Magnesium in PDB 5tye: Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min)

All present enzymatic activity of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min):
2.7.7.7;

The structure of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min), PDB code: 5tye 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)	21.36 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.998, 68.573, 110.478, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.8

The structure of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min) (pdb code 5tye). 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 Product Complex, 10 Mm MG2+ (60 Min), PDB code: 5tye:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 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 Product Complex, 10 Mm MG2+ (60 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:19.4 occ:1.00 O A:HOH709 2.0 26.5 0.7 O A:HOH666 2.1 19.9 1.0 OD1 A:ASP330 2.1 23.2 1.0 OD2 A:ASP332 2.1 19.4 1.0 OP1 P:DT5 2.1 19.5 1.0 O32 A:PPV512 2.1 18.2 0.8 O31 A:PPV512 2.8 27.3 0.3 CG A:ASP330 3.0 30.8 1.0 CG A:ASP332 3.2 20.6 1.0 P2 A:PPV512 3.2 25.4 0.8 OD2 A:ASP330 3.4 33.0 1.0 OPP A:PPV512 3.4 29.7 0.8 MG A:MG502 3.4 16.7 0.7 NA A:NA503 3.4 19.1 0.3 P P:DT5 3.5 21.6 1.0 OD1 A:ASP332 3.6 16.6 1.0 P1 A:PPV512 3.7 29.9 0.3 O22 A:PPV512 3.9 33.1 0.8 O5' P:DT5 4.0 18.7 1.0 O A:ASP330 4.1 19.8 1.0 C5' P:DT5 4.1 17.7 1.0 O A:HOH602 4.2 34.8 1.0 O A:HOH610 4.2 19.5 1.0 N A:GLY320 4.3 14.9 1.0 O A:HOH801 4.4 30.3 1.0 CB A:ASP330 4.4 22.8 1.0 O A:HOH627 4.4 28.1 1.0 OP2 P:DT5 4.4 20.8 1.0 C A:ASP330 4.5 21.1 1.0 CB A:ASP332 4.5 17.8 1.0 O12 A:PPV512 4.5 18.7 0.8 O3' P:DA4 4.5 20.5 1.0 CA A:GLY319 4.5 16.9 1.0 O21 A:PPV512 4.7 28.5 0.3 O11 A:PPV512 4.7 27.6 0.3 CA A:ASP330 4.9 23.4 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 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 Product Complex, 10 Mm MG2+ (60 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:16.7 occ:0.74 NA A:NA503 0.0 19.1 0.3 OD1 A:ASP332 2.1 16.6 1.0 OD2 A:ASP418 2.2 19.9 1.0 OP1 P:DT5 2.3 19.5 1.0 OD1 A:ASP330 2.6 23.2 1.0 O A:HOH627 2.7 28.1 1.0 O3' P:DA4 2.7 20.5 1.0 CG A:ASP332 3.1 20.6 1.0 P P:DT5 3.1 21.6 1.0 CG A:ASP330 3.2 30.8 1.0 CG A:ASP418 3.2 20.5 1.0 OD2 A:ASP332 3.3 19.4 1.0 MG A:MG501 3.4 19.4 1.0 OD2 A:ASP330 3.7 33.0 1.0 CB A:ASP418 3.8 19.4 1.0 C3' P:DA4 3.9 18.7 1.0 CB A:ASP330 4.0 22.8 1.0 C4' P:DA4 4.0 19.2 1.0 C5' P:DA4 4.0 21.1 1.0 OP2 P:DT5 4.1 20.8 1.0 OD1 A:ASP418 4.2 21.1 1.0 O5' P:DT5 4.3 18.7 1.0 CB A:ASP332 4.4 17.8 1.0 C5' P:DT5 4.4 17.7 1.0 NH2 A:ARG416 4.5 18.2 1.0 O A:HOH709 4.6 26.5 0.7 O A:VAL331 4.6 18.1 1.0 CZ3 A:TRP434 4.8 19.0 1.0 O5' P:DA4 4.9 21.8 1.0 C A:VAL331 4.9 20.1 1.0 N A:ASP418 4.9 16.9 1.0 CA A:ASP332 4.9 18.2 1.0 OP1 P:DA4 5.0 20.1 1.0 O A:HOH666 5.0 19.9 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