Magnesium in PDB 6wie: Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate

All present enzymatic activity of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate:
2.7.7.7;

The structure of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wie was solved by A.M.Kaminski, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.90 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.073, 62.247, 118.318, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 18.7

The structure of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate (pdb code 6wie). 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 Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wie:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:16.6 occ:0.60 NA A:NA502 0.1 17.8 0.4 OD2 A:ASP418 1.8 19.4 1.0 OD1 A:ASP332 1.9 15.0 1.0 OD2 A:ASP330 1.9 22.3 1.0 OP1 P:DT5 2.3 15.4 1.0 O3' P:DA4 2.6 17.2 1.0 CG A:ASP330 2.8 18.2 1.0 CG A:ASP332 2.9 13.2 1.0 CG A:ASP418 2.9 16.3 1.0 OD1 A:ASP330 3.1 14.3 1.0 P P:DT5 3.2 16.1 1.0 OD2 A:ASP332 3.2 14.6 1.0 MG A:MG503 3.5 13.6 1.0 CB A:ASP418 3.6 12.0 1.0 C3' P:DA4 3.8 13.4 1.0 C4' P:DA4 3.8 15.9 1.0 OD1 A:ASP418 3.9 17.1 1.0 C5' P:DA4 3.9 14.4 1.0 CB A:ASP330 4.0 12.9 1.0 OP2 P:DT5 4.2 13.8 1.0 O5' P:DT5 4.2 12.2 1.0 CB A:ASP332 4.2 10.7 1.0 C5' P:DT5 4.3 13.0 1.0 CZ3 A:TRP434 4.5 19.0 1.0 O32 A:PPV507 4.5 23.8 0.4 O A:HOH629 4.6 17.1 0.6 CE1 A:HIS329 4.6 28.4 1.0 NH2 A:ARG416 4.7 13.1 1.0 O A:VAL331 4.7 12.7 1.0 CA A:ASP332 4.7 10.4 1.0 C A:VAL331 4.9 12.7 1.0 N A:ASP418 4.9 11.1 1.0 CA A:ASP418 4.9 10.4 1.0 C2' P:DA4 4.9 15.3 1.0 N A:ASP332 4.9 10.5 1.0 O5' P:DA4 4.9 13.2 1.0

Magnesium binding site 2 out of 2 in the Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:13.6 occ:1.00 O A:HOH629 1.9 17.1 0.6 O32 A:PPV507 2.0 23.8 0.4 O4 A:SO4506 2.1 14.7 0.6 OD1 A:ASP330 2.1 14.3 1.0 O11 A:PPV507 2.2 18.5 0.4 OP1 P:DT5 2.2 15.4 1.0 O A:HOH745 2.2 13.0 1.0 OD2 A:ASP332 2.2 14.6 1.0 P2 A:PPV507 3.1 18.8 0.4 CG A:ASP330 3.2 18.2 1.0 OPP A:PPV507 3.2 22.3 0.4 S A:SO4506 3.2 15.9 0.6 CG A:ASP332 3.3 13.2 1.0 P1 A:PPV507 3.3 31.3 0.4 O2 A:SO4506 3.3 22.4 0.6 NA A:NA502 3.5 17.8 0.4 OD2 A:ASP330 3.5 22.3 1.0 MG A:MG501 3.5 16.6 0.6 P P:DT5 3.5 16.1 1.0 OD1 A:ASP332 3.7 15.0 1.0 O12 A:PPV507 3.8 28.5 0.4 O3 A:SO4506 3.9 27.9 0.6 C5' P:DT5 4.0 13.0 1.0 O5' P:DT5 4.0 12.2 1.0 O A:ASP330 4.1 13.1 1.0 O21 A:PPV507 4.1 26.7 0.4 O A:HOH635 4.2 17.3 1.0 O A:HOH656 4.3 13.7 1.0 N A:GLY320 4.3 12.0 1.0 O22 A:PPV507 4.4 28.5 0.4 O31 A:PPV507 4.4 27.4 0.4 C A:ASP330 4.4 12.8 1.0 OP2 P:DT5 4.5 13.8 1.0 O1 A:SO4506 4.5 10.6 0.6 CB A:ASP330 4.5 12.9 1.0 O3' P:DA4 4.5 17.2 1.0 CA A:GLY319 4.5 11.1 1.0 CB A:ASP332 4.6 10.7 1.0 CE1 A:HIS329 4.6 28.4 1.0 ND1 A:HIS329 4.6 28.5 1.0 N A:ASP330 4.8 12.9 1.0 CA A:ASP330 4.8 11.7 1.0 N A:ASP332 4.9 10.5 1.0

A.M.Kaminski, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Structural Snapshots of Human Dna Polymerase Mu Engaged on A Dna Double-Strand Break. Nat Commun V. 11 4784 2020.
ISSN: ESSN 2041-1723
PubMed: 32963245
DOI: 10.1038/S41467-020-18506-5