Atomistry » Sodium » PDB 6vf7-6w0r » 6vf7
Atomistry »
  Sodium »
    PDB 6vf7-6w0r »
      6vf7 »

Sodium in PDB 6vf7: Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf7 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) 35.04 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.159, 68.927, 110.446, 90, 90, 90
R / Rfree (%) 16.6 / 19.7

Other elements in 6vf7:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) (pdb code 6vf7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf7:

Sodium binding site 1 out of 1 in 6vf7

Go back to Sodium Binding Sites List in 6vf7
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:27.1
occ:1.00
 O A:VAL246 2.3 29.0 1.0
O A:THR241 2.3 30.4 1.0
O A:ILE243 2.3 27.1 1.0
O A:HOH814 2.4 27.2 1.0
O P:HOH111 2.6 29.4 1.0
OP1 P:DT3 2.8 24.6 1.0
C A:ILE243 3.3 21.3 1.0
C A:VAL246 3.4 22.1 1.0
C A:THR241 3.4 29.9 1.0
O P:HOH107 3.6 32.2 1.0
N A:VAL246 3.7 26.1 1.0
P P:DT3 3.8 25.2 1.0
OP2 P:DT3 3.9 24.7 1.0
N A:ILE243 4.0 26.1 1.0
CA A:VAL246 4.0 25.6 1.0
N A:PHE244 4.1 30.1 1.0
C A:GLN242 4.2 30.6 1.0
O A:HOH788 4.2 45.2 1.0
N A:GLY245 4.2 22.7 1.0
CA A:PHE244 4.2 28.6 1.0
CA A:THR241 4.2 29.1 1.0
CA A:ILE243 4.3 27.3 1.0
N A:GLN242 4.3 25.8 1.0
CA A:GLN242 4.3 27.5 1.0
CB A:VAL246 4.4 26.6 1.0
N A:GLY247 4.4 31.7 1.0
C A:PHE244 4.6 28.8 1.0
O3' P:DG2 4.7 24.2 1.0
O A:GLN242 4.7 28.6 1.0
C A:GLY245 4.7 27.1 1.0
O A:PHE240 4.7 26.4 1.0
CA A:GLY247 4.8 31.8 1.0
CB A:THR241 5.0 26.5 1.0

Reference:

J.A.Jamsen, A.Sassa, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) To Be Published.
Page generated: Tue Oct 8 14:22:54 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy