Atomistry » Magnesium » PDB 6psr-6q70 » 6q4u
Atomistry »
  Magnesium »
    PDB 6psr-6q70 »
      6q4u »

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

Last articles

Al in 8SHD
Al in 8SHA
Al in 8SGL
Al in 8SH9
Al in 8SGC
Al in 8SG9
Al in 8SFF
Al in 8SG8
Al in 8R1A
Al in 8Q75
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy