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Magnesium in PDB 6nkz: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Methylene Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Methylene Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant 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 K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Methylene Dgtp, PDB code: 6nkz 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) 21.33 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.642, 80.043, 55.249, 90.00, 107.92, 90.00
R / Rfree (%) 18.6 / 23.5

Other elements in 6nkz:

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Methylene Dgtp also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Methylene Dgtp (pdb code 6nkz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Methylene Dgtp, PDB code: 6nkz:

Magnesium binding site 1 out of 1 in 6nkz

Go back to Magnesium Binding Sites List in 6nkz
Magnesium binding site 1 out of 1 in the Ternary Complex Crystal Structure of K289M Variant 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 K289M Variant 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:19.3
occ:1.00
 OD1 A:ASP190 2.0 23.0 1.0
O1G A:GGH403 2.1 22.8 1.0
OD2 A:ASP192 2.1 21.8 1.0
O2B A:GGH403 2.1 20.6 1.0
O1A A:GGH403 2.1 21.9 1.0
O A:HOH585 2.2 23.4 1.0
CG A:ASP190 3.1 24.8 1.0
CG A:ASP192 3.1 21.4 1.0
P2 A:GGH403 3.2 19.0 1.0
P3 A:GGH403 3.3 27.1 1.0
P1 A:GGH403 3.3 24.0 1.0
NA A:NA402 3.4 24.6 1.0
OD1 A:ASP192 3.5 20.7 1.0
OD2 A:ASP190 3.5 26.4 1.0
O3A A:GGH403 3.7 24.6 1.0
O3G A:GGH403 3.7 23.8 1.0
C3B A:GGH403 3.9 24.5 1.0
O A:ASP190 4.1 24.9 1.0
C5' A:GGH403 4.2 23.2 1.0
O A:HOH624 4.2 27.6 1.0
N A:ASP190 4.3 19.6 1.0
O5' A:GGH403 4.3 22.2 1.0
C A:ASP190 4.3 21.8 1.0
O A:HOH602 4.3 21.7 1.0
O2A A:GGH403 4.4 23.4 1.0
CB A:ASP190 4.4 22.3 1.0
CB A:ASP192 4.4 22.3 1.0
O2G A:GGH403 4.5 30.9 1.0
O1B A:GGH403 4.5 22.3 1.0
OG A:SER180 4.5 29.6 1.0
CA A:GLY179 4.5 22.3 1.0
CA A:ASP190 4.5 22.6 1.0
N A:SER180 4.6 23.8 1.0
O A:HOH587 4.8 33.9 1.0
N A:ASP192 4.8 21.9 1.0
N A:MET191 4.9 21.3 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Methylene Dgtp To Be Published.
Page generated: Tue Oct 1 12:45:37 2024

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