Magnesium in PDB 7ksw: Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN), PDB code: 7ksw 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)	35.00 / 1.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.043, 68.736, 110.548, 90, 90, 90
R / Rfree (%)	15.4 / 17.2

The structure of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) (pdb code 7ksw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN), PDB code: 7ksw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)


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, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:15.4 occ:1.00 OD2 A:ASP330 1.7 20.2 0.5 OD2 A:ASP418 2.1 20.3 1.0 OD1 A:ASP332 2.2 16.1 1.0 OP1 P:DG5 2.2 12.9 0.6 O A:HOH602 2.3 28.8 1.0 O2A A:DGT505 2.6 15.2 0.4 O3' P:DA4 2.6 16.6 0.6 OD1 A:ASP330 2.7 16.3 0.6 O3' P:DA4 2.7 21.1 0.4 CG A:ASP330 2.8 21.3 0.5 P P:DG5 3.0 12.3 0.6 OD1 A:ASP330 3.2 17.0 0.5 CG A:ASP332 3.2 15.4 1.0 CG A:ASP418 3.2 16.6 1.0 CG A:ASP330 3.4 18.7 0.6 OD2 A:ASP332 3.5 14.7 1.0 MG A:MG502 3.5 14.6 1.0 PA A:DGT505 3.5 16.4 0.4 C3' P:DA4 3.8 17.7 0.6 C3' P:DA4 3.9 17.6 0.4 CB A:ASP418 3.9 15.5 1.0 O1A A:DGT505 3.9 15.1 0.4 C4' P:DA4 3.9 15.8 0.6 C5' P:DA4 4.0 17.2 0.4 C5' P:DA4 4.0 16.2 0.6 OP2 P:DG5 4.0 15.9 0.6 OD2 A:ASP330 4.0 23.7 0.6 O5' A:DGT505 4.0 16.1 0.4 C4' P:DA4 4.1 16.5 0.4 CB A:ASP330 4.1 15.8 0.5 CB A:ASP330 4.2 17.8 0.6 OD1 A:ASP418 4.2 16.8 1.0 O5' P:DG5 4.2 13.2 0.6 CE1 A:HIS329 4.3 36.6 0.5 C5' P:DG5 4.4 15.6 0.6 C5' A:DGT505 4.4 12.9 0.4 OP1 P:DA4 4.5 18.0 0.4 CB A:ASP332 4.5 13.3 1.0 NH2 A:ARG416 4.5 17.2 1.0 O5' P:DA4 4.7 17.0 0.6 OP1 P:DA4 4.7 18.9 0.6 O12 A:PPV506 4.8 20.6 0.6 O2G A:DGT505 4.8 20.2 0.4 O5' P:DA4 4.8 18.2 0.4 CZ3 A:TRP434 4.8 18.7 1.0 NE2 A:HIS329 4.9 38.3 0.5 O A:VAL331 4.9 15.8 1.0 C2' P:DA4 4.9 18.5 0.6

Magnesium binding site 2 out of 3 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)


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, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:14.6 occ:1.00 O2A A:DGT505 1.6 15.2 0.4 O2B A:DGT505 2.0 14.5 0.4 O2G A:DGT505 2.0 20.2 0.4 O11 A:PPV506 2.1 14.8 0.6 OD1 A:ASP330 2.1 16.3 0.6 OD2 A:ASP332 2.2 14.7 1.0 O A:HOH623 2.2 19.3 1.0 OD1 A:ASP330 2.3 17.0 0.5 OP1 P:DG5 2.4 12.9 0.6 O12 A:PPV506 2.4 20.6 0.6 PA A:DGT505 2.8 16.4 0.4 PB A:DGT505 2.9 17.1 0.4 O3A A:DGT505 3.1 15.9 0.4 CG A:ASP330 3.1 18.7 0.6 PG A:DGT505 3.2 22.9 0.4 CG A:ASP332 3.2 15.4 1.0 CG A:ASP330 3.3 21.3 0.5 O3B A:DGT505 3.3 18.9 0.4 P1 A:PPV506 3.4 15.4 0.6 OD2 A:ASP330 3.4 23.7 0.6 MG A:MG501 3.5 15.4 1.0 OD1 A:ASP332 3.5 16.1 1.0 OD2 A:ASP330 3.6 20.2 0.5 P P:DG5 3.7 12.3 0.6 OPP A:PPV506 3.7 16.6 0.6 P2 A:PPV506 3.8 22.6 0.6 O5' A:DGT505 3.8 16.1 0.4 C5' A:DGT505 3.8 12.9 0.4 O A:HOH654 3.8 25.3 0.6 O A:ASP330 4.0 17.1 0.5 O1A A:DGT505 4.0 15.1 0.4 CE1 A:HIS329 4.0 36.6 0.5 O3G A:DGT505 4.1 21.6 0.4 C5' P:DG5 4.1 15.6 0.6 ND1 A:HIS329 4.2 38.2 0.5 O21 A:PPV506 4.2 17.6 0.6 O5' P:DG5 4.2 13.2 0.6 O A:HOH653 4.3 16.4 1.0 O1B A:DGT505 4.4 14.9 0.4 O1G A:DGT505 4.4 32.0 0.4 O A:ASP330 4.4 14.0 0.6 N A:GLY320 4.4 12.3 1.0 CB A:ASP330 4.4 17.8 0.6 O A:HOH613 4.4 25.7 0.6 O A:HOH602 4.4 28.8 1.0 C A:ASP330 4.4 14.3 0.5 O31 A:PPV506 4.5 16.7 0.6 O22 A:PPV506 4.5 32.6 0.6 C A:ASP330 4.6 14.5 0.6 CB A:ASP332 4.6 13.3 1.0 CB A:ASP330 4.6 15.8 0.5 O A:HOH654 4.6 14.6 0.4 OP2 P:DG5 4.6 15.9 0.6 CA A:GLY319 4.7 12.6 1.0 O3' P:DA4 4.7 16.6 0.6 O32 A:PPV506 4.8 32.0 0.6 N A:ASP330 4.8 14.4 0.5 O3' P:DA4 4.8 21.1 0.4 CA A:ASP330 4.9 16.8 0.5 CA A:ASP330 4.9 17.0 0.6

Magnesium binding site 3 out of 3 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:29.8 occ:0.62 O1A A:DGT505 1.9 15.1 0.4 OP2 P:DG5 2.1 15.9 0.6 O22 A:PPV506 2.1 32.6 0.6 O P:HOH215 2.1 21.3 0.6 O P:HOH203 2.2 35.0 0.6 PA A:DGT505 3.3 16.4 0.4 O A:HOH761 3.4 21.1 0.4 P P:DG5 3.4 12.3 0.6 P2 A:PPV506 3.6 22.6 0.6 O3A A:DGT505 3.8 15.9 0.4 CE1 A:HIS329 3.8 36.6 0.5 O A:HOH602 4.0 28.8 1.0 O A:HOH761 4.0 24.3 0.6 OP1 P:DG5 4.0 12.9 0.6 O A:HOH731 4.1 24.2 1.0 O12 A:PPV506 4.1 20.6 0.6 OPP A:PPV506 4.2 16.6 0.6 O A:HOH806 4.2 23.4 0.4 O5' A:DGT505 4.3 16.1 0.4 O5' P:DG5 4.3 13.2 0.6 NE2 A:HIS329 4.3 38.3 0.5 O2A A:DGT505 4.4 15.2 0.4 O3' P:DA4 4.4 16.6 0.6 OP2 P:DA4 4.4 19.3 0.4 OP2 P:DA4 4.4 19.7 0.6 OP1 P:DA4 4.6 18.0 0.4 O5' P:DA4 4.6 17.0 0.6 C3' P:DA4 4.6 17.7 0.6 ND1 A:HIS329 4.7 38.2 0.5 O32 A:PPV506 4.7 32.0 0.6 OP1 P:DA4 4.7 18.9 0.6 P P:DA4 4.8 17.4 0.4 O1G A:DGT505 4.8 32.0 0.4 P P:DA4 4.8 17.3 0.6 O3' P:DA4 4.8 21.1 0.4 O5' P:DA4 4.8 18.2 0.4 O P:HOH202 4.8 37.6 1.0 OD2 A:ASP330 4.8 23.7 0.6 C3' P:DA4 4.9 17.6 0.4

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) To Be Published.