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Sodium in PDB 4jzb: Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+

Enzymatic activity of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+

All present enzymatic activity of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+:
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 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+, PDB code: 4jzb was solved by S.Aripirala, L.M.Amzel, S.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.96 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.361, 85.967, 107.074, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21

Other elements in 4jzb:

The structure of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+ also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+ (pdb code 4jzb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+, PDB code: 4jzb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4jzb

Go back to Sodium Binding Sites List in 4jzb
Sodium binding site 1 out of 2 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+


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 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:33.9
occ:1.00
 O A:HOH561 2.0 22.1 1.0
O A:HOH554 2.2 20.0 1.0
OE1 A:GLU270 2.9 24.8 1.0
O A:HOH671 2.9 29.4 1.0
O A:HOH637 3.5 23.8 1.0
O A:GLY266 3.5 23.9 1.0
OE2 A:GLU270 3.6 25.6 1.0
CD A:GLU270 3.6 25.6 1.0
CG1 A:VAL305 3.9 20.1 1.0
O A:HOH746 4.0 27.8 1.0
CE A:LYS309 4.1 20.2 1.0
CB A:ILE269 4.1 21.1 1.0
CD1 A:ILE269 4.1 19.9 1.0
NZ A:LYS309 4.2 22.1 1.0
CG1 A:ILE269 4.3 20.6 1.0
CA A:THR267 4.3 24.6 1.0
C A:GLY266 4.4 24.2 1.0
OD1 A:ASP254 4.4 22.8 1.0
O A:HOH840 4.5 39.7 1.0
N A:ILE269 4.5 21.9 1.0
O A:ASP254 4.7 20.4 1.0
C A:THR267 4.8 23.9 1.0
N A:THR267 4.8 24.5 1.0
N A:ASP268 4.9 22.6 1.0
CA A:ILE269 4.9 21.6 1.0
O A:HOH805 5.0 35.8 1.0
N A:GLU270 5.0 22.3 1.0

Sodium binding site 2 out of 2 in 4jzb

Go back to Sodium Binding Sites List in 4jzb
Sodium binding site 2 out of 2 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+


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 1-(2-Hydroxy-2,2-Diphosphonoethyl)-3- Phenylpyridinium, Ipp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:39.8
occ:1.00
 O B:HOH562 2.2 24.8 1.0
O B:HOH615 2.3 25.7 1.0
O B:HOH766 2.7 32.0 1.0
OE1 B:GLU270 2.8 23.5 1.0
O B:HOH716 3.5 30.0 1.0
CD B:GLU270 3.5 26.0 1.0
OE2 B:GLU270 3.6 25.1 1.0
O B:GLY266 3.6 23.9 1.0
CG1 B:VAL305 3.9 26.5 1.0
CE B:LYS309 4.0 23.4 1.0
CB B:ILE269 4.1 23.0 1.0
CD1 B:ILE269 4.1 23.5 1.0
O B:HOH694 4.2 30.6 1.0
NZ B:LYS309 4.2 23.8 1.0
CG1 B:ILE269 4.3 22.8 1.0
CA B:THR267 4.4 24.8 1.0
N B:ILE269 4.5 22.6 1.0
C B:GLY266 4.6 24.4 1.0
OD1 B:ASP254 4.6 23.6 1.0
C B:THR267 4.8 24.5 1.0
CA B:ILE269 4.9 22.8 1.0
N B:GLU270 4.9 23.7 1.0
N B:ASP268 4.9 23.7 1.0
O B:ASP254 4.9 22.8 1.0
N B:THR267 4.9 24.5 1.0
CG2 B:VAL305 5.0 26.1 1.0
CG B:GLU270 5.0 24.5 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 16:23:19 2024

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