Magnesium in PDB 5xil: Crystal Structure of Leishmania Major Prolyl-Trna Synthetase (Lmprs)

All present enzymatic activity of Crystal Structure of Leishmania Major Prolyl-Trna Synthetase (Lmprs):
6.1.1.5; 6.1.1.7;

The structure of Crystal Structure of Leishmania Major Prolyl-Trna Synthetase (Lmprs), PDB code: 5xil 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)	40.99 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.294, 98.861, 146.327, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.1

The structure of Crystal Structure of Leishmania Major Prolyl-Trna Synthetase (Lmprs) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Leishmania Major Prolyl-Trna Synthetase (Lmprs) (pdb code 5xil). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Leishmania Major Prolyl-Trna Synthetase (Lmprs), PDB code: 5xil:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Leishmania Major Prolyl-Trna Synthetase (Lmprs)


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 Leishmania Major Prolyl-Trna Synthetase (Lmprs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:17.6 occ:0.66 O A:HOH1199 1.9 24.2 1.0 O A:HOH1297 2.0 29.4 1.0 NE2 A:HIS662 2.0 17.2 1.0 O A:HOH1172 2.2 19.3 1.0 OE2 A:GLU468 2.2 26.6 1.0 O A:HOH1217 2.2 15.8 1.0 CD2 A:HIS662 2.9 14.9 1.0 CE1 A:HIS662 3.0 15.7 1.0 CD A:GLU468 3.4 27.8 1.0 CG A:GLU468 3.9 21.5 1.0 CG A:HIS662 4.0 16.4 1.0 ND1 A:HIS662 4.1 16.1 1.0 O A:LYS679 4.3 11.5 1.0 O A:ARG678 4.4 14.8 1.0 O A:GLU468 4.4 15.3 1.0 O A:HOH1214 4.4 41.6 1.0 OE1 A:GLU468 4.5 29.9 1.0 CB A:LYS679 4.6 17.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Leishmania Major Prolyl-Trna Synthetase (Lmprs)


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 Leishmania Major Prolyl-Trna Synthetase (Lmprs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1006 b:19.5 occ:0.50 O A:HOH1324 1.9 26.0 1.0 O A:HOH1343 1.9 39.0 1.0 O A:HOH1101 2.0 31.6 1.0 O A:HOH1455 2.1 37.1 1.0 NZ A:LYS453 3.4 18.4 0.5 OE1 A:GLU450 4.1 22.2 0.5 OE2 A:GLU450 4.2 17.9 0.5 OD1 A:ASP458 4.2 22.3 1.0 OE1 A:GLU450 4.3 18.9 0.5 O A:ASP458 4.4 13.2 1.0 OE2 A:GLU450 4.4 18.3 0.5 CD A:GLU450 4.6 18.4 0.5 CA A:ASP458 4.7 15.3 1.0 CD A:GLU450 4.7 19.3 0.5 CE A:LYS453 4.8 18.5 0.5 CG A:ASP458 4.9 19.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Leishmania Major Prolyl-Trna Synthetase (Lmprs)


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 Leishmania Major Prolyl-Trna Synthetase (Lmprs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1007 b:24.7 occ:0.45 O A:HOH1319 1.8 42.7 1.0 O A:HOH1275 1.8 39.4 1.0 O A:HOH1228 1.9 36.9 1.0 O A:HOH1192 2.1 38.1 1.0 OE1 A:GLU736 2.2 40.2 1.0 CD A:GLU736 3.3 40.5 1.0 OE2 A:GLU736 3.7 47.1 1.0 OE2 A:GLU668 4.0 33.5 1.0 O A:HOH1269 4.0 46.0 1.0 ND1 A:HIS735 4.2 20.4 1.0 N A:GLU736 4.3 22.9 1.0 CG A:GLU736 4.6 34.9 1.0 CA A:HIS735 4.7 21.9 1.0 OE1 A:GLU668 4.7 37.5 1.0 CD A:GLU668 4.8 32.1 1.0 O A:THR667 4.8 18.4 1.0 CB A:GLU736 4.9 27.7 1.0 O A:GLY734 5.0 25.5 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