Magnesium in PDB 5tyc: Dna Polymerase Mu Reactant Complex, 10MM MG2+ (15 Min)

All present enzymatic activity of Dna Polymerase Mu Reactant Complex, 10MM MG2+ (15 Min):
2.7.7.7;

The structure of Dna Polymerase Mu Reactant Complex, 10MM MG2+ (15 Min), PDB code: 5tyc 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)	22.02 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.004, 68.577, 110.373, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.7

The structure of Dna Polymerase Mu Reactant Complex, 10MM 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, 10MM MG2+ (15 Min) (pdb code 5tyc). 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, 10MM MG2+ (15 Min), PDB code: 5tyc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Mu Reactant Complex, 10MM 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, 10MM MG2+ (15 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:17.9 occ:1.00 OD1 A:ASP330 2.0 25.0 1.0 O1A A:TTP504 2.1 20.8 0.6 O A:HOH617 2.1 22.6 1.0 OD2 A:ASP332 2.1 16.5 1.0 O1B A:TTP504 2.1 22.5 0.6 O1G A:TTP504 2.2 23.8 0.6 O21 A:PPV503 2.2 22.5 0.4 O32 A:PPV503 2.2 23.9 0.1 OP1 P:DT5 2.2 21.0 0.4 CG A:ASP330 3.0 26.5 1.0 PB A:TTP504 3.0 24.2 0.6 PA A:TTP504 3.1 24.0 0.6 CG A:ASP332 3.1 18.8 1.0 P1 A:PPV503 3.2 23.7 0.4 OD2 A:ASP330 3.2 28.5 1.0 O3A A:TTP504 3.2 26.8 0.6 O31 A:PPV503 3.3 26.1 0.4 PG A:TTP504 3.3 32.0 0.6 P2 A:PPV503 3.4 31.6 0.1 MG A:MG502 3.4 21.0 0.5 CA A:CA508 3.4 20.3 0.5 OD1 A:ASP332 3.5 17.1 1.0 O3B A:TTP504 3.5 26.9 0.6 OPP A:PPV503 3.6 26.5 0.1 P P:DT5 3.6 21.0 0.4 O A:ASP330 4.0 18.9 1.0 C5' A:TTP504 4.0 19.3 0.6 O5' A:TTP504 4.0 20.5 0.6 O2G A:TTP504 4.1 25.1 0.6 O22 A:PPV503 4.1 25.2 0.1 O5' P:DT5 4.1 20.5 0.4 O A:HOH622 4.2 20.2 1.0 C5' P:DT5 4.2 19.3 0.4 O2A A:TTP504 4.3 23.2 0.6 CE1 A:HIS329 4.3 23.8 0.6 C A:ASP330 4.3 19.4 1.0 CB A:ASP330 4.4 20.7 1.0 N A:GLY320 4.4 12.7 1.0 O2B A:TTP504 4.4 22.6 0.6 ND1 A:HIS329 4.4 28.0 0.6 O A:HOH606 4.4 20.3 0.6 CB A:ASP332 4.5 16.3 1.0 O11 A:PPV503 4.5 22.4 0.4 O3G A:TTP504 4.5 30.1 0.6 O12 A:PPV503 4.5 29.7 0.1 OP2 P:DT5 4.5 24.0 0.4 CA A:GLY319 4.6 16.3 1.0 O3' P:DA4 4.6 22.2 0.4 O P:HOH201 4.7 32.0 1.0 CA A:ASP330 4.7 19.6 1.0 N A:ASP330 4.8 19.3 1.0 O3' P:DA4 4.8 22.5 0.6 N A:VAL331 4.9 19.6 1.0 N A:ASP332 5.0 17.2 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Mu Reactant Complex, 10MM 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, 10MM MG2+ (15 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:21.0 occ:0.50 CA A:CA508 0.0 20.3 0.5 OD2 A:ASP330 2.0 28.5 1.0 OD1 A:ASP332 2.0 17.1 1.0 OD2 A:ASP418 2.1 21.3 1.0 OP1 P:DT5 2.1 21.0 0.4 O1A A:TTP504 2.3 20.8 0.6 O3' P:DA4 2.4 22.2 0.4 O3' P:DA4 2.4 22.5 0.6 O P:HOH201 2.6 32.0 1.0 P P:DT5 2.8 21.0 0.4 CG A:ASP330 3.0 26.5 1.0 CG A:ASP332 3.1 18.8 1.0 CG A:ASP418 3.2 20.3 1.0 OD2 A:ASP332 3.4 16.5 1.0 PA A:TTP504 3.4 24.0 0.6 OD1 A:ASP330 3.4 25.0 1.0 MG A:MG501 3.4 17.9 1.0 C3' P:DA4 3.6 22.1 0.4 C3' P:DA4 3.6 22.2 0.6 C4' P:DA4 3.8 22.5 0.4 OP2 P:DT5 3.8 24.0 0.4 O5' A:TTP504 3.8 20.5 0.6 CB A:ASP418 3.8 20.3 1.0 O2A A:TTP504 3.8 23.2 0.6 C4' P:DA4 3.9 22.5 0.6 C5' P:DA4 3.9 23.5 0.4 C5' P:DA4 4.0 23.5 0.6 O5' P:DT5 4.0 20.5 0.4 C5' P:DT5 4.2 19.3 0.4 OD1 A:ASP418 4.2 21.2 1.0 C5' A:TTP504 4.2 19.3 0.6 CB A:ASP330 4.3 20.7 1.0 CB A:ASP332 4.4 16.3 1.0 CZ3 A:TRP434 4.6 23.2 1.0 NH2 A:ARG416 4.6 19.9 1.0 C2' P:DA4 4.7 22.6 0.4 O5' P:DA4 4.7 24.6 0.4 O5' P:DA4 4.7 24.7 0.6 CE1 A:HIS329 4.7 23.8 0.6 O1G A:TTP504 4.8 23.8 0.6 C2' P:DA4 4.8 22.7 0.6 O A:VAL331 4.8 16.9 1.0 O3A A:TTP504 4.8 26.8 0.6 O32 A:PPV503 4.9 23.9 0.1 OP1 P:DA4 4.9 20.0 0.6 O1B A:TTP504 5.0 22.5 0.6 CA A:ASP332 5.0 15.4 1.0

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