Atomistry » Fluorine » PDB 3oyl-3pr2 » 3p5r
Atomistry »
  Fluorine »
    PDB 3oyl-3pr2 »
      3p5r »

Fluorine in PDB 3p5r: Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate

Enzymatic activity of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate

All present enzymatic activity of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate:
4.2.3.17;

Protein crystallography data

The structure of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate, PDB code: 3p5r was solved by M.Koksal, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.41 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.050, 201.980, 81.431, 90.00, 91.60, 90.00
R / Rfree (%) 18.7 / 25

Other elements in 3p5r:

The structure of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate (pdb code 3p5r). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate, PDB code: 3p5r:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3p5r

Go back to Fluorine Binding Sites List in 3p5r
Fluorine binding site 1 out of 2 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F911

b:39.2
occ:1.00
F01 A:FGG911 0.0 39.2 1.0
C02 A:FGG911 1.3 32.7 1.0
C03 A:FGG911 2.3 30.0 1.0
C01 A:FGG911 2.4 30.0 1.0
C04 A:FGG911 2.7 29.2 1.0
O01 A:FGG911 2.8 21.0 1.0
C19 A:FGG911 3.3 38.6 1.0
O A:HOH1263 3.6 18.6 1.0
C16 A:FGG911 3.7 23.8 1.0
CG2 A:VAL610 4.0 13.9 1.0
P02 A:FGG911 4.1 16.8 1.0
C15 A:FGG911 4.1 45.7 1.0
C05 A:FGG911 4.2 28.6 1.0
C20 A:FGG911 4.3 38.8 1.0
O03 A:FGG911 4.3 17.7 1.0
O A:HOH1272 4.4 28.6 1.0
CG1 A:VAL610 4.4 12.4 1.0
O07 A:FGG911 4.5 16.8 1.0
CB A:VAL610 4.5 12.8 1.0
CA A:VAL610 4.6 10.5 1.0
NH2 A:ARG580 4.6 26.5 0.5
C17 A:FGG911 4.8 28.3 1.0
OD2 A:ASP613 4.9 12.0 1.0

Fluorine binding site 2 out of 2 in 3p5r

Go back to Fluorine Binding Sites List in 3p5r
Fluorine binding site 2 out of 2 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F911

b:38.5
occ:1.00
F01 B:FGG911 0.0 38.5 1.0
C02 B:FGG911 1.3 30.8 1.0
C03 B:FGG911 2.3 29.9 1.0
C01 B:FGG911 2.4 26.7 1.0
C04 B:FGG911 2.7 26.9 1.0
O01 B:FGG911 2.8 20.3 1.0
O B:HOH1430 3.3 23.9 1.0
C16 B:FGG911 3.7 20.8 1.0
O B:HOH1289 3.7 15.5 1.0
CG2 B:VAL610 3.8 13.1 1.0
CG1 B:VAL610 4.0 16.9 1.0
P02 B:FGG911 4.0 15.5 1.0
C05 B:FGG911 4.2 27.5 1.0
OD2 B:ASP613 4.2 15.2 1.0
O03 B:FGG911 4.3 16.1 1.0
CB B:VAL610 4.3 16.8 1.0
CA B:VAL610 4.4 17.4 1.0
O07 B:FGG911 4.5 15.4 1.0
C17 B:FGG911 4.7 28.0 1.0
C06 B:FGG911 4.9 33.3 1.0
CG B:ASP613 4.9 12.6 1.0

Reference:

M.Koksal, Y.Jin, R.M.Coates, R.Croteau, D.W.Christianson. Taxadiene Synthase Structure and Evolution of Modular Architecture in Terpene Biosynthesis. Nature V. 469 116 2011.
ISSN: ISSN 0028-0836
PubMed: 21160477
DOI: 10.1038/NATURE09628
Page generated: Sun Dec 13 11:53:04 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy