Magnesium in PDB 7ror: Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp

All present enzymatic activity of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp:
6.1.1.1;

The structure of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp, PDB code: 7ror was solved by R.D.Metcalfe, S.C.Xie, C.J.Morton, L.Tilley, M.D.W.Griffin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.65 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.612, 46.597, 141.402, 90, 93.81, 90
R / Rfree (%)	17.8 / 21.8

The structure of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp (pdb code 7ror). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp, PDB code: 7ror:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:44.7 occ:1.00 O A:ARG304 2.2 44.1 1.0 O A:HOH602 2.3 55.1 1.0 OD1 A:ASP311 2.4 40.3 1.0 O A:HOH647 2.5 47.4 1.0 C A:ARG304 3.3 47.1 1.0 CG A:ASP311 3.3 45.4 1.0 OD2 A:ASP311 3.7 52.5 1.0 O A:HOH662 4.0 59.5 1.0 N A:ARG304 4.0 36.7 1.0 N A:ASP311 4.0 36.6 1.0 N A:LYS305 4.0 46.8 1.0 CA A:LYS305 4.1 43.5 1.0 CA A:ARG304 4.3 44.8 1.0 CB A:ASP311 4.4 37.9 1.0 CG1 A:VAL303 4.5 39.1 1.0 C A:LYS305 4.5 41.6 1.0 N A:GLU306 4.6 45.5 1.0 CA A:ASP311 4.7 38.4 1.0 CA A:GLY310 4.7 44.4 1.0 C A:GLY310 4.8 41.1 1.0 O A:HOH642 4.9 49.2 1.0

Magnesium binding site 2 out of 3 in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:48.4 occ:1.00 O A:HOH654 2.3 46.0 1.0 O A:HOH607 2.4 42.9 1.0 O A:VAL134 2.4 36.5 1.0 O A:MET131 2.4 34.7 1.0 O A:HOH610 2.5 52.2 1.0 O A:HOH645 2.5 54.4 1.0 C A:MET131 3.5 39.6 1.0 C A:VAL134 3.6 34.6 1.0 O A:GLU132 4.2 39.5 1.0 N A:VAL134 4.2 38.8 1.0 N A:MET131 4.2 36.0 1.0 CA A:VAL134 4.3 33.0 1.0 C A:GLU132 4.3 38.5 1.0 CA A:GLU132 4.4 39.6 1.0 N A:GLU132 4.4 38.9 1.0 CB A:VAL134 4.4 37.8 1.0 NZ A:LYS125 4.5 72.5 1.0 CA A:MET131 4.5 39.6 1.0 O A:HOH621 4.5 44.1 1.0 N A:GLN135 4.6 37.0 1.0 CE2 A:PHE136 4.6 40.7 1.0 CA A:GLN135 4.8 38.5 1.0 CG1 A:VAL134 4.8 44.9 1.0 CD2 A:PHE136 4.9 35.4 1.0 O A:HOH648 5.0 62.6 1.0

Magnesium binding site 3 out of 3 in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with Tyrosine-Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:64.0 occ:1.00 O B:ARG304 2.3 65.5 1.0 OD1 B:ASP311 2.5 57.5 1.0 O B:HOH667 2.5 60.3 1.0 O B:HOH588 2.6 56.6 1.0 CG B:ASP311 3.4 66.5 1.0 C B:ARG304 3.5 72.8 1.0 OD2 B:ASP311 3.7 53.1 1.0 N B:ASP311 4.0 54.6 1.0 N B:ARG304 4.1 54.4 1.0 N B:LYS305 4.4 62.1 1.0 CA B:ARG304 4.4 51.2 1.0 CA B:GLY310 4.4 68.0 1.0 C B:GLY310 4.4 58.7 1.0 CA B:LYS305 4.4 73.6 1.0 CG1 B:VAL303 4.5 52.3 1.0 CB B:ASP311 4.5 51.7 1.0 O B:HOH636 4.6 53.7 1.0 CA B:ASP311 4.7 50.8 1.0 C B:LYS305 4.7 73.2 1.0 O8 B:MLI403 4.9 74.4 1.0 N B:GLU306 4.9 85.2 1.0

S.C.Xie, R.D.Metcalfe, E.Dunn, C.J.Morton, S.C.Huang, T.Puhalovich, Y.Du, S.Wittlin, S.Nie, M.R.Luth, L.Ma, M.S.Kim, C.F.A.Pasaje, K.Kumpornsin, C.Giannangelo, F.J.Houghton, A.Churchyard, M.T.Famodimu, D.C.Barry, D.L.Gillett, S.Dey, C.C.Kosasih, W.Newman, J.C.Niles, M.C.S.Lee, J.Baum, S.Ottilie, E.A.Winzeler, D.J.Creek, N.Williamson, M.W.Parker, S.Brand, S.P.Langston, L.R.Dick, M.D.W.Griffin, A.E.Gould, L.Tilley. Reaction Hijacking of Tyrosine Trna Synthetase As A New Whole-of-Life-Cycle Antimalarial Strategy. Science V. 376 1074 2022.
ISSN: ESSN 1095-9203
PubMed: 35653481
DOI: 10.1126/SCIENCE.ABN0611