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: Mon Dec 14 23:51:32 2020

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