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Sodium 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:

Fluorine (F) 4 atoms
Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 6 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4k10

Go back to Sodium Binding Sites List in 4k10
Sodium binding site 1 out of 6 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 Sodium with other atoms in the Na 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:Na401

b:43.3
occ:1.00
 O B:HOH555 2.1 44.4 1.0
O A:HOH531 2.8 30.7 1.0
NH1 A:ARG154 4.1 32.2 1.0
NH1 B:ARG25 4.4 39.5 1.0
OD2 A:ASP158 4.4 29.9 1.0
O A:HOH542 4.5 38.6 1.0
CZ B:ARG25 4.7 39.1 1.0
OD1 A:ASP158 4.9 32.8 1.0

Sodium binding site 2 out of 6 in 4k10

Go back to Sodium Binding Sites List in 4k10
Sodium binding site 2 out of 6 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 Sodium with other atoms in the Na 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
A:Na402

b:32.0
occ:1.00
 OD2 A:ASP160 2.6 30.0 1.0
O B:HOH509 2.7 31.2 1.0
O A:HOH521 2.7 22.9 1.0
ND1 A:HIS157 2.9 38.9 1.0
CG A:ASP160 3.5 32.7 1.0
CB A:ASP160 3.6 31.3 1.0
CA B:ALA133 3.6 35.9 1.0
O A:HIS157 3.6 33.5 1.0
CG A:HIS157 3.8 35.5 1.0
CB A:HIS157 3.8 34.0 1.0
CE1 A:HIS157 3.9 39.5 1.0
CB B:ALA133 4.0 35.6 1.0
CA A:HIS157 4.0 33.8 1.0
CB B:THR136 4.2 36.0 1.0
O B:ALA133 4.2 36.0 1.0
C A:HIS157 4.3 33.8 1.0
OG1 B:THR136 4.3 36.1 1.0
O B:LEU132 4.4 35.1 1.0
O A:HOH505 4.4 23.3 1.0
C B:ALA133 4.5 36.0 1.0
N B:ALA133 4.5 35.3 1.0
N A:LEU161 4.6 32.0 1.0
OD1 A:ASP160 4.7 32.0 1.0
CG2 B:THR136 4.7 35.4 1.0
CA A:ASP160 4.8 31.9 1.0
C B:LEU132 4.8 35.2 1.0
CD2 A:HIS157 4.9 36.7 1.0
C A:ASP160 5.0 31.3 1.0

Sodium binding site 3 out of 6 in 4k10

Go back to Sodium Binding Sites List in 4k10
Sodium binding site 3 out of 6 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 Sodium with other atoms in the Na 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
A:Na403

b:41.8
occ:1.00
 O B:HOH538 2.7 41.3 1.0
NH1 A:ARG25 3.9 35.7 1.0
NH1 B:ARG154 4.3 37.8 1.0
CZ A:ARG25 4.5 36.2 1.0
OD2 A:ASP21 4.6 38.4 1.0
OD2 B:ASP158 4.6 37.1 1.0
OD1 B:ASP158 4.7 37.6 1.0

Sodium binding site 4 out of 6 in 4k10

Go back to Sodium Binding Sites List in 4k10
Sodium binding site 4 out of 6 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 Sodium with other atoms in the Na 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
B:Na401

b:50.8
occ:1.00
 OD2 B:ASP160 2.6 40.1 1.0
O A:HOH527 2.6 34.7 1.0
ND1 B:HIS157 2.8 35.8 1.0
O A:HOH515 3.3 35.0 1.0
CA A:ALA133 3.4 35.8 1.0
CG B:ASP160 3.6 38.2 1.0
CE1 B:HIS157 3.7 37.7 1.0
CG B:HIS157 3.8 35.8 1.0
CB B:ASP160 3.9 37.3 1.0
CB B:HIS157 3.9 34.7 1.0
CB A:ALA133 4.0 35.1 1.0
O B:HIS157 4.0 34.7 1.0
N A:ALA133 4.1 35.5 1.0
OG1 A:THR136 4.2 35.3 1.0
CA B:HIS157 4.2 34.7 1.0
CB A:THR136 4.2 35.8 1.0
O A:ALA133 4.3 36.6 1.0
C A:ALA133 4.4 35.8 1.0
O A:HOH562 4.4 31.6 1.0
O A:LEU132 4.5 35.5 1.0
C A:LEU132 4.6 35.5 1.0
C B:HIS157 4.6 34.7 1.0
CG2 A:THR136 4.8 35.6 1.0
OD1 B:ASP160 4.8 38.0 1.0
NE2 B:HIS157 4.9 38.4 1.0
CD2 B:HIS157 4.9 37.0 1.0
CE1 A:HIS157 5.0 39.5 1.0

Sodium binding site 5 out of 6 in 4k10

Go back to Sodium Binding Sites List in 4k10
Sodium binding site 5 out of 6 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 Sodium with other atoms in the Na binding site number 5 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:Na401

b:43.7
occ:1.00
 O D:HOH507 2.6 34.4 1.0
OD2 C:ASP160 2.7 29.7 1.0
O C:HOH501 2.8 29.1 1.0
ND1 C:HIS157 2.8 34.3 1.0
CA D:ALA133 3.5 33.9 1.0
O C:HIS157 3.6 34.1 1.0
CG C:ASP160 3.6 32.5 1.0
CG C:HIS157 3.6 34.9 1.0
CB C:ASP160 3.7 31.2 1.0
CB C:HIS157 3.7 34.4 1.0
CB D:ALA133 3.7 33.6 1.0
CE1 C:HIS157 3.8 33.0 1.0
CA C:HIS157 4.0 34.5 1.0
O D:ALA133 4.0 34.3 1.0
C C:HIS157 4.2 34.7 1.0
C D:ALA133 4.3 34.5 1.0
CB D:THR136 4.3 35.0 1.0
OG1 D:THR136 4.4 34.1 1.0
N D:ALA133 4.4 32.9 1.0
O C:HOH565 4.5 31.5 1.0
O D:LEU132 4.6 32.3 1.0
N C:LEU161 4.6 32.4 1.0
CG2 D:THR136 4.7 34.1 1.0
OD1 C:ASP160 4.8 33.5 1.0
CD2 C:HIS157 4.8 34.1 1.0
NE2 C:HIS157 4.9 32.9 1.0
C D:LEU132 4.9 32.1 1.0
CA C:ASP160 4.9 31.8 1.0

Sodium binding site 6 out of 6 in 4k10

Go back to Sodium Binding Sites List in 4k10
Sodium binding site 6 out of 6 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 Sodium with other atoms in the Na binding site number 6 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:Na402

b:39.7
occ:1.00
 NH1 C:ARG25 3.8 37.4 1.0
OD2 D:ASP158 4.1 35.2 1.0
CZ C:ARG25 4.1 38.0 1.0
OD1 D:ASP158 4.2 36.1 1.0
CG D:ASP158 4.5 34.4 1.0
NE C:ARG25 4.6 38.2 1.0
NH1 D:ARG154 4.6 40.7 1.0
OD2 C:ASP21 4.6 42.2 1.0
NH2 C:ARG25 4.6 37.9 1.0
OE1 C:GLN137 4.7 41.8 1.0
CD C:ARG25 4.8 39.0 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: Mon Oct 7 16:24:27 2024

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