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

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

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with 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 Dgtp, PDB code: 6nkx 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) 26.25 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.516, 79.884, 55.200, 90.00, 107.99, 90.00
R / Rfree (%) 18.1 / 23.2

Other elements in 6nkx:

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

Chlorine (Cl) 1 atom
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 Dgtp (pdb code 6nkx). 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 Dgtp, PDB code: 6nkx:

Magnesium binding site 1 out of 1 in 6nkx

Go back to Magnesium Binding Sites List in 6nkx
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 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 Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:17.4
occ:1.00
 OD1 A:ASP190 2.0 21.1 1.0
O1G A:DGT404 2.0 19.1 1.0
OD2 A:ASP192 2.1 19.2 1.0
O1B A:DGT404 2.1 14.4 1.0
O A:HOH536 2.1 20.3 1.0
O1A A:DGT404 2.1 16.9 1.0
CG A:ASP190 3.1 18.9 1.0
PB A:DGT404 3.1 18.2 1.0
CG A:ASP192 3.1 19.5 1.0
PG A:DGT404 3.3 21.0 1.0
PA A:DGT404 3.3 22.9 1.0
NA A:NA402 3.4 22.7 1.0
OD1 A:ASP192 3.5 19.0 1.0
OD2 A:ASP190 3.5 23.0 1.0
O3A A:DGT404 3.5 23.1 1.0
O3B A:DGT404 3.6 21.8 1.0
O3G A:DGT404 4.0 19.5 1.0
C5' A:DGT404 4.1 19.6 1.0
O A:ASP190 4.1 24.5 1.0
O A:HOH620 4.2 19.8 1.0
C A:ASP190 4.3 17.8 1.0
O5' A:DGT404 4.3 19.2 1.0
N A:ASP190 4.3 17.6 1.0
CB A:ASP190 4.4 17.5 1.0
OG A:SER180 4.4 25.7 1.0
O2A A:DGT404 4.4 22.3 1.0
O2G A:DGT404 4.4 23.2 1.0
O2B A:DGT404 4.4 20.0 1.0
CB A:ASP192 4.4 18.5 1.0
N A:SER180 4.5 18.8 1.0
CA A:GLY179 4.5 17.1 1.0
CA A:ASP190 4.5 18.6 1.0
N A:MET191 4.8 18.0 1.0
N A:ASP192 4.8 20.6 1.0
C A:MET191 5.0 19.4 1.0

Reference:

V.K.Batra, S.H.Wilson. PDBX_DESCRIPTOR Ternary Complex Crystal Structure To Be Published.
Page generated: Tue Oct 1 12:45:12 2024

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