Atomistry » Magnesium » PDB 6pry-6q57 » 6q4t
Atomistry »
  Magnesium »
    PDB 6pry-6q57 »
      6q4t »

Magnesium in PDB 6q4t: Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp

Enzymatic activity of Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp

All present enzymatic activity of Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp:
2.7.7.7;

Protein crystallography data

The structure of Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp, PDB code: 6q4t was solved by H.M.Kropp, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.22 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.940, 146.424, 71.477, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.1

Other elements in 6q4t:

The structure of Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp (pdb code 6q4t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp, PDB code: 6q4t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6q4t

Go back to Magnesium Binding Sites List in 6q4t
Magnesium binding site 1 out of 2 in the Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:43.5
occ:1.00
 OD2 A:ASP404 2.3 45.6 1.0
OD1 A:ASP542 2.3 45.5 1.0
O A:HOH1040 2.3 39.0 1.0
O3 A:HHZ810 2.4 32.8 1.0
O A:HOH1058 2.5 31.8 1.0
H3'2 P:DOC12 2.9 47.5 1.0
HH A:TYR402 3.1 64.3 1.0
CG A:ASP404 3.2 42.9 1.0
CG A:ASP542 3.4 43.2 1.0
P A:HHZ810 3.4 33.0 1.0
OD1 A:ASP404 3.4 47.0 1.0
H11 A:HHZ810 3.4 40.6 1.0
H3'1 P:DOC12 3.5 47.5 1.0
H5'' P:DOC12 3.6 48.0 1.0
C3' P:DOC12 3.6 39.5 1.0
MN A:MN801 3.6 33.2 1.0
OH A:TYR402 3.6 53.5 1.0
O A:HOH1105 3.7 32.7 1.0
O2 A:HHZ810 3.7 33.7 1.0
H9 A:HHZ810 3.8 38.8 1.0
OD2 A:ASP542 3.8 47.1 1.0
O1 A:HHZ810 3.8 33.1 1.0
HA3 A:GLY543 4.0 44.9 1.0
H10 A:HHZ810 4.0 38.8 1.0
C8 A:HHZ810 4.1 32.2 1.0
H A:ASP542 4.2 41.8 1.0
N A:GLY543 4.3 35.7 1.0
C5' P:DOC12 4.3 39.9 1.0
C4' P:DOC12 4.4 39.6 1.0
O A:ASP540 4.4 31.4 1.0
H A:GLY543 4.4 43.0 1.0
H4' P:DOC12 4.4 47.6 1.0
C A:ASP542 4.5 34.5 1.0
CB A:ASP404 4.6 38.1 1.0
CA A:GLY543 4.6 37.3 1.0
HB2 A:ASP404 4.6 45.9 1.0
CB A:ASP542 4.7 38.9 1.0
H5' P:DOC12 4.7 48.0 1.0
O P:HOH103 4.7 34.6 1.0
O A:ASP542 4.7 33.1 1.0
O10 A:HHZ810 4.8 33.1 1.0
N A:ASP542 4.8 34.7 1.0
HB A:THR541 4.8 40.5 1.0
O4 A:HHZ810 4.8 33.6 1.0
HE1 A:TYR402 4.8 59.6 1.0
CZ A:TYR402 4.9 51.6 1.0
CA A:ASP542 4.9 35.5 1.0
C2' P:DOC12 4.9 39.1 1.0

Magnesium binding site 2 out of 2 in 6q4t

Go back to Magnesium Binding Sites List in 6q4t
Magnesium binding site 2 out of 2 in the Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kod Dna Pol in A Closed Ternary Complex with 7-Deaza-7-(2-(2- Hydroxyethoxy)-N-(Prop-2-Yn-1-Yl)Acetamide)-2-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:80.0
occ:1.00
 O T:HOH223 2.4 66.6 1.0
O P:HOH107 2.8 63.3 1.0
O T:HOH204 2.9 49.8 1.0
O P:HOH106 3.2 54.2 1.0
O6 T:DG8 3.4 38.0 1.0
O P:HOH101 3.6 53.2 1.0
O6 P:DG8 3.7 36.3 1.0
H42 P:DC9 4.0 46.9 1.0
O T:HOH221 4.1 62.8 1.0
H42 T:DC9 4.2 44.5 1.0
C6 T:DG8 4.3 38.4 1.0
H41 T:DC9 4.4 44.5 1.0
H41 P:DC9 4.6 46.9 1.0
N7 T:DG8 4.6 37.7 1.0
N4 P:DC9 4.6 39.0 1.0
N7 P:DG7 4.6 46.0 1.0
N4 T:DC9 4.6 37.0 1.0
O6 P:DG7 4.7 45.7 1.0
C5 T:DG8 4.8 38.2 1.0
C6 P:DG8 4.8 37.4 1.0

Reference:

H.M.Kropp, K.Diederichs, A.Marx. The Structure of An Archaeal B-Family Dna Polymerase in Complex with A Chemically Modified Nucleotide. Angew.Chem.Int.Ed.Engl. V. 58 5457 2019.
ISSN: ESSN 1521-3773
PubMed: 30761722
DOI: 10.1002/ANIE.201900315
Page generated: Tue Oct 1 15:23:05 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy