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Fluorine in PDB 4k10: Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+

Enzymatic activity of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+

All present enzymatic activity of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+, PDB code: 4k10 was solved by S.Aripirala, S.Gabelli, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 115.47 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.168, 143.743, 194.333, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 27.6

Other elements in 4k10:

The structure of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Sodium (Na) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ (pdb code 4k10). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+, PDB code: 4k10:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4k10

Go back to Fluorine Binding Sites List in 4k10
Fluorine binding site 1 out of 4 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


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 Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:88.2
occ:1.00
 F A:NI9406 0.0 88.2 1.0
C7 A:NI9406 1.3 87.9 1.0
C4 A:NI9406 2.4 87.8 1.0
C3 A:NI9406 2.4 87.9 1.0
CD A:GLN167 2.9 40.5 1.0
NE2 A:GLN167 3.1 40.5 1.0
OE1 A:GLN167 3.2 40.4 1.0
CG A:GLN167 3.4 38.1 1.0
N A:NI9406 3.6 87.9 1.0
C6 A:NI9406 3.6 88.1 1.0
CE A:LYS207 4.0 39.9 1.0
CG A:LYS207 4.0 40.0 1.0
CB A:PHE94 4.0 38.7 1.0
C5 A:NI9406 4.1 88.2 1.0
CD2 A:PHE94 4.2 39.8 1.0
CG A:PHE94 4.3 39.5 1.0
CG2 A:THR163 4.3 35.9 1.0
CD A:LYS207 4.6 39.8 1.0
O A:LYS207 4.6 40.2 1.0
OD1 A:ASP98 4.7 40.0 1.0
O A:PHE94 4.7 39.2 1.0
CG A:ASP98 4.8 39.2 1.0
CB A:ASP98 4.8 38.1 1.0
C2 A:NI9406 4.8 87.6 1.0
CB A:GLN167 4.9 37.5 1.0

Fluorine binding site 2 out of 4 in 4k10

Go back to Fluorine Binding Sites List in 4k10
Fluorine binding site 2 out of 4 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


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 Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F405

b:0.2
occ:1.00
 F B:NI9405 0.0 0.2 1.0
C7 B:NI9405 1.3 0.1 1.0
C4 B:NI9405 2.3 0.2 1.0
C3 B:NI9405 2.3 0.4 1.0
NE2 B:GLN167 2.9 36.4 1.0
CD B:GLN167 3.1 36.7 1.0
OE1 B:GLN167 3.1 37.5 1.0
N B:NI9405 3.5 0.7 1.0
C6 B:NI9405 3.6 0.4 1.0
CB B:ASP98 3.6 41.3 1.0
CG B:ASP98 3.7 41.5 1.0
OD1 B:ASP98 3.7 38.6 1.0
O B:PHE94 3.8 36.7 1.0
C5 B:NI9405 4.0 0.6 1.0
CG B:GLN167 4.0 37.3 1.0
CB B:PHE94 4.2 35.7 1.0
OD2 B:ASP98 4.3 42.8 1.0
C B:PHE94 4.4 37.1 1.0
O B:HOH560 4.5 51.6 1.0
CD2 B:PHE94 4.5 35.1 1.0
CG B:PHE94 4.7 36.3 1.0
C2 B:NI9405 4.7 0.0 1.0
CG B:LYS207 4.8 41.3 1.0
CD B:LYS207 4.8 43.2 1.0
O4 B:NI9405 4.8 0.5 1.0
CA B:PHE94 4.8 36.2 1.0
CA B:ASP98 4.9 41.2 1.0

Fluorine binding site 3 out of 4 in 4k10

Go back to Fluorine Binding Sites List in 4k10
Fluorine binding site 3 out of 4 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F405

b:100.0
occ:1.00
 F D:NI9405 0.0 100.0 1.0
C7 D:NI9405 1.3 99.5 1.0
C4 D:NI9405 2.4 99.2 1.0
C3 D:NI9405 2.4 99.8 1.0
CD D:GLN167 2.9 44.2 1.0
NE2 D:GLN167 2.9 45.6 1.0
OE1 D:GLN167 3.1 43.5 1.0
CG D:GLN167 3.5 43.5 1.0
N D:NI9405 3.6 99.9 1.0
C6 D:NI9405 3.6 99.8 1.0
CB D:PHE94 3.8 37.4 1.0
CD2 D:PHE94 4.0 36.6 1.0
C5 D:NI9405 4.1 99.9 1.0
CG D:PHE94 4.1 37.7 1.0
O D:PHE94 4.2 38.1 1.0
CB D:ASP98 4.3 39.0 1.0
CG D:ASP98 4.4 40.3 1.0
OD1 D:ASP98 4.5 43.0 1.0
O D:HOH504 4.5 42.6 1.0
CG D:LYS207 4.6 40.9 1.0
C D:PHE94 4.6 37.7 1.0
CG2 D:THR163 4.7 36.3 1.0
CA D:PHE94 4.7 37.5 1.0
C2 D:NI9405 4.8 0.1 1.0
O C:HOH503 4.8 47.7 1.0
CE2 D:PHE94 4.9 34.0 1.0
CB D:GLN167 4.9 42.8 1.0
CD D:LYS207 5.0 40.1 1.0

Fluorine binding site 4 out of 4 in 4k10

Go back to Fluorine Binding Sites List in 4k10
Fluorine binding site 4 out of 4 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F405

b:83.8
occ:1.00
 F C:NI9405 0.0 83.8 1.0
C7 C:NI9405 1.3 83.5 1.0
C4 C:NI9405 2.4 83.4 1.0
C3 C:NI9405 2.4 83.6 1.0
NE2 C:GLN167 2.8 41.9 1.0
CD C:GLN167 3.1 41.9 1.0
OE1 C:GLN167 3.1 43.9 1.0
CD2 C:PHE94 3.4 33.6 1.0
N C:NI9405 3.6 83.7 1.0
C6 C:NI9405 3.6 83.9 1.0
CB C:PHE94 3.6 34.2 1.0
CG C:PHE94 3.8 33.4 1.0
C5 C:NI9405 4.1 83.9 1.0
CG C:LYS207 4.2 35.7 1.0
CG2 C:THR163 4.2 33.0 1.0
CG C:GLN167 4.3 40.8 1.0
CE2 C:PHE94 4.4 32.8 1.0
O C:PHE94 4.4 35.9 1.0
CB C:GLN167 4.6 37.9 1.0
OD1 C:ASP98 4.6 35.5 1.0
O D:HOH531 4.6 41.4 1.0
CA C:PHE94 4.7 34.6 1.0
CE C:LYS207 4.7 36.9 1.0
C C:PHE94 4.8 35.1 1.0
CB C:ASP98 4.8 35.5 1.0
C2 C:NI9405 4.8 83.8 1.0
CD C:LYS207 4.9 34.8 1.0
CG C:ASP98 4.9 35.7 1.0
O C:HOH561 4.9 39.1 1.0
O C:THR163 5.0 33.5 1.0
CD1 C:PHE94 5.0 32.7 1.0

Reference:

S.Aripirala, D.Gonzalez-Pacanowska, E.Oldfield, M.Kaiser, L.M.Amzel, S.B.Gabelli. Structural and Thermodynamic Basis of the Inhibition of Leishmania Major Farnesyl Diphosphate Synthase By Nitrogen-Containing Bisphosphonates. Acta Crystallogr.,Sect.D V. 70 802 2014.
ISSN: ISSN 0907-4449
PubMed: 24598749
DOI: 10.1107/S1399004713033221
Page generated: Thu Aug 1 03:04:39 2024

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