Magnesium in PDB 5xip: Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone

The structure of Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone, PDB code: 5xip was solved by V.Jain, Y.Manickam, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.77 / 3.10
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	138.757, 138.757, 425.671, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 23

The structure of Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone (pdb code 5xip). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone, PDB code: 5xip:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:19.0 occ:1.00 O A:HOH1103 1.8 18.7 1.0 O1B A:ANP1001 1.9 21.5 1.0 O A:HOH1104 1.9 53.9 1.0 O A:HOH1102 2.0 20.2 1.0 O3G A:ANP1001 2.0 22.9 1.0 O A:HOH1101 2.1 20.9 1.0 PB A:ANP1001 3.1 22.9 1.0 PG A:ANP1001 3.1 24.1 1.0 O1G A:ANP1001 3.3 23.1 1.0 NH1 A:ARG390 3.5 25.2 1.0 O2B A:ANP1001 3.6 21.2 1.0 N3B A:ANP1001 3.7 22.6 1.0 N7 A:ANP1001 4.3 15.8 1.0 N1 A:HFG1003 4.3 31.7 1.0 O3A A:ANP1001 4.3 22.7 1.0 NH2 A:ARG401 4.3 17.0 1.0 OE2 A:GLU338 4.4 35.2 1.0 O2G A:ANP1001 4.4 24.8 1.0 OE2 A:GLU392 4.6 29.5 1.0 CZ A:ARG390 4.6 24.3 1.0 OE1 A:GLU338 4.7 33.9 1.0 O1A A:ANP1001 4.7 22.4 1.0 OE1 A:GLU392 4.8 33.0 1.0 C2 A:HFG1003 4.8 32.1 1.0 CD A:ARG390 4.8 25.9 1.0 C8 A:ANP1001 4.9 16.6 1.0 CD A:GLU338 4.9 34.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:33.8 occ:1.00 O B:HOH1104 1.8 25.4 1.0 O B:HOH1103 1.9 63.1 1.0 O2B B:ANP1001 1.9 27.0 1.0 O B:HOH1102 2.0 17.7 1.0 O B:HOH1101 2.0 31.9 1.0 O2G B:ANP1001 2.2 26.4 1.0 O1G B:ANP1001 2.6 26.7 1.0 PG B:ANP1001 2.9 26.7 1.0 PB B:ANP1001 3.3 27.1 1.0 NH1 B:ARG390 3.7 24.5 1.0 N3B B:ANP1001 3.7 26.3 1.0 O3A B:ANP1001 4.0 26.2 1.0 OE1 B:GLU338 4.2 32.4 1.0 O3G B:ANP1001 4.2 27.0 1.0 O1B B:ANP1001 4.4 26.5 1.0 N1 B:HFG1003 4.4 37.2 1.0 OE2 B:GLU392 4.4 24.7 1.0 OE1 B:GLU392 4.5 27.0 1.0 NH2 B:ARG401 4.5 17.4 1.0 N7 B:ANP1001 4.6 15.8 1.0 C2 B:HFG1003 4.6 34.7 1.0 CD B:GLU338 4.8 33.2 1.0 OE2 B:GLU338 4.8 33.8 1.0 CD B:GLU392 4.9 26.8 1.0 CZ B:ARG390 4.9 22.6 1.0 CD B:ARG390 4.9 23.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:31.3 occ:1.00 O C:HOH1101 1.8 30.2 1.0 O C:HOH1103 1.8 13.1 1.0 O1B C:ANP1001 1.8 39.5 1.0 O C:HOH1102 1.8 21.4 1.0 O1G C:ANP1001 1.8 38.1 1.0 O C:HOH1104 2.0 28.3 1.0 PB C:ANP1001 3.0 44.3 1.0 PG C:ANP1001 3.2 43.8 1.0 N3B C:ANP1001 3.5 43.4 1.0 NH1 C:ARG390 3.8 33.0 1.0 O2B C:ANP1001 3.8 44.5 1.0 O2G C:ANP1001 3.9 43.2 1.0 OE2 C:GLU392 3.9 44.0 1.0 OE1 C:GLU392 4.0 39.9 1.0 N1 C:HFG1003 4.1 53.7 1.0 N7 C:ANP1001 4.2 44.9 1.0 O3G C:ANP1001 4.2 45.1 1.0 O3A C:ANP1001 4.2 43.1 1.0 NH2 C:ARG401 4.3 31.3 1.0 CD C:GLU392 4.4 46.0 1.0 C2 C:HFG1003 4.4 53.0 1.0 OE1 C:GLU338 4.5 40.9 1.0 OE2 C:GLU338 4.6 37.3 1.0 CD C:ARG390 4.6 38.0 1.0 C8 C:ANP1001 4.7 44.1 1.0 CZ C:ARG390 4.9 34.8 1.0 CD C:GLU338 4.9 37.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Eimeria Tenella Prolyl-Trna Synthetase (Etprs) in Complex with Halofuginone within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:44.7 occ:1.00 O2G D:ANP1001 1.8 41.2 1.0 O D:HOH1104 1.8 34.6 1.0 O D:HOH1101 1.9 34.0 1.0 O D:HOH1103 2.0 24.6 1.0 O D:HOH1102 2.0 13.5 1.0 O2B D:ANP1001 2.2 41.4 1.0 PG D:ANP1001 3.1 43.9 1.0 PB D:ANP1001 3.2 44.7 1.0 N3B D:ANP1001 3.6 42.6 1.0 O1G D:ANP1001 3.6 46.2 1.0 NH1 D:ARG390 3.6 31.1 1.0 O1B D:ANP1001 3.8 45.1 1.0 OE2 D:GLU392 3.8 37.4 1.0 OE1 D:GLU392 4.0 33.0 1.0 N1 D:HFG1003 4.0 55.0 1.0 O3G D:ANP1001 4.2 42.5 1.0 OE2 D:GLU338 4.3 33.0 1.0 CD D:ARG390 4.3 34.6 1.0 CD D:GLU392 4.3 39.7 1.0 C2 D:HFG1003 4.4 51.6 1.0 OE1 D:GLU338 4.4 37.8 1.0 N7 D:ANP1001 4.5 38.9 1.0 O3A D:ANP1001 4.6 43.3 1.0 CZ D:ARG390 4.6 32.6 1.0 NH2 D:ARG401 4.7 28.7 1.0 CD D:GLU338 4.8 35.0 1.0 NE D:ARG390 4.9 33.2 1.0

V.Jain, M.Yogavel, H.Kikuchi, Y.Oshima, N.Hariguchi, M.Matsumoto, P.Goel, B.Touquet, R.S.Jumani, F.Tacchini-Cottier, K.Harlos, C.D.Huston, M.A.Hakimi, A.Sharma. Targeting Prolyl-Trna Synthetase to Accelerate Drug Discovery Against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis Structure V. 25 1495 2017.
ISSN: ISSN 1878-4186
PubMed: 28867614
DOI: 10.1016/J.STR.2017.07.015