Atomistry » Magnesium » PDB 7klu-7ku7 » 7ktf
Atomistry »
  Magnesium »
    PDB 7klu-7ku7 »
      7ktf »

Magnesium in PDB 7ktf: Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN), PDB code: 7ktf 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) 34.97 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.947, 68.515, 110.696, 90, 90, 90
R / Rfree (%) 16.7 / 18.7

Other elements in 7ktf:

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN) (pdb code 7ktf). 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-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN), PDB code: 7ktf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7ktf

Go back to Magnesium Binding Sites List in 7ktf
Magnesium binding site 1 out of 2 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN)


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-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:27.5
occ:1.00
O11 A:PPV504 2.0 18.6 0.6
OD1 A:ASP330 2.1 28.0 1.0
O32 A:PPV504 2.1 28.5 0.6
OD2 A:ASP332 2.1 23.9 1.0
O A:HOH766 2.2 28.9 1.0
OP1 P:8OG5 2.4 25.2 1.0
P1 A:PPV504 3.1 22.4 0.6
CG A:ASP330 3.1 43.1 1.0
CG A:ASP332 3.2 23.4 1.0
O31 A:PPV504 3.3 33.3 0.8
P2 A:PPV504 3.4 22.6 0.4
MG A:MG502 3.5 22.7 1.0
OD2 A:ASP330 3.6 38.9 1.0
OD1 A:ASP332 3.6 23.0 1.0
OPP A:PPV504 3.6 27.2 0.8
P P:8OG5 3.7 27.3 1.0
O12 A:PPV504 4.0 44.2 1.0
O5' P:8OG5 4.0 23.3 1.0
O A:ASP330 4.1 21.5 1.0
O A:HOH831 4.1 45.0 1.0
C5' P:8OG5 4.2 23.0 1.0
N A:GLY320 4.3 12.8 1.0
C A:ASP330 4.3 21.9 1.0
O A:HOH613 4.3 17.5 1.0
O21 A:PPV504 4.4 23.7 0.9
OP2 P:8OG5 4.4 30.0 1.0
CB A:ASP330 4.4 27.6 1.0
CA A:GLY319 4.5 13.6 1.0
CB A:ASP332 4.5 14.9 1.0
O A:HOH605 4.6 31.0 1.0
O22 A:PPV504 4.6 41.1 0.7
CA A:ASP330 4.7 22.4 1.0
N A:ASP330 4.7 20.6 1.0
N A:VAL331 4.8 20.3 1.0
O A:HOH645 4.8 30.8 1.0
N A:ASP332 4.9 13.9 1.0
O3' P:DA4 5.0 27.4 1.0
C A:GLY319 5.0 11.8 1.0

Magnesium binding site 2 out of 2 in 7ktf

Go back to Magnesium Binding Sites List in 7ktf
Magnesium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN)


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-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:22.7
occ:1.00
OD2 A:ASP330 1.7 38.9 1.0
OP1 P:8OG5 1.9 25.2 1.0
OD2 A:ASP418 2.1 21.7 1.0
OD1 A:ASP332 2.1 23.0 1.0
O A:HOH605 2.5 31.0 1.0
CG A:ASP330 2.7 43.1 1.0
P P:8OG5 2.8 27.3 1.0
O3' P:DA4 2.9 27.4 1.0
CG A:ASP332 3.1 23.4 1.0
OD1 A:ASP330 3.2 28.0 1.0
CG A:ASP418 3.2 17.2 1.0
OD2 A:ASP332 3.4 23.9 1.0
MG A:MG501 3.5 27.5 1.0
OP2 P:8OG5 3.7 30.0 1.0
CB A:ASP418 3.9 15.9 1.0
CB A:ASP330 4.1 27.6 1.0
C3' P:DA4 4.1 23.0 1.0
C5' P:DA4 4.1 22.1 1.0
OD1 A:ASP418 4.1 20.1 1.0
O5' P:8OG5 4.1 23.3 1.0
O A:HOH831 4.2 45.0 1.0
C4' P:DA4 4.2 19.0 1.0
C5' P:8OG5 4.4 23.0 1.0
CB A:ASP332 4.5 14.9 1.0
NH2 A:ARG416 4.5 18.3 1.0
O32 A:PPV504 4.7 28.5 0.6
OP1 P:DA4 4.7 20.4 1.0
O A:VAL331 4.7 16.4 1.0
O5' P:DA4 4.9 20.1 1.0
CZ3 A:TRP434 4.9 19.6 1.0
N A:ASP418 4.9 14.0 1.0
C A:VAL331 5.0 15.6 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN) To Be Published.
Page generated: Fri Dec 17 10:32:43 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy