Sodium in PDB 5vzi: Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Dttp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Dttp:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Dttp, PDB code: 5vzi 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)	32.88 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.132, 68.838, 111.023, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.4

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Dttp (pdb code 5vzi). 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 (W434H) Mutant with Incoming Dttp, PDB code: 5vzi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:9.6 occ:1.00 OP1 P:DT5 2.2 23.7 0.6 O A:HOH1001 2.2 16.4 0.4 O A:THR241 2.4 17.4 1.0 O P:HOH216 2.4 20.6 1.0 O A:VAL246 2.4 15.1 1.0 O A:ILE243 2.4 16.3 1.0 OP1 P:DT3 2.5 13.7 1.0 C A:VAL246 3.5 16.7 1.0 C A:ILE243 3.5 20.2 1.0 C A:THR241 3.5 15.7 1.0 P P:DT3 3.6 13.7 1.0 P P:DT5 3.7 17.0 0.6 N A:VAL246 3.8 16.0 1.0 OP2 P:DT3 3.9 12.6 1.0 N A:ILE243 4.1 16.2 1.0 C5' P:DT5 4.2 17.7 0.6 CA A:VAL246 4.2 16.4 1.0 C A:GLN242 4.2 18.0 1.0 N A:GLY245 4.2 15.2 1.0 CA A:THR241 4.2 14.9 1.0 N A:PHE244 4.2 15.0 1.0 CA A:PHE244 4.3 17.0 1.0 N A:GLY247 4.4 16.9 1.0 CA A:ILE243 4.4 16.9 1.0 O5' P:DT5 4.5 18.3 0.6 N A:GLN242 4.5 17.6 1.0 O A:GLN242 4.5 21.5 1.0 OP2 P:DT5 4.5 23.4 0.6 OP2 P:DA4 4.6 13.2 0.6 O3' P:DA4 4.6 16.5 0.6 C3' P:DA4 4.6 14.9 0.6 CA A:GLN242 4.6 18.4 1.0 O3' P:DG2 4.6 15.0 1.0 CB A:VAL246 4.6 16.6 1.0 C A:PHE244 4.7 19.8 1.0 CA A:GLY247 4.7 17.4 1.0 O5' P:DT3 4.7 13.0 1.0 O2 P:DT5 4.7 23.0 0.6 C A:GLY245 4.9 16.9 1.0 CB A:THR241 4.9 18.5 1.0 O A:PHE240 4.9 15.4 1.0

Sodium binding site 2 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:9.0 occ:0.58 MG A:MG704 0.0 9.2 0.4 OD2 A:ASP330 1.9 15.7 1.0 OD1 A:ASP332 2.1 10.7 1.0 OD2 A:ASP418 2.1 12.5 1.0 O P:HOH209 2.1 8.5 0.6 O A:HOH921 2.2 12.7 0.6 OP1 P:DT5 2.3 9.6 0.4 O3' P:DA4 2.3 9.4 0.4 O2A A:TTP702 2.4 7.7 0.6 CG A:ASP330 2.9 16.6 1.0 P P:DT5 2.9 9.4 0.4 CG A:ASP332 3.1 7.5 1.0 OD1 A:ASP330 3.1 8.5 1.0 CG A:ASP418 3.2 13.0 1.0 OD2 A:ASP332 3.4 6.3 1.0 PA A:TTP702 3.4 6.8 0.6 C3' P:DA4 3.5 11.1 0.4 MG A:MG703 3.5 9.2 1.0 C4' P:DA4 3.6 9.9 0.4 C5' P:DA4 3.6 12.4 0.4 CB A:ASP418 3.8 10.1 1.0 O5' A:TTP702 3.9 5.9 0.6 O1A A:TTP702 4.0 8.6 0.6 OP2 P:DT5 4.0 9.4 0.4 O P:HOH207 4.0 14.7 0.4 O5' P:DT5 4.1 12.6 0.4 CE1 A:HIS329 4.1 10.2 0.6 C5' A:TTP702 4.2 6.5 0.6 C5' P:DT5 4.2 15.0 0.4 CB A:ASP330 4.2 10.1 1.0 OD1 A:ASP418 4.3 12.3 1.0 O A:HOH1019 4.3 19.0 1.0 O5' P:DA4 4.4 13.8 0.4 CB A:ASP332 4.4 7.2 1.0 OP1 P:DA4 4.4 11.9 0.6 C2' P:DA4 4.6 9.4 0.4 NH2 A:ARG416 4.6 13.7 1.0 O2B A:TTP701 4.6 8.3 0.4 O3A A:TTP702 4.8 5.6 0.6 OP1 P:DA4 4.8 13.4 0.4 O3G A:TTP702 4.9 9.1 0.6 NE2 A:HIS329 4.9 9.0 0.6 O2G A:TTP701 5.0 6.0 0.4 ND1 A:HIS329 5.0 14.2 0.6 O4' P:DA4 5.0 11.0 0.4

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