Magnesium in PDB 6vf0: Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min):
2.7.7.7;

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min), PDB code: 6vf0 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)	34.96 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.982, 68.437, 110.615, 90, 90, 90
R / Rfree (%)	16.4 / 18.7

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) (pdb code 6vf0). 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 Reaction State Ternary Complex, 50 Mm MG2+ (30 Min), PDB code: 6vf0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 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 Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:26.1 occ:1.00 OD2 A:ASP330 1.8 58.5 1.0 OP1 P:8GM5 1.9 25.2 0.4 OD2 A:ASP418 2.1 27.2 1.0 OD1 A:ASP332 2.1 27.4 1.0 O A:HOH605 2.2 44.7 1.0 O2A A:8GT505 2.5 46.7 0.6 P P:8GM5 2.7 33.2 0.4 O3' P:DA4 2.7 47.7 0.4 CG A:ASP330 2.8 61.4 1.0 O3' P:DA4 2.9 45.7 0.6 CG A:ASP332 3.1 28.8 1.0 CG A:ASP418 3.2 19.6 1.0 OD1 A:ASP330 3.2 32.0 1.0 OD2 A:ASP332 3.4 33.1 1.0 MG A:MG502 3.5 29.2 1.0 PA A:8GT505 3.5 64.9 0.6 OP2 P:8GM5 3.6 42.3 0.4 O1A A:8GT505 3.8 63.7 0.6 C3' P:DA4 3.8 37.2 0.4 C5' P:DA4 3.9 30.5 0.6 C5' P:DA4 3.9 33.6 0.4 CB A:ASP418 3.9 19.3 1.0 C3' P:DA4 3.9 36.3 0.6 C4' P:DA4 4.0 33.5 0.4 C4' P:DA4 4.0 32.1 0.6 O5' P:8GM5 4.0 32.9 0.4 O5' A:8GT505 4.1 65.8 0.6 OD1 A:ASP418 4.1 22.5 1.0 CB A:ASP330 4.1 45.0 1.0 C5' P:8GM5 4.4 28.3 0.4 CE1 A:HIS329 4.5 38.5 0.6 CB A:ASP332 4.5 17.0 1.0 C5' A:8GT505 4.5 57.4 0.6 NH2 A:ARG416 4.5 21.5 1.0 OP1 P:DA4 4.6 23.8 0.6 O5' P:DA4 4.7 29.6 0.4 O5' P:DA4 4.7 27.3 0.6 OP1 P:DA4 4.8 25.7 0.4 O A:VAL331 4.8 19.5 1.0 O1G A:8GT505 4.9 42.0 0.6 CZ3 A:TRP434 4.9 31.2 1.0 O3A A:8GT505 5.0 71.7 0.6

Magnesium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 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 Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:29.2 occ:1.00 O2A A:8GT505 2.0 46.7 0.6 OD1 A:ASP330 2.0 32.0 1.0 O21 P:PPV102 2.0 19.5 0.4 O A:HOH661 2.1 31.2 1.0 OD2 A:ASP332 2.1 33.1 1.0 O2B A:8GT505 2.1 62.6 0.6 O1G A:8GT505 2.3 42.0 0.6 OP1 P:8GM5 2.4 25.2 0.4 CG A:ASP330 3.1 61.4 1.0 PB A:8GT505 3.2 74.0 0.6 PA A:8GT505 3.2 64.9 0.6 P1 P:PPV102 3.2 36.8 0.4 CG A:ASP332 3.2 28.8 1.0 O3A A:8GT505 3.4 71.7 0.6 O31 P:PPV102 3.4 38.1 0.4 OD2 A:ASP330 3.5 58.5 1.0 MG A:MG501 3.5 26.1 1.0 PG A:8GT505 3.5 53.1 0.6 OD1 A:ASP332 3.6 27.4 1.0 O3B A:8GT505 3.7 68.0 0.6 P P:8GM5 3.8 33.2 0.4 O A:ASP330 3.9 22.4 1.0 OPP P:PPV102 3.9 33.9 0.4 O5' P:8GM5 4.1 32.9 0.4 C A:ASP330 4.2 23.6 1.0 O A:HOH611 4.2 20.6 1.0 N A:GLY320 4.2 15.2 1.0 O5' A:8GT505 4.2 65.8 0.6 O1A A:8GT505 4.2 63.7 0.6 O3G A:8GT505 4.3 46.9 0.6 C5' A:8GT505 4.3 57.4 0.6 CB A:ASP330 4.4 45.0 1.0 ND1 A:HIS329 4.4 44.5 0.6 C5' P:8GM5 4.5 28.3 0.4 O A:HOH605 4.5 44.7 1.0 CA A:GLY319 4.5 16.5 1.0 O1B A:8GT505 4.5 71.2 0.6 O11 P:PPV102 4.5 25.2 0.4 CE1 A:HIS329 4.5 38.5 0.6 CB A:ASP332 4.6 17.0 1.0 OP2 P:8GM5 4.6 42.3 0.4 CA A:ASP330 4.6 26.5 1.0 O2G A:8GT505 4.7 58.2 0.6 N A:VAL331 4.7 20.8 1.0 N A:ASP330 4.7 22.8 1.0 O A:HOH779 4.7 35.2 1.0 N A:ASP332 4.8 16.5 1.0 O3' P:DA4 4.9 47.7 0.4 C A:GLY319 4.9 15.9 1.0 C A:VAL331 4.9 17.4 1.0 CA A:VAL331 5.0 17.3 1.0

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) To Be Published.