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Calcium in PDB 4jzx: Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+

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

All present enzymatic activity of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, 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 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+, PDB code: 4jzx 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) 25.94 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.428, 85.805, 106.867, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+ (pdb code 4jzx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+, PDB code: 4jzx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4jzx

Go back to Calcium Binding Sites List in 4jzx
Calcium binding site 1 out of 6 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:24.7
occ:1.00
 O A:HOH501 2.3 28.1 1.0
OD1 A:ASP98 2.4 23.1 1.0
O A:HOH504 2.4 22.3 1.0
O A:HOH543 2.4 24.4 1.0
O15 A:476402 2.4 22.9 1.0
OD2 A:ASP102 2.4 27.6 1.0
OD1 A:ASP102 3.0 28.6 1.0
CG A:ASP102 3.1 27.2 1.0
CG A:ASP98 3.1 23.2 1.0
OD2 A:ASP98 3.1 22.1 1.0
CA A:CA405 3.5 27.0 1.0
P9 A:476402 3.6 24.7 1.0
O14 A:476402 3.7 23.9 1.0
OD2 A:ASP170 4.1 27.0 1.0
NE2 A:GLN167 4.3 22.1 1.0
O A:HOH578 4.4 28.5 1.0
OE1 A:GLN167 4.5 23.9 1.0
CB A:ASP102 4.5 26.1 1.0
O A:HOH534 4.5 24.4 1.0
CB A:ASP98 4.5 22.3 1.0
CG A:ASP170 4.6 25.1 1.0
OD1 A:ASP170 4.6 27.5 1.0
O16 A:476402 4.6 23.6 1.0
C1 A:476402 4.8 24.8 1.0
CD A:GLN167 4.8 23.3 1.0
C7 A:476402 4.8 24.4 1.0
C8 A:476402 4.8 23.3 1.0
O A:HOH503 4.9 28.9 1.0
O A:ASP98 4.9 22.3 1.0
N2 A:476402 5.0 24.9 1.0
NZ A:LYS273 5.0 34.6 1.0

Calcium binding site 2 out of 6 in 4jzx

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Calcium binding site 2 out of 6 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:23.9
occ:1.00
 O16 A:476402 2.2 23.6 1.0
O12 A:476402 2.3 23.2 1.0
OD2 A:ASP250 2.3 21.7 1.0
O A:HOH505 2.4 21.4 1.0
O A:HOH506 2.4 25.3 1.0
O A:HOH545 2.5 25.9 1.0
CG A:ASP250 3.4 22.0 1.0
P9 A:476402 3.5 24.7 1.0
P10 A:476402 3.6 24.1 1.0
C8 A:476402 3.8 23.3 1.0
O A:HOH562 3.9 27.2 1.0
OD1 A:ASP250 3.9 21.0 1.0
O A:HOH534 4.0 24.4 1.0
NE2 A:GLN247 4.2 21.4 1.0
O15 A:476402 4.3 22.9 1.0
O A:ASP250 4.3 21.9 1.0
OD2 A:ASP268 4.4 25.8 1.0
O A:HOH621 4.4 32.4 1.0
NZ A:LYS264 4.5 23.0 1.0
O13 A:476402 4.5 22.5 1.0
OD1 A:ASP268 4.5 26.3 1.0
O11 A:476402 4.6 23.1 1.0
O A:HOH503 4.6 28.9 1.0
CB A:ASP250 4.6 21.7 1.0
C A:ASP250 4.6 22.0 1.0
O14 A:476402 4.6 23.9 1.0
CE A:LYS264 4.7 24.6 1.0
OD1 A:ASP251 4.8 21.8 1.0
CG A:ASP268 4.9 26.6 1.0
OD2 A:ASP254 4.9 30.1 1.0
CB A:ASP254 4.9 27.4 1.0

Calcium binding site 3 out of 6 in 4jzx

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Calcium binding site 3 out of 6 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:27.0
occ:1.00
 O13 A:476402 2.2 22.5 1.0
OD2 A:ASP102 2.3 27.6 1.0
O A:HOH502 2.3 25.1 1.0
O A:HOH503 2.3 28.9 1.0
OD2 A:ASP98 2.3 22.1 1.0
O15 A:476402 2.4 22.9 1.0
P10 A:476402 3.4 24.1 1.0
CG A:ASP102 3.4 27.2 1.0
CG A:ASP98 3.5 23.2 1.0
CA A:CA403 3.5 24.7 1.0
P9 A:476402 3.6 24.7 1.0
C8 A:476402 3.8 23.3 1.0
OD1 A:ASP98 4.0 23.1 1.0
CB A:ASP102 4.0 26.1 1.0
C7 A:476402 4.0 24.4 1.0
O12 A:476402 4.0 23.2 1.0
O A:HOH864 4.1 39.5 1.0
NH2 A:ARG107 4.2 21.3 1.0
OG A:SER104 4.3 28.2 1.0
O16 A:476402 4.3 23.6 1.0
OD1 A:ASP99 4.4 23.5 1.0
OD1 A:ASP102 4.4 28.6 1.0
O A:HOH562 4.5 27.2 1.0
O A:ASP98 4.6 22.3 1.0
O11 A:476402 4.6 23.1 1.0
CB A:ASP98 4.7 22.3 1.0
O A:HOH625 4.7 37.0 1.0
O14 A:476402 4.7 23.9 1.0
O A:HOH501 4.8 28.1 1.0
O A:HOH565 4.9 25.5 1.0
O A:HOH506 4.9 25.3 1.0
C A:ASP98 4.9 22.3 1.0

Calcium binding site 4 out of 6 in 4jzx

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Calcium binding site 4 out of 6 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:24.3
occ:1.00
 OD2 B:ASP98 2.3 24.2 1.0
O B:HOH504 2.4 23.7 1.0
OD2 B:ASP102 2.4 28.9 1.0
O B:HOH527 2.4 22.7 1.0
O15 B:476402 2.4 24.7 1.0
O B:HOH502 2.4 28.5 1.0
OD1 B:ASP102 3.0 28.0 1.0
CG B:ASP102 3.0 27.9 1.0
CG B:ASP98 3.1 22.4 1.0
OD1 B:ASP98 3.2 22.0 1.0
CA B:CA405 3.5 28.7 1.0
P9 B:476402 3.6 25.1 1.0
O14 B:476402 3.7 25.2 1.0
OD2 B:ASP170 4.0 27.9 1.0
NE2 B:GLN167 4.2 24.6 1.0
OE1 B:GLN167 4.4 24.9 1.0
O B:HOH566 4.5 31.4 1.0
CB B:ASP102 4.5 27.2 1.0
CG B:ASP170 4.5 26.1 1.0
CB B:ASP98 4.5 22.3 1.0
O B:HOH595 4.6 25.9 1.0
OD1 B:ASP170 4.6 27.6 1.0
O16 B:476402 4.6 24.6 1.0
C1 B:476402 4.7 24.4 1.0
CD B:GLN167 4.8 23.9 1.0
C7 B:476402 4.8 24.8 1.0
NZ B:LYS273 4.8 36.9 1.0
C8 B:476402 4.9 24.7 1.0
O B:HOH503 4.9 32.1 1.0
O B:ASP98 5.0 22.7 1.0
N2 B:476402 5.0 23.8 1.0

Calcium binding site 5 out of 6 in 4jzx

Go back to Calcium Binding Sites List in 4jzx
Calcium binding site 5 out of 6 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:24.1
occ:1.00
 O16 B:476402 2.2 24.6 1.0
O12 B:476402 2.3 25.1 1.0
OD2 B:ASP250 2.3 24.5 1.0
O B:HOH525 2.4 26.7 1.0
O B:HOH505 2.4 21.6 1.0
O B:HOH506 2.5 30.9 1.0
CG B:ASP250 3.4 23.5 1.0
P10 B:476402 3.5 24.2 1.0
P9 B:476402 3.5 25.1 1.0
C8 B:476402 3.7 24.7 1.0
O B:HOH608 3.8 27.3 1.0
OD1 B:ASP250 3.9 23.6 1.0
O B:HOH595 3.9 25.9 1.0
NE2 B:GLN247 4.3 22.0 1.0
O15 B:476402 4.3 24.7 1.0
O B:HOH629 4.3 32.5 1.0
O B:ASP250 4.4 23.0 1.0
NZ B:LYS264 4.4 25.3 1.0
OD2 B:ASP268 4.4 28.4 1.0
O13 B:476402 4.5 23.3 1.0
O11 B:476402 4.5 24.5 1.0
OD1 B:ASP268 4.5 28.1 1.0
CB B:ASP250 4.6 23.5 1.0
O B:HOH503 4.6 32.1 1.0
O14 B:476402 4.6 25.2 1.0
C B:ASP250 4.7 23.5 1.0
CE B:LYS264 4.7 27.2 1.0
OD2 B:ASP254 4.7 32.1 1.0
OD1 B:ASP251 4.8 23.4 1.0
CG B:ASP268 4.9 28.9 1.0
CB B:ASP254 4.9 28.7 1.0

Calcium binding site 6 out of 6 in 4jzx

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Calcium binding site 6 out of 6 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Butyl-1-(2,2-Diphosphonoethyl)Pyridinium, Ipp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:28.7
occ:1.00
 O13 B:476402 2.1 23.3 1.0
O B:HOH790 2.2 26.3 1.0
OD1 B:ASP98 2.3 22.0 1.0
O B:HOH503 2.3 32.1 1.0
OD2 B:ASP102 2.4 28.9 1.0
O15 B:476402 2.4 24.7 1.0
P10 B:476402 3.4 24.2 1.0
CG B:ASP98 3.4 22.4 1.0
CG B:ASP102 3.5 27.9 1.0
CA B:CA403 3.5 24.3 1.0
P9 B:476402 3.6 25.1 1.0
C8 B:476402 3.8 24.7 1.0
OD2 B:ASP98 3.9 24.2 1.0
O12 B:476402 3.9 25.1 1.0
C7 B:476402 4.0 24.8 1.0
CB B:ASP102 4.0 27.2 1.0
NH2 B:ARG107 4.1 21.9 1.0
O B:HOH842 4.1 39.8 1.0
OG B:SER104 4.3 26.6 1.0
O16 B:476402 4.3 24.6 1.0
OD1 B:ASP99 4.4 23.4 1.0
OD1 B:ASP102 4.5 28.0 1.0
O B:HOH608 4.6 27.3 1.0
O11 B:476402 4.6 24.5 1.0
CB B:ASP98 4.7 22.3 1.0
O B:HOH599 4.7 36.3 1.0
O B:ASP98 4.7 22.7 1.0
O14 B:476402 4.8 25.2 1.0
O B:HOH568 4.8 30.1 1.0
O B:HOH502 4.9 28.5 1.0
O B:HOH506 4.9 30.9 1.0
C B:ASP98 4.9 22.6 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: Sun Jul 14 08:43:18 2024

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