Atomistry » Magnesium » PDB 6njw-6nol » 6nkw
Atomistry »
  Magnesium »
    PDB 6njw-6nol »
      6nkw »

Magnesium in PDB 6nkw: Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp, PDB code: 6nkw was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.16 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.441, 79.186, 55.352, 90.00, 107.60, 90.00
R / Rfree (%) 17.4 / 21.7

Other elements in 6nkw:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp (pdb code 6nkw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp, PDB code: 6nkw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6nkw

Go back to Magnesium Binding Sites List in 6nkw
Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:35.2
occ:1.00
 O T:HOH210 2.0 29.4 1.0
O T:HOH244 2.2 35.2 1.0
O T:HOH237 2.2 31.4 1.0
O D:HOH217 2.3 36.4 1.0
O A:HOH754 4.2 27.7 1.0
O D:HOH210 4.3 31.2 1.0
N3 T:DA4 4.3 29.4 1.0
O4' T:DA5 4.4 31.0 1.0
O D:HOH214 4.4 42.7 1.0
OE1 A:GLU288 4.5 33.5 1.0
C4' T:DA5 4.5 34.5 1.0
O2 D:DC3 4.5 36.2 1.0
O T:HOH208 4.6 31.9 1.0
O T:HOH240 4.7 34.3 1.0
O D:HOH218 4.7 37.6 1.0
C5' T:DA5 4.7 35.1 1.0
C2 T:DA4 4.7 28.8 1.0

Magnesium binding site 2 out of 2 in 6nkw

Go back to Magnesium Binding Sites List in 6nkw
Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:16.5
occ:1.00
 OD1 A:ASP190 2.0 20.8 1.0
OD2 A:ASP192 2.0 14.9 1.0
O1A A:GGH407 2.0 17.4 1.0
O2B A:GGH407 2.1 16.4 1.0
O1G A:GGH407 2.1 22.1 1.0
O A:HOH617 2.3 16.6 1.0
CG A:ASP192 3.1 17.1 1.0
CG A:ASP190 3.1 21.8 1.0
P2 A:GGH407 3.2 17.4 1.0
P1 A:GGH407 3.3 17.7 1.0
P3 A:GGH407 3.3 24.0 1.0
OD1 A:ASP192 3.4 18.5 1.0
OD2 A:ASP190 3.5 24.6 1.0
O3A A:GGH407 3.6 18.8 1.0
NA A:NA402 3.6 24.4 1.0
O3G A:GGH407 3.8 20.2 1.0
C3B A:GGH407 3.9 18.1 1.0
C5' A:GGH407 4.1 16.7 1.0
O A:ASP190 4.1 18.1 1.0
O5' A:GGH407 4.2 18.4 1.0
C A:ASP190 4.3 16.7 1.0
O A:HOH627 4.3 16.3 1.0
O2A A:GGH407 4.3 19.5 1.0
N A:ASP190 4.4 17.8 1.0
CB A:ASP190 4.4 19.7 1.0
CB A:ASP192 4.4 15.6 1.0
CA A:GLY179 4.4 15.7 1.0
O A:HOH725 4.5 32.0 1.0
O1B A:GGH407 4.5 16.3 1.0
O2G A:GGH407 4.5 24.3 1.0
N A:SER180 4.5 20.3 1.0
CA A:ASP190 4.6 18.7 1.0
O A:HOH638 4.7 43.5 1.0
OG A:SER180 4.7 23.9 1.0
N A:ASP192 4.8 17.8 1.0
N A:MET191 4.8 18.1 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.
Page generated: Tue Oct 1 12:45:09 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