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Fluorine in PDB 2c94: Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate

Enzymatic activity of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate

All present enzymatic activity of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate:
2.5.1.9;

Protein crystallography data

The structure of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate, PDB code: 2c94 was solved by E.Morgunova, B.Illarionov, G.Jin, I.Haase, M.Fischer, M.Cushman, A.Bacher, R.Ladenstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.384, 81.251, 85.883, 90.00, 120.25, 90.00
R / Rfree (%) 17.5 / 21.9

Other elements in 2c94:

The structure of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate also contains other interesting chemical elements:

Potassium (K) 17 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate (pdb code 2c94). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate, PDB code: 2c94:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 2c94

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Fluorine binding site 1 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:37.9
occ:1.00
 F1 A:TSF701 0.0 37.9 1.0
C19 A:TSF701 1.3 37.4 1.0
F2 A:TSF701 2.2 39.2 1.0
C18 A:TSF701 2.3 36.9 1.0
P A:TSF701 2.6 36.8 1.0
O1P A:TSF701 2.9 35.3 1.0
O2P A:TSF701 3.0 34.9 1.0
C17 A:TSF701 3.1 36.4 1.0
O A:HOH2091 3.5 55.3 1.0
C15 A:TSF701 3.6 33.9 1.0
O3P A:TSF701 3.8 35.9 1.0
C16 A:TSF701 4.0 34.8 1.0
O A:HOH2115 4.6 36.8 1.0
OE2 B:GLU136 4.7 39.9 1.0
O A:HOH2055 4.9 30.1 1.0
CA A:GLY85 5.0 27.7 1.0
N5 A:TSF701 5.0 33.0 1.0

Fluorine binding site 2 out of 10 in 2c94

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Fluorine binding site 2 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:39.2
occ:1.00
 F2 A:TSF701 0.0 39.2 1.0
C19 A:TSF701 1.3 37.4 1.0
F1 A:TSF701 2.2 37.9 1.0
C18 A:TSF701 2.3 36.9 1.0
P A:TSF701 2.5 36.8 1.0
C17 A:TSF701 2.7 36.4 1.0
O2P A:TSF701 2.9 34.9 1.0
O3P A:TSF701 3.0 35.9 1.0
CA A:GLY85 3.0 27.7 1.0
N A:GLY85 3.0 27.6 1.0
O A:HOH2055 3.2 30.1 1.0
O A:ILE83 3.6 26.0 1.0
O1P A:TSF701 3.8 35.3 1.0
C A:ARG84 3.8 27.1 1.0
C16 A:TSF701 4.1 34.8 1.0
C A:GLY85 4.1 28.2 1.0
N A:GLN86 4.3 28.3 1.0
O A:ARG84 4.3 27.2 1.0
O A:HOH2091 4.4 55.3 1.0
C15 A:TSF701 4.4 33.9 1.0
O A:HOH2115 4.5 36.8 1.0
CA A:ARG84 4.6 27.0 1.0
C A:ILE83 4.7 26.0 1.0

Fluorine binding site 3 out of 10 in 2c94

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Fluorine binding site 3 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:40.8
occ:1.00
 F1 B:TSF701 0.0 40.8 1.0
C19 B:TSF701 1.3 40.3 1.0
F2 B:TSF701 2.1 41.2 1.0
C18 B:TSF701 2.3 40.0 1.0
P B:TSF701 2.6 39.8 1.0
C17 B:TSF701 2.6 39.2 1.0
N B:GLY85 2.8 31.1 1.0
CA B:GLY85 2.9 31.5 1.0
O2P B:TSF701 2.9 39.0 1.0
O B:HOH2110 2.9 35.4 1.0
O3P B:TSF701 3.0 39.5 1.0
C B:ARG84 3.7 30.9 1.0
O B:ILE83 3.7 29.1 1.0
O1P B:TSF701 3.8 39.5 1.0
C B:GLY85 3.9 31.6 1.0
C16 B:TSF701 4.1 38.2 1.0
N B:GLN86 4.1 31.9 1.0
O B:ARG84 4.4 30.5 1.0
C15 B:TSF701 4.5 36.3 1.0
CA B:ARG84 4.5 30.6 1.0
O B:HOH2109 4.7 50.0 1.0
C B:ILE83 4.8 29.1 1.0
O B:GLY85 4.9 31.7 1.0
O C:HOH2073 5.0 53.1 1.0

Fluorine binding site 4 out of 10 in 2c94

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Fluorine binding site 4 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:41.2
occ:1.00
 F2 B:TSF701 0.0 41.2 1.0
C19 B:TSF701 1.3 40.3 1.0
F1 B:TSF701 2.1 40.8 1.0
C18 B:TSF701 2.3 40.0 1.0
P B:TSF701 2.6 39.8 1.0
O C:HOH2073 3.0 53.1 1.0
O1P B:TSF701 3.0 39.5 1.0
O2P B:TSF701 3.0 39.0 1.0
C17 B:TSF701 3.2 39.2 1.0
C15 B:TSF701 3.7 36.3 1.0
O3P B:TSF701 3.8 39.5 1.0
C16 B:TSF701 4.1 38.2 1.0
O B:HOH2109 4.5 50.0 1.0
CA B:GLY85 4.7 31.5 1.0
O B:HOH2110 4.7 35.4 1.0
CZ3 B:TRP27 4.9 40.4 1.0
N B:GLY85 4.9 31.1 1.0
O B:ILE83 4.9 29.1 1.0

Fluorine binding site 5 out of 10 in 2c94

Go back to Fluorine Binding Sites List in 2c94
Fluorine binding site 5 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:43.1
occ:1.00
 F1 C:TSF701 0.0 43.1 1.0
C19 C:TSF701 1.3 42.6 1.0
F2 C:TSF701 2.1 43.5 1.0
C18 C:TSF701 2.3 41.6 1.0
P C:TSF701 2.6 42.6 1.0
O1P C:TSF701 2.7 41.5 1.0
C17 C:TSF701 2.8 40.6 1.0
O2P C:TSF701 3.3 41.5 1.0
C15 C:TSF701 3.6 36.6 1.0
O3P C:TSF701 3.7 42.2 1.0
C16 C:TSF701 3.8 39.0 1.0
O C:HOH2070 3.8 57.0 1.0
O C:HOH2084 4.5 61.3 1.0
OE2 D:GLU136 4.7 41.8 1.0
O C:HOH2082 4.8 39.6 1.0
N5 C:TSF701 4.9 35.2 1.0
CZ3 C:TRP27 5.0 38.9 1.0
CH2 C:TRP27 5.0 39.0 1.0

Fluorine binding site 6 out of 10 in 2c94

Go back to Fluorine Binding Sites List in 2c94
Fluorine binding site 6 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:43.5
occ:1.00
 F2 C:TSF701 0.0 43.5 1.0
C19 C:TSF701 1.3 42.6 1.0
F1 C:TSF701 2.1 43.1 1.0
C18 C:TSF701 2.3 41.6 1.0
P C:TSF701 2.6 42.6 1.0
O2P C:TSF701 2.7 41.5 1.0
CA C:GLY85 3.2 29.1 1.0
O3P C:TSF701 3.4 42.2 1.0
N C:GLY85 3.6 28.9 1.0
C17 C:TSF701 3.6 40.6 1.0
O1P C:TSF701 3.7 41.5 1.0
O C:HOH2070 4.1 57.0 1.0
O C:HOH2085 4.2 37.1 1.0
O C:ILE83 4.2 28.4 1.0
C C:GLY85 4.3 29.0 1.0
C C:ARG84 4.3 29.0 1.0
O C:HOH2082 4.4 39.6 1.0
N C:GLN86 4.4 28.8 1.0
C16 C:TSF701 4.5 39.0 1.0
C15 C:TSF701 4.6 36.6 1.0
O C:ARG84 4.6 28.9 1.0

Fluorine binding site 7 out of 10 in 2c94

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Fluorine binding site 7 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F701

b:38.8
occ:1.00
 F1 D:TSF701 0.0 38.8 1.0
C19 D:TSF701 1.3 38.6 1.0
F2 D:TSF701 2.2 39.4 1.0
C18 D:TSF701 2.4 37.5 1.0
P D:TSF701 2.6 38.1 1.0
C17 D:TSF701 2.8 36.0 1.0
O2P D:TSF701 2.8 37.4 1.0
CA D:GLY85 2.9 29.8 1.0
N D:GLY85 3.1 29.8 1.0
O3P D:TSF701 3.1 38.0 1.0
O D:HOH2064 3.6 37.7 1.0
O1P D:TSF701 3.8 38.0 1.0
O D:ILE83 3.8 28.1 1.0
C D:ARG84 3.9 29.5 1.0
C D:GLY85 4.0 30.1 1.0
N D:GLN86 4.1 30.3 1.0
C16 D:TSF701 4.2 34.2 1.0
O D:HOH2118 4.4 38.3 1.0
O D:HOH2098 4.5 46.5 1.0
O D:ARG84 4.5 29.6 1.0
O D:HOH2047 4.5 53.9 1.0
C15 D:TSF701 4.5 31.9 1.0
CA D:ARG84 4.8 29.5 1.0
O D:HOH2063 4.8 56.6 1.0
C D:ILE83 4.9 28.0 1.0

Fluorine binding site 8 out of 10 in 2c94

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Fluorine binding site 8 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F701

b:39.4
occ:1.00
 F2 D:TSF701 0.0 39.4 1.0
C19 D:TSF701 1.3 38.6 1.0
F1 D:TSF701 2.2 38.8 1.0
C18 D:TSF701 2.3 37.5 1.0
P D:TSF701 2.6 38.1 1.0
O D:HOH2047 2.7 53.9 1.0
O1P D:TSF701 2.9 38.0 1.0
C17 D:TSF701 3.1 36.0 1.0
O2P D:TSF701 3.2 37.4 1.0
C15 D:TSF701 3.5 31.9 1.0
O3P D:TSF701 3.8 38.0 1.0
O D:HOH2098 3.8 46.5 1.0
C16 D:TSF701 3.9 34.2 1.0
O D:HOH2118 4.5 38.3 1.0
N5 D:TSF701 4.9 31.1 1.0
CA D:GLY85 5.0 29.8 1.0

Fluorine binding site 9 out of 10 in 2c94

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Fluorine binding site 9 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F701

b:41.5
occ:1.00
 F1 E:TSF701 0.0 41.5 1.0
C19 E:TSF701 1.3 41.0 1.0
F2 E:TSF701 2.2 43.2 1.0
C18 E:TSF701 2.3 40.0 1.0
P E:TSF701 2.6 40.1 1.0
C17 E:TSF701 2.6 38.3 1.0
CA E:GLY85 2.8 27.9 1.0
N E:GLY85 2.8 27.6 1.0
O3P E:TSF701 2.9 39.2 1.0
O2P E:TSF701 3.0 39.5 1.0
O E:HOH2117 3.1 28.8 1.0
O E:ILE83 3.7 26.6 1.0
C E:ARG84 3.7 27.6 1.0
O1P E:TSF701 3.8 39.4 1.0
C E:GLY85 3.9 28.2 1.0
C16 E:TSF701 4.0 36.2 1.0
N E:GLN86 4.1 28.2 1.0
O E:ARG84 4.3 27.4 1.0
O E:HOH2115 4.4 37.0 1.0
C15 E:TSF701 4.5 33.5 1.0
CA E:ARG84 4.5 27.4 1.0
O E:HOH2093 4.6 46.2 1.0
C E:ILE83 4.7 26.9 1.0
O E:GLY85 4.9 28.3 1.0

Fluorine binding site 10 out of 10 in 2c94

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Fluorine binding site 10 out of 10 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl) 1,1 Difluoropentane-1- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F701

b:43.2
occ:1.00
 F2 E:TSF701 0.0 43.2 1.0
C19 E:TSF701 1.3 41.0 1.0
F1 E:TSF701 2.2 41.5 1.0
C18 E:TSF701 2.3 40.0 1.0
P E:TSF701 2.6 40.1 1.0
O2P E:TSF701 3.0 39.5 1.0
O1P E:TSF701 3.0 39.4 1.0
C17 E:TSF701 3.3 38.3 1.0
O E:HOH2093 3.5 46.2 1.0
O3P E:TSF701 3.8 39.2 1.0
C15 E:TSF701 4.0 33.5 1.0
C16 E:TSF701 4.3 36.2 1.0
O E:HOH2115 4.6 37.0 1.0
CA E:GLY85 4.6 27.9 1.0
CZ3 E:TRP27 4.8 39.6 1.0
O E:HOH2117 4.9 28.8 1.0
NZ A:LYS138 4.9 43.1 1.0
N E:GLY85 4.9 27.6 1.0

Reference:

E.Morgunova, B.Illarionov, T.Sambaiah, I.Haase, A.Bacher, M.Cushman, M.Fischer, R.Ladenstein. Structural and Thermodynamic Insights Into the Binding Mode of Five Novel Inhibitors of Lumazine Synthase From Mycobacterium Tuberculosis. Febs J. V. 273 4790 2006.
ISSN: ISSN 1742-464X
PubMed: 16984393
DOI: 10.1111/J.1742-4658.2006.05481.X
Page generated: Sun Dec 13 11:35:21 2020

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