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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: Wed Jul 31 10:53:12 2024

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