Magnesium in PDB 6a88: Crystal Structure of T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog

All present enzymatic activity of Crystal Structure of T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog:
6.1.1.15;

The structure of Crystal Structure of T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog, PDB code: 6a88 was solved by S.Kumari, S.Mishra, M.Yogavel, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.94 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	76.910, 90.882, 93.028, 89.91, 80.30, 75.58
R / Rfree (%)	17.2 / 22

The binding sites of Magnesium atom in the Crystal Structure of T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog (pdb code 6a88). 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 T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog, PDB code: 6a88:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog


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 T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:29.5 occ:1.00 O A:HOH1118 2.0 32.3 1.0 O3G A:ANP1001 2.0 41.1 1.0 O A:HOH1117 2.1 26.8 1.0 O A:HOH1121 2.1 26.5 1.0 O2B A:ANP1001 2.3 26.1 1.0 PG A:ANP1001 3.4 30.5 1.0 PB A:ANP1001 3.7 26.3 1.0 OE2 A:GLU472 3.9 41.6 1.0 O2G A:ANP1001 3.9 32.5 1.0 OE1 A:GLU418 4.0 49.3 1.0 NH1 A:ARG470 4.0 26.4 1.0 NH1 A:ARG481 4.0 34.0 1.0 OE2 A:GLU418 4.1 55.8 1.0 OE1 A:GLU472 4.1 45.0 1.0 N3B A:ANP1001 4.2 48.9 1.0 O A:HOH1119 4.2 41.9 1.0 CD A:GLU472 4.4 37.9 1.0 CD A:GLU418 4.4 45.5 1.0 O1G A:ANP1001 4.5 38.1 1.0 N1 A:9SF1003 4.5 36.5 1.0 N7 A:ANP1001 4.5 32.6 1.0 O1B A:ANP1001 4.6 19.8 1.0 O3A A:ANP1001 4.7 39.2 1.0 CD A:ARG470 4.8 28.8 1.0 C2 A:9SF1003 4.9 32.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog


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 T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:32.1 occ:1.00 O B:HOH1102 1.9 35.8 1.0 O1B B:ANP1001 2.0 35.6 1.0 O3G B:ANP1001 2.0 33.0 1.0 O B:HOH1106 2.1 38.5 1.0 O B:HOH1115 2.3 32.5 1.0 O B:HOH1109 2.3 29.6 1.0 PG B:ANP1001 3.4 37.4 1.0 PB B:ANP1001 3.4 30.6 1.0 NH1 B:ARG470 3.8 28.2 1.0 OE2 B:GLU418 3.9 54.2 1.0 N1 B:9SF1003 4.0 37.1 1.0 N3B B:ANP1001 4.0 53.2 1.0 O2G B:ANP1001 4.0 56.2 1.0 OE1 B:GLU418 4.1 48.5 1.0 O2B B:ANP1001 4.2 27.5 1.0 O B:HOH1151 4.3 46.6 1.0 C2 B:9SF1003 4.3 31.6 1.0 CD B:GLU418 4.4 49.7 1.0 OE2 B:GLU472 4.4 43.3 1.0 O3A B:ANP1001 4.4 47.9 1.0 OE1 B:GLU472 4.5 43.5 1.0 NH1 B:ARG481 4.5 31.6 1.0 O1G B:ANP1001 4.5 44.1 1.0 CD B:ARG470 4.7 29.9 1.0 N7 B:ANP1001 4.7 33.0 1.0 CZ B:ARG470 4.8 30.1 1.0 CD B:GLU472 4.9 43.8 1.0 CE1 B:PHE415 4.9 57.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog


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 T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:29.0 occ:1.00 O3G C:ANP1001 2.0 50.9 1.0 O C:HOH1108 2.0 33.1 1.0 O C:HOH1116 2.1 34.3 1.0 O2B C:ANP1001 2.1 29.6 1.0 O C:HOH1107 2.1 40.8 1.0 O C:HOH1113 2.2 29.2 1.0 PG C:ANP1001 3.1 37.1 1.0 O2G C:ANP1001 3.3 42.3 1.0 PB C:ANP1001 3.4 30.8 1.0 N3B C:ANP1001 3.7 53.4 1.0 NH1 C:ARG470 3.8 31.7 1.0 NZ C:LYS474 3.8 42.2 1.0 NH1 C:ARG481 4.0 39.9 1.0 OE2 C:GLU472 4.1 42.5 1.0 OE1 C:GLU418 4.2 47.7 1.0 OE1 C:GLU472 4.3 43.6 1.0 O1B C:ANP1001 4.3 40.7 1.0 O1G C:ANP1001 4.3 40.5 1.0 N1 C:9SF1003 4.4 40.8 1.0 N7 C:ANP1001 4.4 31.7 1.0 O3A C:ANP1001 4.4 41.8 1.0 OE2 C:GLU418 4.4 50.0 1.0 C2 C:9SF1003 4.6 31.4 1.0 CD C:GLU472 4.7 39.7 1.0 CE C:LYS474 4.7 43.5 1.0 CD C:GLU418 4.8 47.0 1.0 C8 C:ANP1001 4.9 34.8 1.0 CD C:ARG470 4.9 30.7 1.0 CZ C:ARG470 4.9 35.7 1.0 O2A C:ANP1001 5.0 39.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog


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 T. Gondii Prolyl Trna Synthetase with Febrifugine and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:25.0 occ:1.00 O D:HOH1115 2.0 39.9 1.0 O D:HOH1122 2.1 30.3 1.0 O2B D:ANP1001 2.1 28.7 1.0 O D:HOH1107 2.1 34.9 1.0 O3G D:ANP1001 2.2 34.2 1.0 O D:HOH1114 2.3 32.1 1.0 PG D:ANP1001 3.4 39.8 1.0 PB D:ANP1001 3.5 30.0 1.0 O2G D:ANP1001 3.7 50.2 1.0 NH1 D:ARG470 3.9 26.2 1.0 OE2 D:GLU418 4.0 43.9 1.0 N3B D:ANP1001 4.0 42.1 1.0 OE1 D:GLU418 4.1 46.4 1.0 O D:HOH1157 4.1 53.6 1.0 OE2 D:GLU472 4.1 35.5 1.0 OE1 D:GLU472 4.3 35.3 1.0 NH1 D:ARG481 4.3 33.0 1.0 N1 D:9SF1003 4.3 32.3 1.0 O1B D:ANP1001 4.3 30.7 1.0 CD D:GLU418 4.5 44.2 1.0 O3A D:ANP1001 4.5 38.4 1.0 O1G D:ANP1001 4.6 42.1 1.0 C2 D:9SF1003 4.6 28.3 1.0 CD D:GLU472 4.6 36.6 1.0 N7 D:ANP1001 4.6 34.6 1.0 CD D:ARG470 4.8 20.9 1.0 CZ D:ARG470 5.0 28.9 1.0

S.Mishra, N.Malhotra, S.Kumari, M.Sato, H.Kikuchi, M.Yogavel, A.Sharma. Conformational Heterogeneity in Apo and Drug-Bound Structures of Toxoplasma Gondii Prolyl-Trna Synthetase. Acta Crystallogr.,Sect.F V. 75 714 2019.
ISSN: ESSN 2053-230X
PubMed: 31702585
DOI: 10.1107/S2053230X19014808