Atomistry » Calcium » PDB 4jo1-4k0g » 4jzx
Atomistry »
  Calcium »
    PDB 4jo1-4k0g »
      4jzx »

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

Go back to Calcium Binding Sites List in 4jzx
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

Go back to Calcium Binding Sites List in 4jzx
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

Go back to Calcium Binding Sites List in 4jzx
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

Go back to Calcium Binding Sites List in 4jzx
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy