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Magnesium in PDB 6q4u: Klentaq 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 Klentaq 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 Klentaq 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 Klentaq 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: 6q4u 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) 47.35 / 2.01
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.359, 109.359, 90.893, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 22

Other elements in 6q4u:

The structure of Klentaq 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 Klentaq 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 6q4u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Klentaq 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: 6q4u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6q4u

Go back to Magnesium Binding Sites List in 6q4u
Magnesium binding site 1 out of 2 in the Klentaq 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 Klentaq 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:Mg901

b:37.5
occ:1.00
 OD2 A:ASP610 2.2 44.4 1.0
OD1 A:ASP785 2.3 42.3 1.0
O A:HOH1078 2.3 41.3 1.0
O3 A:HHZ903 2.4 43.0 1.0
O A:HOH1034 2.4 31.7 1.0
H3'2 B:DOC112 2.9 42.9 1.0
CG A:ASP610 2.9 42.6 1.0
OD1 A:ASP610 3.1 47.9 1.0
CG A:ASP785 3.2 43.9 1.0
HB2 A:GLU786 3.3 53.5 1.0
OD2 A:ASP785 3.4 46.6 1.0
MN A:MN902 3.5 41.7 1.0
P A:HHZ903 3.5 43.9 1.0
H3'1 B:DOC112 3.6 42.9 1.0
H5' B:DOC112 3.6 41.8 1.0
C3' B:DOC112 3.6 35.8 1.0
H11 A:HHZ903 3.6 46.1 1.0
H13 A:HHZ903 3.7 47.8 1.0
O A:HOH1136 3.8 36.2 1.0
HZ1 A:LYS831 3.8 78.6 1.0
O2 A:HHZ903 3.9 38.4 1.0
HZ2 A:LYS831 3.9 78.6 1.0
H9 A:HHZ903 4.1 51.7 1.0
OE1 A:GLU786 4.1 44.8 1.0
CB A:GLU786 4.2 44.6 1.0
O1 A:HHZ903 4.2 39.7 1.0
H4' B:DOC112 4.2 42.2 1.0
HB3 A:GLU786 4.2 53.5 1.0
NZ A:LYS831 4.2 65.5 1.0
H10 A:HHZ903 4.2 51.7 1.0
C4' B:DOC112 4.3 35.2 1.0
C5' B:DOC112 4.3 34.8 1.0
CB A:ASP610 4.3 42.5 1.0
H A:ASP785 4.3 36.5 1.0
HZ3 A:LYS831 4.4 78.6 1.0
HB2 A:ASP610 4.4 51.0 1.0
C8 A:HHZ903 4.4 43.0 1.0
O8 A:HHZ903 4.5 39.8 1.0
O A:VAL783 4.6 31.3 1.0
C A:ASP785 4.6 34.8 1.0
CB A:ASP785 4.6 40.2 1.0
O A:ASP785 4.7 37.0 1.0
N A:GLU786 4.8 44.1 1.0
HA A:ASP610 4.8 43.7 1.0
O5' B:DOC112 4.8 32.6 1.0
O4 A:HHZ903 4.9 43.2 1.0
HB3 A:ASP610 4.9 51.0 1.0
C2' B:DOC112 4.9 31.1 1.0
CA A:ASP785 5.0 34.2 1.0
CD A:GLU786 5.0 45.9 1.0
O6 A:HHZ903 5.0 42.0 1.0

Magnesium binding site 2 out of 2 in 6q4u

Go back to Magnesium Binding Sites List in 6q4u
Magnesium binding site 2 out of 2 in the Klentaq 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 Klentaq 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
B:Mg201

b:50.5
occ:1.00
 O B:HOH311 2.6 41.2 1.0
O B:HOH302 3.0 37.1 1.0
O6 B:DG107 3.0 28.9 1.0
H5 B:DC106 3.4 35.8 1.0
O B:HOH314 3.5 42.8 1.0
H42 C:DC209 3.5 41.0 1.0
H41 C:DC209 3.6 41.0 1.0
O6 B:DG108 3.6 31.0 1.0
O C:HOH422 3.7 42.3 1.0
H41 B:DC106 3.7 36.4 1.0
C5 B:DC106 3.8 29.8 1.0
N4 C:DC209 3.8 34.2 1.0
C6 B:DG107 4.0 33.6 1.0
N7 B:DG107 4.0 30.0 1.0
O C:HOH435 4.1 50.7 1.0
N4 B:DC106 4.1 30.3 1.0
C4 B:DC106 4.2 29.9 1.0
H42 C:DC210 4.2 37.6 1.0
C5 B:DG107 4.4 31.5 1.0
C6 B:DG108 4.5 31.7 1.0
C6 B:DC106 4.5 31.8 1.0
H6 B:DC106 4.7 38.2 1.0
H42 B:DC106 4.7 36.4 1.0
N4 C:DC210 4.8 31.3 1.0
H41 C:DC210 4.9 37.6 1.0
C4 C:DC209 4.9 30.0 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

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