Atomistry » Manganese » PDB 6oe2-6q9f » 6q4t
Atomistry »
  Manganese »
    PDB 6oe2-6q9f »
      6q4t »

Manganese 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:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total only one binding site of Manganese was 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:

Manganese binding site 1 out of 1 in 6q4t

Go back to Manganese Binding Sites List in 6q4t
Manganese binding site 1 out of 1 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 Manganese with other atoms in the Mn 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:Mn801

b:33.2
occ:1.00
 OD1 A:ASP404 2.0 47.0 1.0
OD2 A:ASP542 2.1 47.1 1.0
O6 A:HHZ810 2.2 33.1 1.0
O3 A:HHZ810 2.2 32.8 1.0
O10 A:HHZ810 2.2 33.1 1.0
O A:PHE405 2.2 31.7 1.0
CG A:ASP542 3.1 43.2 1.0
CG A:ASP404 3.2 42.9 1.0
H10 A:HHZ810 3.2 38.8 1.0
P1 A:HHZ810 3.2 32.8 1.0
OD1 A:ASP542 3.4 45.5 1.0
P A:HHZ810 3.4 33.0 1.0
C A:PHE405 3.4 31.7 1.0
P2 A:HHZ810 3.4 34.2 1.0
O4 A:HHZ810 3.6 33.6 1.0
MG A:MG802 3.6 43.5 1.0
OD2 A:ASP404 3.6 45.6 1.0
O7 A:HHZ810 3.6 34.0 1.0
O A:HOH991 3.8 30.2 1.0
H A:PHE405 3.9 36.5 1.0
N A:PHE405 3.9 30.3 1.0
H A:LEU408 3.9 39.2 1.0
O A:HOH1105 3.9 32.7 1.0
HB2 A:PHE405 4.0 37.6 1.0
H A:SER407 4.0 43.0 1.0
CA A:PHE405 4.1 31.1 1.0
C8 A:HHZ810 4.1 32.2 1.0
HB2 A:LEU408 4.2 37.8 1.0
O8 A:HHZ810 4.3 33.7 1.0
O1 A:HHZ810 4.3 33.1 1.0
HA A:ARG406 4.3 44.2 1.0
C A:ASP404 4.4 31.5 1.0
CB A:ASP404 4.4 38.1 1.0
N A:SER407 4.4 35.7 1.0
CB A:ASP542 4.4 38.9 1.0
CB A:PHE405 4.5 31.2 1.0
N A:ARG406 4.5 34.3 1.0
H9 A:HHZ810 4.5 38.8 1.0
HB2 A:ASP542 4.5 46.8 1.0
O2 A:HHZ810 4.5 33.7 1.0
O9 A:HHZ810 4.6 33.9 1.0
HB3 A:ASP404 4.6 45.9 1.0
O5 A:HHZ810 4.6 33.1 1.0
HB3 A:PHE405 4.6 37.6 1.0
O A:ASP542 4.7 33.1 1.0
N A:LEU408 4.7 32.5 1.0
H14 A:HHZ810 4.7 40.9 1.0
CA A:ARG406 4.8 36.8 1.0
H13 A:HHZ810 4.8 40.6 1.0
C A:ARG406 4.8 34.9 1.0
O A:ASP404 4.8 32.3 1.0
HA A:SER407 4.8 43.3 1.0
HB3 A:LEU408 4.9 37.8 1.0
CA A:ASP404 4.9 33.8 1.0
HB3 A:ASP542 4.9 46.8 1.0
HA A:ASP404 4.9 40.7 1.0
O A:HOH1058 4.9 31.8 1.0
CB A:LEU408 4.9 31.4 1.0
HZ3 A:LYS487 5.0 46.4 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: Sun Oct 6 05:53:53 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy