Magnesium in PDB 4m04: Human Dna Polymerase Mu Ternary Complex

All present enzymatic activity of Human Dna Polymerase Mu Ternary Complex:
2.7.7.7;

The structure of Human Dna Polymerase Mu Ternary Complex, PDB code: 4m04 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)	23.17 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.892, 68.467, 109.773, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.6

The structure of Human Dna Polymerase Mu Ternary Complex also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Human Dna Polymerase Mu Ternary Complex (pdb code 4m04). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Mu Ternary Complex, PDB code: 4m04:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Mu Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Mu Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:6.5 occ:1.00 OD2 A:ASP330 2.0 6.0 1.0 OD1 A:ASP332 2.0 4.8 1.0 OD1 A:ASP418 2.0 6.5 1.0 O A:HOH807 2.1 7.7 1.0 O3' P:DA4 2.1 4.2 1.0 O1A A:DUP701 2.3 3.0 1.0 CG A:ASP332 3.1 5.4 1.0 CG A:ASP330 3.1 5.8 1.0 CG A:ASP418 3.2 9.0 1.0 C3' P:DA4 3.3 7.3 1.0 PA A:DUP701 3.3 4.8 1.0 OD2 A:ASP332 3.5 3.3 1.0 OD1 A:ASP330 3.5 5.5 1.0 MG A:MG703 3.6 2.8 1.0 O5' A:DUP701 3.7 4.1 1.0 O2A A:DUP701 3.7 6.6 1.0 C4' P:DA4 3.8 9.7 1.0 CB A:ASP418 3.9 6.4 1.0 C5' P:DA4 3.9 9.6 1.0 C5' A:DUP701 4.0 2.5 1.0 CE1 A:HIS329 4.1 4.6 0.8 OD2 A:ASP418 4.2 8.8 1.0 CB A:ASP332 4.4 2.5 1.0 CB A:ASP330 4.4 3.8 1.0 O5' P:DA4 4.5 14.2 1.0 OP1 P:DA4 4.5 7.9 1.0 C2' P:DA4 4.6 6.6 1.0 CZ3 A:TRP434 4.6 7.7 1.0 NH2 A:ARG416 4.6 7.6 1.0 O3G A:DUP701 4.7 6.5 1.0 ND1 A:HIS329 4.8 6.0 0.8 N3A A:DUP701 4.9 3.8 1.0 O2B A:DUP701 5.0 2.9 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Mu Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Mu Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:2.8 occ:1.00 OD1 A:ASP330 2.0 5.5 1.0 O2B A:DUP701 2.0 2.9 1.0 OD2 A:ASP332 2.0 3.3 1.0 O3G A:DUP701 2.1 6.5 1.0 O1A A:DUP701 2.1 3.0 1.0 O A:HOH821 2.1 5.1 1.0 CG A:ASP330 3.1 5.8 1.0 CG A:ASP332 3.1 5.4 1.0 PB A:DUP701 3.2 4.5 1.0 PA A:DUP701 3.3 4.8 1.0 PG A:DUP701 3.4 7.4 1.0 OD2 A:ASP330 3.4 6.0 1.0 OD1 A:ASP332 3.5 4.8 1.0 N3A A:DUP701 3.5 3.8 1.0 O3B A:DUP701 3.6 4.9 1.0 MG A:MG702 3.6 6.5 1.0 O A:ASP330 4.1 5.3 1.0 C5' A:DUP701 4.1 2.5 1.0 O A:HOH828 4.1 7.0 1.0 ND1 A:HIS329 4.1 6.0 0.8 O2G A:DUP701 4.2 7.6 1.0 N A:GLY320 4.2 3.9 1.0 O A:HOH803 4.2 4.4 1.0 O5' A:DUP701 4.3 4.1 1.0 C A:ASP330 4.3 7.2 1.0 CB A:ASP330 4.4 3.8 1.0 CB A:ASP332 4.4 2.5 1.0 O2A A:DUP701 4.4 6.6 1.0 CE1 A:HIS329 4.5 4.6 0.8 O1B A:DUP701 4.5 5.2 1.0 CA A:GLY319 4.5 5.7 1.0 O1G A:DUP701 4.5 6.7 1.0 N A:ASP330 4.5 5.5 1.0 CA A:ASP330 4.7 5.7 1.0 O A:HOH807 4.7 7.7 1.0 N A:ASP332 4.7 5.3 1.0 C A:GLY319 4.9 6.0 1.0 N A:VAL331 4.9 3.4 1.0

A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Sustained Active Site Rigidity During Synthesis By Human Dna Polymerase Mu. Nat.Struct.Mol.Biol. V. 21 253 2014.
ISSN: ISSN 1545-9993
PubMed: 24487959
DOI: 10.1038/NSMB.2766