Magnesium in PDB 5tyd: Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min)

All present enzymatic activity of Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min):
2.7.7.7;

The structure of Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min), PDB code: 5tyd 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)	34.94 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.891, 68.590, 110.476, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.2

The structure of Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min) (pdb code 5tyd). 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, 10 Mm MG2+ (45 Min), PDB code: 5tyd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 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, 10 Mm MG2+ (45 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:12.2 occ:1.00 OD2 A:ASP330 1.8 18.7 0.6 OD1 A:ASP332 2.1 11.9 1.0 OD2 A:ASP418 2.1 13.8 1.0 OP1 P:DT5 2.3 12.5 0.6 O A:HOH604 2.4 23.5 1.0 O3' P:DA4 2.4 15.1 0.6 O3' P:DA4 2.4 15.0 0.4 O2A A:TTP505 2.5 13.2 0.4 OD2 A:ASP330 2.7 15.9 0.4 P P:DT5 2.9 14.4 0.6 CG A:ASP330 2.9 18.7 0.6 CG A:ASP332 3.1 12.9 1.0 CG A:ASP418 3.3 16.5 1.0 OD1 A:ASP330 3.3 14.0 0.6 CG A:ASP330 3.3 18.5 0.4 OD2 A:ASP332 3.5 11.9 1.0 MG A:MG502 3.5 12.5 1.0 C3' P:DA4 3.5 14.6 0.4 PA A:TTP505 3.5 16.1 0.4 C3' P:DA4 3.6 13.7 0.6 C4' P:DA4 3.8 14.7 0.6 C5' P:DA4 3.8 15.6 0.4 C4' P:DA4 3.9 14.7 0.4 O1A A:TTP505 3.9 15.7 0.4 O5' A:TTP505 3.9 14.7 0.4 CB A:ASP418 3.9 11.9 1.0 OP2 P:DT5 3.9 14.8 0.6 C5' P:DA4 3.9 15.7 0.6 OD1 A:ASP330 4.0 18.7 0.4 CB A:ASP330 4.1 16.1 0.4 O5' P:DT5 4.1 14.8 0.6 CB A:ASP330 4.2 15.8 0.6 C5' A:TTP505 4.2 12.2 0.4 OD1 A:ASP418 4.2 16.0 1.0 C5' P:DT5 4.3 12.2 0.6 CB A:ASP332 4.4 9.7 1.0 NH2 A:ARG416 4.6 13.1 1.0 O3G A:TTP505 4.6 19.7 0.4 CZ3 A:TRP434 4.7 15.1 1.0 O5' P:DA4 4.7 15.3 0.4 C2' P:DA4 4.7 15.1 0.6 O5' P:DA4 4.7 15.3 0.6 OP1 P:DA4 4.8 13.8 0.4 O2B A:TTP505 4.8 16.2 0.4 C2' P:DA4 4.8 15.1 0.4 O32 A:PPV510 4.9 20.2 0.3 OP1 P:DA4 4.9 13.7 0.6 CE1 A:HIS329 4.9 22.1 0.4 O A:VAL331 4.9 10.7 1.0 O3A A:TTP505 5.0 20.9 0.4 CA A:ASP332 5.0 9.7 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 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, 10 Mm MG2+ (45 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:12.5 occ:1.00 O2A A:TTP505 1.9 13.2 0.4 OD2 A:ASP330 2.0 15.9 0.4 O2B A:TTP505 2.0 16.2 0.4 OD2 A:ASP332 2.0 11.9 1.0 O21 A:PPV510 2.1 17.1 0.6 O A:HOH629 2.1 14.9 1.0 OD1 A:ASP330 2.1 14.0 0.6 O3G A:TTP505 2.1 19.7 0.4 OP1 P:DT5 2.2 12.5 0.6 O32 A:PPV510 2.2 20.2 0.3 CG A:ASP330 3.0 18.5 0.4 PB A:TTP505 3.0 18.6 0.4 CG A:ASP330 3.1 18.7 0.6 CG A:ASP332 3.1 12.9 1.0 PA A:TTP505 3.1 16.1 0.4 P1 A:PPV510 3.2 18.2 0.6 PG A:TTP505 3.3 39.6 0.4 O3A A:TTP505 3.3 20.9 0.4 OD2 A:ASP330 3.4 18.7 0.6 OD1 A:ASP330 3.4 18.7 0.4 O31 A:PPV510 3.4 21.9 0.6 OD1 A:ASP332 3.4 11.9 1.0 MG A:MG501 3.5 12.2 1.0 O3B A:TTP505 3.5 28.5 0.4 P2 A:PPV510 3.5 38.9 0.3 P P:DT5 3.6 14.4 0.6 OPP A:PPV510 3.8 29.0 0.3 O A:ASP330 3.8 14.0 0.4 O2G A:TTP505 4.0 28.8 0.4 C5' A:TTP505 4.1 12.2 0.4 O5' A:TTP505 4.1 14.7 0.4 O5' P:DT5 4.2 14.8 0.6 O A:HOH603 4.2 25.0 1.0 O A:ASP330 4.2 13.0 0.6 O1A A:TTP505 4.2 15.7 0.4 O A:HOH641 4.2 10.1 1.0 C5' P:DT5 4.2 12.2 0.6 O12 A:PPV510 4.2 28.6 0.3 CB A:ASP330 4.2 16.1 0.4 C A:ASP330 4.3 15.3 0.4 N A:GLY320 4.3 10.2 1.0 O1B A:TTP505 4.4 16.8 0.4 CB A:ASP332 4.4 9.7 1.0 C A:ASP330 4.4 15.3 0.6 O A:HOH604 4.4 23.5 1.0 CB A:ASP330 4.4 15.8 0.6 O11 A:PPV510 4.5 15.6 0.6 O1G A:TTP505 4.5 47.8 0.4 OP2 P:DT5 4.5 14.8 0.6 CA A:GLY319 4.5 8.5 1.0 O3' P:DA4 4.6 15.1 0.6 O22 A:PPV510 4.6 45.7 0.3 CA A:ASP330 4.7 16.8 0.4 O3' P:DA4 4.8 15.0 0.4 CA A:ASP330 4.8 16.7 0.6 ND1 A:HIS329 4.9 27.3 0.4 N A:ASP332 4.9 9.9 1.0 N A:ASP330 4.9 16.4 0.4 N A:ASP330 4.9 16.3 0.6 CE1 A:HIS329 4.9 22.1 0.4 N A:VAL331 4.9 12.9 1.0 C A:GLY319 5.0 9.4 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