Magnesium 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:

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

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Dttp, PDB code: 5vzc:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg501 b:7.6 occ:1.00 OD2 A:ASP332 2.1 6.9 1.0 OP1 P:DT5 2.1 7.8 1.0 O2G A:TTP505 2.1 7.5 1.0 OD1 A:ASP330 2.1 8.5 1.0 O A:HOH737 2.1 8.7 1.0 O2B A:TTP505 2.2 9.6 0.8 CG A:ASP332 3.1 7.5 1.0 CG A:ASP330 3.2 22.4 1.0 PG A:TTP505 3.2 12.4 1.0 PB A:TTP505 3.3 15.9 0.8 NA A:NA503 3.4 7.7 1.0 O3B A:TTP505 3.5 15.0 1.0 OD1 A:ASP332 3.5 10.3 1.0 P P:DT5 3.5 8.6 1.0 OD2 A:ASP330 3.5 33.6 1.0 O A:HOH709 4.0 23.6 1.0 O5' P:DT5 4.1 6.8 1.0 C5' P:DT5 4.1 8.6 1.0 O3G A:TTP505 4.2 15.5 1.0 O A:ASP330 4.2 8.0 1.0 O1B A:TTP505 4.2 19.9 0.8 O A:HOH637 4.2 9.2 1.0 N A:GLY320 4.4 5.5 1.0 OP2 P:DT5 4.4 10.3 1.0 O1G A:TTP505 4.4 9.1 1.0 C A:ASP330 4.4 7.6 1.0 O3' P:DA4 4.4 8.7 1.0 CB A:ASP332 4.5 6.6 1.0 O A:HOH639 4.5 32.6 1.0 CB A:ASP330 4.5 11.3 1.0 O3A A:TTP505 4.5 20.7 0.8 CA A:GLY319 4.6 5.7 1.0 CA A:ASP330 4.9 9.9 1.0 O A:HOH719 4.9 24.3 1.0 N A:ASP332 4.9 5.9 1.0 N A:VAL331 5.0 7.1 1.0 N A:ASP330 5.0 8.8 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 P:Mg101 b:8.6 occ:0.58 O1B A:TTP505 2.0 19.9 0.8 O A:HOH774 2.1 23.0 1.0 O P:HOH213 2.1 16.2 1.0 OP2 P:DT5 2.1 10.3 1.0 O A:HOH719 2.1 24.3 1.0 O A:HOH731 2.1 17.5 0.6 PB A:TTP505 3.4 15.9 0.8 P P:DT5 3.4 8.6 1.0 O P:HOH217 3.7 15.2 1.0 O3B A:TTP505 4.0 15.0 1.0 O5' A:TTP505 4.0 48.1 0.8 OP1 P:DT5 4.0 7.8 1.0 C7 P:DT5 4.2 9.1 1.0 O P:HOH221 4.2 29.1 1.0 O2B A:TTP505 4.3 9.6 0.8 O3' P:DA4 4.4 8.7 1.0 O5' P:DT5 4.5 6.8 1.0 OP2 P:DA4 4.5 12.2 1.0 OP1 P:DA4 4.5 11.1 1.0 O3A A:TTP505 4.5 20.7 0.8 O5' P:DA4 4.5 8.8 1.0 OD2 A:ASP330 4.6 33.6 1.0 C3' P:DA4 4.6 7.8 1.0 P P:DA4 4.7 9.9 1.0 PA A:TTP505 4.8 37.2 0.8 O P:HOH204 4.8 36.7 1.0 O1A A:TTP505 4.9 43.4 0.8

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