Atomistry » Fluorine » PDB 16pk-1bw7 » 1bs1
Atomistry »
  Fluorine »
    PDB 16pk-1bw7 »
      1bs1 »

Fluorine in PDB 1bs1: Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium

Enzymatic activity of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium

All present enzymatic activity of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium:
6.3.3.3;

Protein crystallography data

The structure of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium, PDB code: 1bs1 was solved by H.Kaeck, J.Sandmark, K.J.Gibson, G.Schneider, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.900, 48.200, 60.900, 90.00, 107.00, 90.00
R / Rfree (%) 17.2 / 20.6

Other elements in 1bs1:

The structure of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium (pdb code 1bs1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium, PDB code: 1bs1:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 1bs1

Go back to Fluorine Binding Sites List in 1bs1
Fluorine binding site 1 out of 3 in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F850

b:18.1
occ:1.00
F1 A:DAA850 0.0 18.1 1.0
AL A:DAA850 1.6 14.2 1.0
MG A:MG901 2.1 20.2 1.0
F3 A:DAA850 2.6 17.3 1.0
F2 A:DAA850 2.6 19.4 1.0
O11 A:DAA850 2.8 15.7 1.0
OD2 A:ASP54 2.9 9.4 1.0
O2B A:ADP802 3.0 9.8 1.0
OE2 A:GLU115 3.1 12.1 1.0
NZ A:LYS37 3.2 7.5 1.0
O3B A:ADP802 3.2 10.7 1.0
MG A:MG902 3.3 16.0 1.0
NZ A:LYS15 3.4 15.6 1.0
O A:HOH444 3.4 23.8 1.0
CE A:LYS15 3.4 13.3 1.0
PB A:ADP802 3.6 11.0 1.0
CG A:ASP54 4.0 9.9 1.0
CN1 A:DAA850 4.1 16.1 1.0
OG1 A:THR16 4.2 8.4 1.0
O A:HOH717 4.2 13.6 1.0
CD A:GLU115 4.3 11.7 1.0
O1B A:ADP802 4.3 10.3 1.0
N A:GLY118 4.4 9.1 1.0
O A:GLY116 4.4 8.7 1.0
OD1 A:ASP54 4.6 7.9 1.0
CE A:LYS37 4.6 8.0 1.0
O12 A:DAA850 4.6 12.9 1.0
N2 A:DAA850 4.8 19.0 1.0
CA A:ALA117 4.8 9.6 1.0
CD A:LYS15 4.9 13.2 1.0
CB A:LYS15 4.9 11.6 1.0
OG1 A:THR11 4.9 11.7 1.0
CZ A:DAA850 4.9 16.5 1.0

Fluorine binding site 2 out of 3 in 1bs1

Go back to Fluorine Binding Sites List in 1bs1
Fluorine binding site 2 out of 3 in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F850

b:19.4
occ:1.00
F2 A:DAA850 0.0 19.4 1.0
AL A:DAA850 1.6 14.2 1.0
MG A:MG902 2.3 16.0 1.0
N2 A:DAA850 2.3 19.0 1.0
F3 A:DAA850 2.5 17.3 1.0
F1 A:DAA850 2.6 18.1 1.0
O11 A:DAA850 2.6 15.7 1.0
CH A:DAA850 3.1 17.2 1.0
O A:HOH754 3.2 17.4 1.0
CZ A:DAA850 3.2 16.5 1.0
CN1 A:DAA850 3.2 16.1 1.0
O3B A:ADP802 3.4 10.7 1.0
OG1 A:THR11 3.4 11.7 1.0
O A:HOH717 3.4 13.6 1.0
N1 A:DAA850 3.6 16.5 1.0
O A:HOH833 3.8 24.9 1.0
O A:HOH444 3.8 23.8 1.0
OD2 A:ASP54 4.1 9.4 1.0
O12 A:DAA850 4.1 12.9 1.0
MG A:MG901 4.1 20.2 1.0
CS A:DAA850 4.5 17.5 1.0
PB A:ADP802 4.6 11.0 1.0
CE A:DAA850 4.6 15.2 1.0
NZ A:LYS37 4.6 7.5 1.0
N A:GLY118 4.6 9.1 1.0
O2B A:ADP802 4.7 9.8 1.0
CB A:THR11 4.7 10.5 1.0
NZ A:LYS15 4.8 15.6 1.0
O A:HOH832 4.9 35.1 1.0
OE1 A:GLU12 4.9 24.8 1.0
CG A:ASP54 5.0 9.9 1.0

Fluorine binding site 3 out of 3 in 1bs1

Go back to Fluorine Binding Sites List in 1bs1
Fluorine binding site 3 out of 3 in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F850

b:17.3
occ:1.00
F3 A:DAA850 0.0 17.3 1.0
AL A:DAA850 1.6 14.2 1.0
F2 A:DAA850 2.5 19.4 1.0
F1 A:DAA850 2.6 18.1 1.0
NZ A:LYS15 2.6 15.6 1.0
OG1 A:THR11 2.8 11.7 1.0
N A:GLY118 2.8 9.1 1.0
CA A:GLY118 3.1 9.2 1.0
O11 A:DAA850 3.2 15.7 1.0
O3B A:ADP802 3.3 10.7 1.0
CB A:THR11 3.5 10.5 1.0
CE A:LYS15 3.6 13.3 1.0
CA A:THR11 3.6 10.1 1.0
CZ A:DAA850 3.9 16.5 1.0
MG A:MG902 3.9 16.0 1.0
O A:GLY118 4.0 9.6 1.0
C A:GLY118 4.0 9.3 1.0
C A:ALA117 4.1 8.9 1.0
PB A:ADP802 4.1 11.0 1.0
N A:GLU12 4.3 10.7 1.0
O1B A:ADP802 4.3 10.3 1.0
CH A:DAA850 4.4 17.2 1.0
N2 A:DAA850 4.4 19.0 1.0
CN1 A:DAA850 4.4 16.1 1.0
C A:THR11 4.5 9.3 1.0
MG A:MG901 4.5 20.2 1.0
O2B A:ADP802 4.5 9.8 1.0
CA A:ALA117 4.5 9.6 1.0
N1 A:DAA850 4.7 16.5 1.0
N A:THR11 4.7 9.5 1.0
CE A:DAA850 4.8 15.2 1.0
O A:ASP10 4.8 9.1 1.0
CD A:DAA850 4.8 14.4 1.0
O A:HOH833 4.8 24.9 1.0
CD A:LYS15 4.9 13.2 1.0
CG2 A:THR11 5.0 12.2 1.0

Reference:

H.Kack, J.Sandmark, K.J.Gibson, G.Schneider, Y.Lindqvist. Crystal Structure of Two Quaternary Complexes of Dethiobiotin Synthetase, Enzyme-Mgadp-ALF3-Diaminopelargonic Acid and Enzyme-Mgadp-Dethiobiotin-Phosphate; Implications For Catalysis. Protein Sci. V. 7 2560 1998.
ISSN: ISSN 0961-8368
PubMed: 9865950
Page generated: Sun Dec 13 11:28:24 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy