Magnesium 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:

Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Dttp, PDB code: 5vz9:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg501 b:7.3 occ:1.00 O2G A:TTP505 2.1 6.9 1.0 OP1 P:DT5 2.1 7.5 1.0 OD2 A:ASP332 2.1 6.8 1.0 O A:HOH711 2.1 9.0 1.0 O2B A:TTP505 2.1 8.7 0.8 OD1 A:ASP330 2.2 8.4 1.0 CG A:ASP332 3.2 6.6 1.0 CG A:ASP330 3.2 25.2 1.0 PG A:TTP505 3.2 11.3 1.0 PB A:TTP505 3.3 16.5 0.8 NA A:NA503 3.4 5.7 1.0 O3B A:TTP505 3.5 8.2 0.7 P P:DT5 3.5 7.4 1.0 OD1 A:ASP332 3.5 10.2 1.0 OD2 A:ASP330 3.5 36.1 1.0 O A:HOH750 4.0 22.8 1.0 O5' P:DT5 4.1 6.1 1.0 C5' P:DT5 4.1 6.2 1.0 O3G A:TTP505 4.1 13.6 1.0 O1B A:TTP505 4.2 18.7 0.8 O A:ASP330 4.2 7.5 1.0 O A:HOH643 4.2 6.8 1.0 N A:GLY320 4.3 5.1 1.0 OP2 P:DT5 4.3 8.8 1.0 O A:HOH658 4.4 36.5 1.0 O1G A:TTP505 4.4 7.7 1.0 O3' P:DA4 4.5 8.0 1.0 C A:ASP330 4.5 6.6 1.0 O3A A:TTP505 4.5 22.3 0.8 CB A:ASP332 4.5 5.1 1.0 CA A:GLY319 4.6 4.8 1.0 CB A:ASP330 4.6 9.9 1.0 CA A:ASP330 4.9 8.3 1.0 O A:HOH754 5.0 20.4 0.8 N A:ASP332 5.0 5.7 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 P:Mg101 b:12.9 occ:0.78 O P:HOH216 2.0 15.2 1.0 OP2 P:DT5 2.1 8.8 1.0 O1B A:TTP505 2.1 18.7 0.8 O A:HOH754 2.1 20.4 0.8 O A:HOH792 2.1 17.2 0.8 O A:HOH753 2.1 20.5 0.8 P P:DT5 3.5 7.4 1.0 PB A:TTP505 3.5 16.5 0.8 O A:HOH830 3.8 13.8 1.0 O3B A:TTP505 4.1 8.2 0.7 OP1 P:DT5 4.1 7.5 1.0 O5' A:TTP505 4.1 50.5 0.8 C7 P:DT5 4.1 7.2 1.0 O P:HOH221 4.2 26.7 1.0 O2B A:TTP505 4.3 8.7 0.8 O3' P:DA4 4.4 8.0 1.0 OP2 P:DA4 4.4 10.5 1.0 O5' P:DT5 4.5 6.1 1.0 OP1 P:DA4 4.5 11.4 1.0 O5' P:DA4 4.6 8.6 1.0 C3' P:DA4 4.6 6.9 1.0 OD2 A:ASP330 4.6 36.1 1.0 O3A A:TTP505 4.7 22.3 0.8 P P:DA4 4.7 9.0 1.0 O1A A:TTP505 4.8 49.5 0.8 PA A:TTP505 4.8 44.5 0.8 O P:HOH205 4.9 30.8 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