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

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of 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 Chf Analogue of Dgtp, PDB code: 6nkv 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) 23.73 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.636, 79.707, 55.412, 90.00, 107.63, 90.00
R / Rfree (%) 16.4 / 20.3

Other elements in 6nkv:

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

Fluorine (F) 1 atom
Chlorine (Cl) 3 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 Chf Analogue of Dgtp (pdb code 6nkv). 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 Chf Analogue of Dgtp, PDB code: 6nkv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6nkv

Go back to Magnesium Binding Sites List in 6nkv
Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of 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 Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:29.2
occ:1.00
 O T:HOH227 1.8 25.1 1.0
O A:HOH883 2.1 32.0 1.0
O T:HOH254 2.2 29.2 1.0
O D:HOH116 2.2 26.4 1.0
O A:HOH544 2.3 32.9 1.0
O A:HOH656 4.1 31.5 1.0
OE1 A:GLU288 4.4 32.6 1.0
O D:HOH108 4.4 22.4 1.0
O T:HOH246 4.4 37.1 1.0
O A:HOH737 4.4 24.6 1.0
N3 T:DA4 4.5 27.4 1.0
O T:HOH245 4.5 31.2 1.0
O2 D:DC3 4.5 29.3 1.0
O4' T:DA5 4.5 25.4 1.0
O D:HOH122 4.6 30.0 1.0
C4' T:DA5 4.6 30.2 1.0
O T:HOH204 4.7 28.5 1.0
C5' T:DA5 4.8 30.7 1.0
C2 T:DA4 4.9 23.5 1.0
C5' D:DG4 4.9 26.8 1.0

Magnesium binding site 2 out of 2 in 6nkv

Go back to Magnesium Binding Sites List in 6nkv
Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of 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 Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:11.8
occ:1.00
 OD2 A:ASP192 2.0 11.6 1.0
OD1 A:ASP190 2.0 11.7 1.0
O1A A:GFH408 2.1 11.9 1.0
O1G A:GFH408 2.1 16.0 1.0
O A:HOH577 2.1 13.6 1.0
O2B A:GFH408 2.1 12.0 1.0
CG A:ASP192 3.0 12.2 1.0
CG A:ASP190 3.1 16.5 1.0
PB A:GFH408 3.2 11.3 1.0
PG A:GFH408 3.3 18.4 1.0
PA A:GFH408 3.3 13.6 1.0
OD1 A:ASP192 3.4 13.4 1.0
NA A:NA402 3.5 17.4 1.0
OD2 A:ASP190 3.5 17.6 1.0
O3A A:GFH408 3.6 14.2 1.0
O3G A:GFH408 3.7 16.3 1.0
C3B A:GFH408 3.9 15.1 1.0
O A:ASP190 4.0 15.0 1.0
C5' A:GFH408 4.0 13.0 1.0
O5' A:GFH408 4.2 13.6 1.0
O A:HOH691 4.2 12.3 1.0
O A:HOH755 4.3 23.3 1.0
C A:ASP190 4.3 13.5 1.0
CB A:ASP192 4.3 11.7 1.0
CB A:ASP190 4.4 14.3 1.0
N A:ASP190 4.4 12.7 1.0
CA A:GLY179 4.4 10.8 1.0
O1B A:GFH408 4.5 12.0 1.0
O2A A:GFH408 4.5 14.2 1.0
O2G A:GFH408 4.6 21.5 1.0
CA A:ASP190 4.6 11.3 1.0
N A:SER180 4.7 14.0 1.0
N A:ASP192 4.7 11.2 1.0
N A:MET191 4.8 10.1 1.0
F3B A:GFH408 4.9 20.7 1.0
C A:MET191 5.0 12.0 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.
Page generated: Wed Aug 13 12:50:14 2025

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