Atomistry » Magnesium » PDB 6nkb-6noo » 6nkv
Atomistry »
  Magnesium »
    PDB 6nkb-6noo »
      6nkv »

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: Tue Oct 1 12:44:34 2024

Last articles

Ca in 2RGD
Ca in 2RGE
Ca in 2RGC
Ca in 2RGB
Ca in 2RGA
Ca in 2RDZ
Ca in 2RDJ
Ca in 2REX
Ca in 2RE1
Ca in 2R8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy