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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

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