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Calcium 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:

Sodium (Na) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 4jzb

Go back to Calcium Binding Sites List in 4jzb
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca401

b:22.8
occ:1.00
 O16 A:P2H405 2.1 18.0 1.0
OD2 A:ASP102 2.2 21.3 1.0
OD2 A:ASP98 2.2 19.4 1.0
O A:HOH502 2.2 18.9 1.0
O10 A:P2H405 2.3 17.4 1.0
O A:HOH503 2.3 17.7 1.0
CG A:ASP98 3.2 18.9 1.0
CG A:ASP102 3.4 21.8 1.0
P14 A:P2H405 3.4 17.9 1.0
CA A:CA402 3.4 19.4 1.0
P9 A:P2H405 3.5 19.5 1.0
OD1 A:ASP98 3.6 17.7 1.0
C8 A:P2H405 3.8 18.4 1.0
CB A:ASP102 3.9 20.0 1.0
O15 A:P2H405 4.0 16.8 1.0
C7 A:P2H405 4.0 17.1 1.0
NH2 A:ARG107 4.2 17.4 1.0
O A:HOH576 4.2 25.4 1.0
O11 A:P2H405 4.3 19.8 1.0
OG A:SER104 4.3 21.1 1.0
OD1 A:ASP102 4.4 22.7 1.0
OD1 A:ASP99 4.5 20.0 1.0
O A:HOH513 4.5 17.4 1.0
CB A:ASP98 4.6 17.2 1.0
O17 A:P2H405 4.6 18.5 1.0
O A:ASP98 4.6 16.7 1.0
O A:HOH628 4.7 26.3 1.0
O12 A:P2H405 4.7 19.4 1.0
O A:HOH501 4.8 18.7 1.0
C A:ASP98 4.9 17.1 1.0
O A:HOH540 5.0 20.4 1.0

Calcium binding site 2 out of 6 in 4jzb

Go back to Calcium Binding Sites List in 4jzb
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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
A:Ca402

b:19.4
occ:1.00
 O A:HOH504 2.3 16.2 1.0
O10 A:P2H405 2.3 17.4 1.0
OD1 A:ASP98 2.3 17.7 1.0
O A:HOH501 2.4 18.7 1.0
OD2 A:ASP102 2.4 21.3 1.0
O A:HOH511 2.5 18.3 1.0
OD1 A:ASP102 2.9 22.7 1.0
CG A:ASP102 3.0 21.8 1.0
CG A:ASP98 3.3 18.9 1.0
CA A:CA401 3.4 22.8 1.0
OD2 A:ASP98 3.5 19.4 1.0
P9 A:P2H405 3.5 19.5 1.0
O12 A:P2H405 3.6 19.4 1.0
OD2 A:ASP170 4.2 21.4 1.0
NE2 A:GLN167 4.2 20.4 1.0
O A:HOH591 4.4 24.9 1.0
OE1 A:GLN167 4.5 21.0 1.0
CB A:ASP102 4.5 20.0 1.0
O11 A:P2H405 4.5 19.8 1.0
O A:HOH532 4.5 19.9 1.0
OD1 A:ASP170 4.6 21.3 1.0
CG A:ASP170 4.6 20.1 1.0
CB A:ASP98 4.6 17.2 1.0
C17 A:P2H405 4.7 17.8 1.0
CD A:GLN167 4.8 19.3 1.0
C8 A:P2H405 4.8 18.4 1.0
C7 A:P2H405 4.8 17.1 1.0
O A:HOH503 4.8 17.7 1.0
O A:HOH749 4.8 39.3 1.0
O A:ASP98 4.9 16.7 1.0
O16 A:P2H405 5.0 18.0 1.0
N12 A:P2H405 5.0 18.6 1.0
NZ A:LYS273 5.0 30.8 1.0

Calcium binding site 3 out of 6 in 4jzb

Go back to Calcium Binding Sites List in 4jzb
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca binding site number 3 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:Ca403

b:20.1
occ:1.00
 O11 A:P2H405 2.2 19.8 1.0
O15 A:P2H405 2.3 16.8 1.0
OD2 A:ASP250 2.4 19.4 1.0
O A:HOH505 2.4 16.3 1.0
O A:HOH506 2.4 20.0 1.0
O A:HOH512 2.5 20.4 1.0
CG A:ASP250 3.4 19.4 1.0
P9 A:P2H405 3.5 19.5 1.0
P14 A:P2H405 3.6 17.9 1.0
O13 A:P2H405 3.6 18.1 1.0
C8 A:P2H405 3.7 18.4 1.0
O A:HOH513 3.8 17.4 1.0
OD1 A:ASP250 3.9 19.1 1.0
O A:HOH532 4.0 19.9 1.0
O A:ASP250 4.3 17.7 1.0
OD2 A:ASP268 4.3 22.4 1.0
O10 A:P2H405 4.3 17.4 1.0
O A:HOH514 4.4 24.6 1.0
NE2 A:GLN247 4.4 16.9 1.0
O A:HOH503 4.4 17.7 1.0
OD1 A:ASP268 4.5 24.2 1.0
O16 A:P2H405 4.5 18.0 1.0
CB A:ASP250 4.6 17.9 1.0
C A:ASP250 4.6 17.6 1.0
O17 A:P2H405 4.6 18.5 1.0
O12 A:P2H405 4.6 19.4 1.0
NZ A:LYS264 4.7 20.3 1.0
CE A:LYS264 4.7 20.6 1.0
CB A:ASP254 4.8 20.9 1.0
OD1 A:ASP251 4.8 19.6 1.0
CG A:ASP268 4.8 23.1 1.0
OD2 A:ASP254 4.9 22.9 1.0

Calcium binding site 4 out of 6 in 4jzb

Go back to Calcium Binding Sites List in 4jzb
Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca binding site number 4 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:Ca403

b:24.8
occ:1.00
 O16 B:P2H402 2.1 16.9 1.0
O B:HOH511 2.2 18.3 1.0
OD1 B:ASP98 2.2 18.6 1.0
OD2 B:ASP102 2.3 22.1 1.0
O B:HOH503 2.3 20.3 1.0
O10 B:P2H402 2.3 18.1 1.0
CG B:ASP98 3.3 15.3 1.0
P14 B:P2H402 3.3 18.1 1.0
CG B:ASP102 3.4 22.4 1.0
P9 B:P2H402 3.5 19.2 1.0
CA B:CA405 3.5 19.1 1.0
OD2 B:ASP98 3.7 16.8 1.0
C8 B:P2H402 3.8 18.3 1.0
O15 B:P2H402 3.9 20.0 1.0
CB B:ASP102 4.0 21.0 1.0
C7 B:P2H402 4.0 17.1 1.0
NH2 B:ARG107 4.1 16.8 1.0
O B:HOH624 4.1 24.6 1.0
O11 B:P2H402 4.2 18.7 1.0
OG B:SER104 4.3 18.8 1.0
OD1 B:ASP102 4.4 22.0 1.0
OD1 B:ASP99 4.5 17.5 1.0
O17 B:P2H402 4.5 18.0 1.0
CB B:ASP98 4.6 16.2 1.0
O B:HOH545 4.6 17.5 1.0
O B:HOH597 4.7 25.2 1.0
O12 B:P2H402 4.7 19.3 1.0
O B:ASP98 4.8 16.0 1.0
O B:HOH502 4.8 19.7 1.0
O B:HOH567 4.9 21.3 1.0
C B:ASP98 5.0 16.5 1.0

Calcium binding site 5 out of 6 in 4jzb

Go back to Calcium Binding Sites List in 4jzb
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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:Ca404

b:19.0
occ:1.00
 O11 B:P2H402 2.2 18.7 1.0
O15 B:P2H402 2.3 20.0 1.0
OD2 B:ASP250 2.3 17.4 1.0
O B:HOH505 2.4 15.1 1.0
O B:HOH506 2.5 20.2 1.0
O B:HOH514 2.5 17.7 1.0
CG B:ASP250 3.3 18.8 1.0
P9 B:P2H402 3.5 19.2 1.0
P14 B:P2H402 3.5 18.1 1.0
O13 B:P2H402 3.6 18.4 1.0
C8 B:P2H402 3.7 18.3 1.0
OD1 B:ASP250 3.8 19.4 1.0
O B:HOH545 3.8 17.5 1.0
O B:HOH513 4.0 20.6 1.0
O B:HOH581 4.3 23.9 1.0
O B:ASP250 4.3 18.0 1.0
O10 B:P2H402 4.3 18.1 1.0
NE2 B:GLN247 4.4 15.7 1.0
OD2 B:ASP268 4.4 22.7 1.0
O B:HOH503 4.4 20.3 1.0
O16 B:P2H402 4.5 16.9 1.0
CB B:ASP250 4.5 19.0 1.0
OD1 B:ASP268 4.5 23.6 1.0
O17 B:P2H402 4.5 18.0 1.0
NZ B:LYS264 4.6 20.6 1.0
C B:ASP250 4.6 18.3 1.0
O12 B:P2H402 4.6 19.3 1.0
OD2 B:ASP254 4.7 23.9 1.0
CB B:ASP254 4.8 23.0 1.0
CE B:LYS264 4.8 22.5 1.0
OD1 B:ASP251 4.8 19.9 1.0
CG B:ASP268 4.9 23.5 1.0

Calcium binding site 6 out of 6 in 4jzb

Go back to Calcium Binding Sites List in 4jzb
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca405

b:19.1
occ:1.00
 O B:HOH504 2.3 20.7 1.0
OD2 B:ASP98 2.3 16.8 1.0
O B:HOH512 2.4 19.6 1.0
OD2 B:ASP102 2.4 22.1 1.0
O10 B:P2H402 2.4 18.1 1.0
O B:HOH502 2.4 19.7 1.0
OD1 B:ASP102 2.9 22.0 1.0
CG B:ASP102 3.0 22.4 1.0
CG B:ASP98 3.2 15.3 1.0
OD1 B:ASP98 3.5 18.6 1.0
CA B:CA403 3.5 24.8 1.0
P9 B:P2H402 3.5 19.2 1.0
O12 B:P2H402 3.6 19.3 1.0
OD2 B:ASP170 4.1 21.9 1.0
NE2 B:GLN167 4.2 19.4 1.0
O B:HOH536 4.4 23.4 1.0
CB B:ASP102 4.5 21.0 1.0
OE1 B:GLN167 4.5 18.8 1.0
O11 B:P2H402 4.6 18.7 1.0
CG B:ASP170 4.6 19.5 1.0
OD1 B:ASP170 4.6 20.4 1.0
CB B:ASP98 4.6 16.2 1.0
O B:HOH513 4.7 20.6 1.0
C17 B:P2H402 4.8 17.5 1.0
CD B:GLN167 4.8 18.4 1.0
C7 B:P2H402 4.8 17.1 1.0
O B:HOH503 4.8 20.3 1.0
C8 B:P2H402 4.8 18.3 1.0
O B:HOH645 4.9 35.8 1.0
O B:ASP98 5.0 16.0 1.0
O16 B:P2H402 5.0 16.9 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 08:42:54 2024

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