Magnesium in PDB 5txz: Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min)

All present enzymatic activity of Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min):
2.7.7.7;

The structure of Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min), PDB code: 5txz was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.45 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.900, 68.571, 110.498, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.4

The structure of Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min) also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min) (pdb code 5txz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min), PDB code: 5txz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:14.6 occ:1.00 O1A A:TTP501 1.9 13.0 0.5 OD1 A:ASP330 2.0 16.9 1.0 OD2 A:ASP332 2.0 13.2 1.0 O A:HOH680 2.1 17.4 1.0 O1B A:TTP501 2.1 12.9 0.5 O1G A:TTP501 2.2 17.0 0.5 O21 A:PPV514 2.2 14.7 0.5 O32 A:PPV514 2.2 16.8 0.2 OP1 P:DT5 2.5 14.3 0.5 CG A:ASP332 3.1 14.6 1.0 CG A:ASP330 3.1 19.6 1.0 P1 A:PPV514 3.1 18.7 0.5 PB A:TTP501 3.2 19.1 0.5 PA A:TTP501 3.2 10.5 0.5 O31 A:PPV514 3.2 17.8 0.5 PG A:TTP501 3.4 19.1 0.5 P2 A:PPV514 3.5 19.4 0.2 OD1 A:ASP332 3.5 15.2 1.0 O3A A:TTP501 3.5 17.7 0.5 OD2 A:ASP330 3.6 22.9 1.0 MG A:MG503 3.6 12.9 0.6 CA A:CA504 3.6 12.5 0.4 O3B A:TTP501 3.6 18.6 0.5 OPP A:PPV514 3.8 18.4 0.2 O A:ASP330 3.9 15.0 1.0 P P:DT5 4.0 18.5 0.5 O2G A:TTP501 4.1 20.4 0.5 C5' A:TTP501 4.1 15.3 0.5 O22 A:PPV514 4.2 20.4 0.2 O5' A:TTP501 4.2 12.8 0.5 ND1 A:HIS329 4.2 21.1 0.5 O A:HOH622 4.2 14.7 1.0 C A:ASP330 4.2 14.6 1.0 O A:HOH606 4.3 21.4 1.0 O2A A:TTP501 4.3 12.5 0.5 N A:GLY320 4.3 12.9 1.0 C5' P:DT5 4.4 15.4 0.5 CB A:ASP332 4.4 11.9 1.0 CE1 A:HIS329 4.4 19.2 0.5 CB A:ASP330 4.4 15.4 1.0 O5' P:DT5 4.5 13.6 0.5 O11 A:PPV514 4.5 17.0 0.5 O2B A:TTP501 4.5 16.9 0.5 O3G A:TTP501 4.6 19.3 0.5 O12 A:PPV514 4.6 19.4 0.2 CA A:GLY319 4.6 11.5 1.0 N A:ASP330 4.6 14.6 1.0 CA A:ASP330 4.6 15.8 1.0 N A:ASP332 4.7 12.2 1.0 N A:VAL331 4.8 13.2 1.0 O3' P:DA4 4.8 18.5 0.5 O P:HOH101 4.9 23.5 1.0 OP2 P:DT5 4.9 17.2 0.5 C A:VAL331 4.9 13.8 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Mu Reactant Complex, 100MM MG2+ (15 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:12.9 occ:0.60 CA A:CA504 0.0 12.5 0.4 OD2 A:ASP330 2.0 22.9 1.0 OD2 A:ASP418 2.2 17.6 1.0 OP1 P:DT5 2.3 14.3 0.5 OD1 A:ASP332 2.3 15.2 1.0 O3' P:DA4 2.3 18.5 0.5 O P:HOH101 2.4 23.5 1.0 O3' P:DA4 2.5 13.3 0.5 O1A A:TTP501 2.6 13.0 0.5 P P:DT5 2.8 18.5 0.5 CG A:ASP330 3.0 19.6 1.0 OD1 A:ASP330 3.3 16.9 1.0 CG A:ASP332 3.3 14.6 1.0 CG A:ASP418 3.3 16.0 1.0 C3' P:DA4 3.5 17.6 0.5 C3' P:DA4 3.5 17.5 0.5 PA A:TTP501 3.5 10.5 0.5 OD2 A:ASP332 3.6 13.2 1.0 MG A:MG502 3.6 14.6 1.0 C4' P:DA4 3.7 18.7 0.5 O5' A:TTP501 3.8 12.8 0.5 C5' P:DA4 3.9 19.1 0.5 OP2 P:DT5 3.9 17.2 0.5 O2A A:TTP501 3.9 12.5 0.5 C5' P:DA4 3.9 18.7 0.5 C4' P:DA4 4.0 18.8 0.5 CB A:ASP418 4.0 12.9 1.0 O5' P:DT5 4.0 13.6 0.5 C5' A:TTP501 4.1 15.3 0.5 CE1 A:HIS329 4.2 19.2 0.5 C5' P:DT5 4.2 15.4 0.5 OD1 A:ASP418 4.3 15.2 1.0 CB A:ASP330 4.4 15.4 1.0 NH2 A:ARG416 4.5 15.9 1.0 O5' P:DA4 4.5 19.5 0.5 OP1 P:DA4 4.6 19.9 0.5 O5' P:DA4 4.6 19.4 0.5 CB A:ASP332 4.6 11.9 1.0 C2' P:DA4 4.6 18.5 0.5 OP1 P:DA4 4.7 20.3 0.5 CZ3 A:TRP434 4.7 20.2 1.0 O1G A:TTP501 4.8 17.0 0.5 O32 A:PPV514 4.8 16.8 0.2 C2' P:DA4 4.8 18.4 0.5 O31 A:PPV514 4.9 17.8 0.5 O1B A:TTP501 4.9 12.9 0.5 ND1 A:HIS329 5.0 21.1 0.5 O3A A:TTP501 5.0 17.7 0.5

J.A.Jamsen, W.A.Beard, L.C.Pedersen, D.D.Shock, A.F.Moon, J.M.Krahn, K.Bebenek, T.A.Kunkel, S.H.Wilson. Time-Lapse Crystallography Snapshots of A Double-Strand Break Repair Polymerase in Action. Nat Commun V. 8 253 2017.
ISSN: ESSN 2041-1723
PubMed: 28811466
DOI: 10.1038/S41467-017-00271-7