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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: Tue Dec 15 04:58:58 2020

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