Magnesium in PDB 6vf1: Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min):
2.7.7.7;

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min), PDB code: 6vf1 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)	35.02 / 1.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.044, 68.415, 111.07, 90, 90, 90
R / Rfree (%)	16.3 / 18.8

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) (pdb code 6vf1). 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, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min), PDB code: 6vf1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 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, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:29.2 occ:0.87 OD1 A:ASP330 2.0 38.4 1.0 O A:HOH606 2.0 37.2 1.0 OD2 A:ASP332 2.1 27.7 1.0 O12 A:GOA506 2.2 32.5 1.0 OP1 P:8GM5 2.3 27.1 1.0 O A:HOH626 2.3 34.3 1.0 CG A:ASP330 3.1 51.9 1.0 CG A:ASP332 3.2 23.6 1.0 C1 A:GOA506 3.3 37.0 1.0 MG A:MG502 3.5 21.0 0.7 OD2 A:ASP330 3.5 46.1 1.0 OD1 A:ASP332 3.5 24.3 1.0 P P:8GM5 3.6 27.0 1.0 O A:HOH816 4.0 18.8 0.5 O A:ASP330 4.0 21.4 1.0 O5' P:8GM5 4.0 24.8 1.0 C2 A:GOA506 4.1 44.2 1.0 C A:ASP330 4.2 21.1 1.0 O11 A:GOA506 4.2 33.9 1.0 N A:GLY320 4.3 11.5 1.0 O A:HOH611 4.3 17.5 1.0 OP2 P:8GM5 4.3 30.7 1.0 C5' P:8GM5 4.3 27.0 1.0 CA A:GLY319 4.4 13.7 1.0 CB A:ASP330 4.4 40.2 1.0 O A:HOH602 4.4 30.4 1.0 CB A:ASP332 4.5 14.8 1.0 O A:HOH764 4.6 46.3 1.0 N A:VAL331 4.7 18.8 1.0 CA A:ASP330 4.7 25.8 1.0 O3' P:DA4 4.8 24.1 1.0 N A:ASP332 4.8 11.7 1.0 N A:ASP330 4.8 22.3 1.0 C A:GLY319 4.9 12.3 1.0 C A:VAL331 5.0 11.1 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 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, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:21.0 occ:0.70 OD2 A:ASP330 1.6 46.1 1.0 OP1 P:8GM5 2.0 27.1 1.0 OD2 A:ASP418 2.1 25.3 1.0 OD1 A:ASP332 2.2 24.3 1.0 O A:HOH602 2.3 30.4 1.0 CG A:ASP330 2.7 51.9 1.0 P P:8GM5 2.8 27.0 1.0 O3' P:DA4 2.9 24.1 1.0 OD1 A:ASP330 3.1 38.4 1.0 CG A:ASP418 3.2 21.5 1.0 CG A:ASP332 3.2 23.6 1.0 OD2 A:ASP332 3.5 27.7 1.0 MG A:MG501 3.5 29.2 0.9 OP2 P:8GM5 3.6 30.7 1.0 C5' P:DA4 3.9 21.2 1.0 CB A:ASP418 3.9 14.3 1.0 CB A:ASP330 4.0 40.2 1.0 C3' P:DA4 4.0 22.0 1.0 OD1 A:ASP418 4.1 22.8 1.0 C4' P:DA4 4.1 22.0 1.0 O5' P:8GM5 4.2 24.8 1.0 NH2 A:ARG416 4.4 18.6 1.0 O A:HOH606 4.5 37.2 1.0 CB A:ASP332 4.6 14.8 1.0 O A:VAL331 4.6 13.7 1.0 OP1 P:DA4 4.6 18.7 1.0 C5' P:8GM5 4.7 27.0 1.0 O5' P:DA4 4.8 20.5 1.0 N A:ASP418 4.9 12.7 1.0 CZ3 A:TRP434 4.9 17.6 1.0 C A:VAL331 4.9 11.1 1.0

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) To Be Published.