP418 3.3 13.9 1.0 OD2 A:ASP332 3.4 6.6 1.0 PA P:TTP701 3.4 7.2 0.4 MG A:MG702 3.5 7.1 1.0 C3' P:DA4 3.5 6.6 0.6 C4' P:DA4 3.6 9.6 0.6 C5' P:DA4 3.7 9.6 0.6 CB A:ASP418 3.9 7.3 1.0 O1A P:TTP701 3.9 8.2 0.4 O5' P:TTP701 4.0 1.7 0.4 OP2 P:DT5 4.0 6.3 0.6 O P:HOH819 4.0 20.1 0.6 O5' P:DT5 4.1 9.8 0.6 CB A:ASP330 4.2 8.9 1.0 C5' P:DT5 4.2 10.0 0.6 C5' P:TTP701 4.2 3.3 0.4 OD1 A:ASP418 4.3 12.5 1.0 O A:HOH1042 4.3 21.7 1.0 CB A:ASP332 4.4 6.2 1.0 CE1 A:HIS329 4.4 18.6 0.4 O5' P:DA4 4.6 8.2 0.6 C2' P:DA4 4.6 6.7 0.6 OP1 P:DA4 4.6 13.6 0.4 NH2 A:ARG416 4.6 12.1 1.0 O2B A:TTP701 4.6 9.3 0.6 O3G P:TTP701 4.7 6.3 0.4 O2B P:TTP701 4.9 4.2 0.4 O3A P:TTP701 4.9 5.3 0.4 OP1 P:DA4 4.9 11.5 0.6 O A:VAL331 5.0 6.8 1.0 CA A:ASP332 5.0 7.0 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