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Magnesium in PDB 5xii: Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6

Enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6

All present enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6, PDB code: 5xii 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) 40.29 / 2.17
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.600, 90.730, 92.996, 89.94, 99.37, 104.31
R / Rfree (%) 17.5 / 22.4

Other elements in 5xii:

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Chlorine (Cl) 15 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 (pdb code 5xii). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6, PDB code: 5xii:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5xii

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Magnesium binding site 1 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:40.1
occ:1.00
 O A:HOH1179 1.6 48.7 1.0
O A:HOH1231 2.0 23.1 0.5
O A:HOH1307 2.1 38.5 1.0
O A:HOH1116 2.3 32.8 1.0
O2G A:ANP1001 2.4 22.0 1.0
PG A:ANP1001 3.6 20.3 1.0
O A:HOH1231 3.7 26.2 0.5
O A:HOH1109 3.9 30.2 1.0
N3B A:ANP1001 4.0 20.7 1.0
O3G A:ANP1001 4.0 19.0 1.0
O A:HOH1107 4.2 19.7 1.0
NZ A:LYS796 4.3 54.5 1.0
OE1 A:GLU532 4.3 30.0 1.0
O A:HOH1216 4.3 43.0 1.0
O2B A:ANP1001 4.4 20.3 1.0
PB A:ANP1001 4.7 19.5 1.0
O1G A:ANP1001 4.8 20.1 1.0
O A:HOH1243 4.9 41.8 1.0
CD A:GLU532 5.0 31.3 1.0

Magnesium binding site 2 out of 8 in 5xii

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Magnesium binding site 2 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:18.7
occ:1.00
 O1G A:ANP1001 1.9 20.1 1.0
O A:HOH1178 2.0 12.7 1.0
O1B A:ANP1001 2.1 20.8 1.0
O A:HOH1158 2.1 17.2 1.0
O A:HOH1150 2.1 20.0 1.0
O A:HOH1107 2.2 19.7 1.0
PG A:ANP1001 3.0 20.3 1.0
PB A:ANP1001 3.2 19.5 1.0
O2G A:ANP1001 3.4 22.0 1.0
N3B A:ANP1001 3.5 20.7 1.0
NH1 A:ARG470 3.8 18.8 1.0
O A:HOH1243 4.0 41.8 1.0
NH1 A:ARG481 4.1 21.1 1.0
O3A A:ANP1001 4.1 21.3 1.0
O A:HOH1134 4.2 40.9 1.0
OE2 A:GLU472 4.2 25.1 1.0
OE1 A:GLU472 4.3 23.5 1.0
O3G A:ANP1001 4.3 19.0 1.0
OE2 A:GLU418 4.3 29.3 1.0
O A:HOH1216 4.3 43.0 1.0
OE1 A:GLU418 4.3 27.0 1.0
O2B A:ANP1001 4.3 20.3 1.0
N09 A:86X1004 4.4 20.7 0.5
N09 A:86X1004 4.5 23.1 0.5
N7 A:ANP1001 4.5 20.2 1.0
CD A:GLU472 4.7 23.9 1.0
C10 A:86X1004 4.7 20.2 0.5
C10 A:86X1004 4.8 22.3 0.5
CD A:ARG470 4.8 17.8 1.0
CD A:GLU418 4.8 28.8 1.0
CZ A:ARG470 4.9 19.0 1.0
C8 A:ANP1001 4.9 19.8 1.0

Magnesium binding site 3 out of 8 in 5xii

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Magnesium binding site 3 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:45.5
occ:1.00
 O B:HOH1122 1.4 52.6 1.0
O B:HOH1192 2.0 39.7 1.0
O B:HOH1202 2.1 48.6 1.0
O1G B:ANP1001 2.2 28.5 1.0
O B:HOH1237 2.5 59.9 1.0
PG B:ANP1001 3.5 26.6 1.0
N3B B:ANP1001 4.0 23.1 1.0
O B:HOH1133 4.0 45.1 1.0
O3G B:ANP1001 4.1 27.7 1.0
O B:HOH1141 4.1 20.8 1.0
NZ B:LYS474 4.2 30.3 1.0
OE1 B:GLU532 4.5 38.5 1.0
O2G B:ANP1001 4.6 25.2 1.0
O2B B:ANP1001 4.8 24.9 1.0
PB B:ANP1001 4.9 22.6 1.0

Magnesium binding site 4 out of 8 in 5xii

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Magnesium binding site 4 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:24.0
occ:1.00
 O2G B:ANP1001 1.9 25.2 1.0
O B:HOH1116 2.0 21.3 1.0
O B:HOH1139 2.0 20.1 1.0
O B:HOH1141 2.1 20.8 1.0
O B:HOH1129 2.1 19.0 1.0
O1B B:ANP1001 2.2 21.5 1.0
PG B:ANP1001 3.2 26.6 1.0
PB B:ANP1001 3.4 22.6 1.0
O1G B:ANP1001 3.7 28.5 1.0
N3B B:ANP1001 3.9 23.1 1.0
NH1 B:ARG470 3.9 19.5 1.0
NZ B:LYS474 3.9 30.3 1.0
NH1 B:ARG481 3.9 22.9 1.0
OE1 B:GLU418 4.1 28.7 1.0
OE1 B:GLU472 4.2 24.3 1.0
OE2 B:GLU418 4.3 31.1 1.0
OE2 B:GLU472 4.3 22.9 1.0
O3G B:ANP1001 4.3 27.7 1.0
N09 B:86X1004 4.3 21.1 0.5
O2B B:ANP1001 4.3 24.9 1.0
N09 B:86X1004 4.3 27.0 0.5
O3A B:ANP1001 4.4 23.4 1.0
N7 B:ANP1001 4.6 20.0 1.0
C10 B:86X1004 4.6 26.6 0.5
CD B:GLU418 4.6 27.8 1.0
C10 B:86X1004 4.7 20.9 0.5
CD B:GLU472 4.7 23.5 1.0
CE B:LYS474 4.7 30.9 1.0
CD B:ARG470 4.8 19.5 1.0
CZ B:ARG470 5.0 20.7 1.0
C8 B:ANP1001 5.0 19.4 1.0

Magnesium binding site 5 out of 8 in 5xii

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Magnesium binding site 5 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:43.8
occ:1.00
 O C:HOH1196 1.9 48.5 1.0
O1G C:ANP1001 2.3 29.6 1.0
PG C:ANP1001 3.6 25.2 1.0
O C:HOH1112 4.1 33.9 1.0
OE1 C:GLU532 4.1 46.9 1.0
NZ C:LYS796 4.1 63.8 1.0
O3G C:ANP1001 4.1 25.1 1.0
O C:HOH1153 4.2 21.7 1.0
N3B C:ANP1001 4.3 23.8 1.0
O C:HOH1104 4.5 42.6 1.0
O2G C:ANP1001 4.7 27.2 1.0
CD C:GLU532 4.9 46.9 1.0
O2B C:ANP1001 4.9 23.6 1.0

Magnesium binding site 6 out of 8 in 5xii

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Magnesium binding site 6 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:23.4
occ:1.00
 O1B C:ANP1001 1.9 23.7 1.0
O2G C:ANP1001 1.9 27.2 1.0
O C:HOH1140 2.0 20.1 1.0
O C:HOH1153 2.1 21.7 1.0
O C:HOH1125 2.1 21.3 1.0
O C:HOH1120 2.2 20.6 1.0
PG C:ANP1001 3.1 25.2 1.0
PB C:ANP1001 3.1 25.8 1.0
O1G C:ANP1001 3.5 29.6 1.0
N3B C:ANP1001 3.5 23.8 1.0
NH1 C:ARG470 3.9 21.0 1.0
O2B C:ANP1001 4.1 23.6 1.0
O C:HOH1128 4.1 40.9 1.0
NH1 C:ARG481 4.1 22.3 1.0
O C:HOH1104 4.2 42.6 1.0
O3A C:ANP1001 4.2 25.6 1.0
OE1 C:GLU472 4.2 27.8 1.0
OE1 C:GLU418 4.3 29.8 1.0
OE2 C:GLU472 4.3 25.3 1.0
OE2 C:GLU418 4.3 35.0 1.0
O3G C:ANP1001 4.4 25.1 1.0
N09 C:86X1004 4.4 27.3 0.5
N09 C:86X1004 4.5 26.4 0.5
N7 C:ANP1001 4.5 23.3 1.0
C10 C:86X1004 4.7 26.2 0.5
CD C:GLU418 4.7 32.1 1.0
CD C:GLU472 4.7 27.4 1.0
CD C:ARG470 4.8 20.0 1.0
C10 C:86X1004 4.8 25.4 0.5
C8 C:ANP1001 5.0 23.4 1.0

Magnesium binding site 7 out of 8 in 5xii

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Magnesium binding site 7 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:45.6
occ:1.00
 O D:HOH1183 1.5 59.5 1.0
O D:HOH1227 1.9 49.3 1.0
O D:HOH1236 2.1 56.7 1.0
O1G D:ANP1001 2.7 28.4 1.0
PG D:ANP1001 3.6 23.6 1.0
O3G D:ANP1001 3.6 24.1 1.0
O D:HOH1231 3.7 48.4 1.0
O D:HOH1120 3.8 38.6 1.0
OE1 D:GLU532 4.1 42.8 1.0
N3B D:ANP1001 4.2 21.3 1.0
O D:HOH1101 4.3 24.5 1.0
O2B D:ANP1001 4.4 22.0 1.0
NZ D:LYS796 4.4 51.9 1.0
O D:HOH1200 4.7 37.7 1.0
OE2 D:GLU532 4.7 41.0 1.0
CD D:GLU532 4.8 40.2 1.0
PB D:ANP1001 4.9 22.1 1.0
O2G D:ANP1001 5.0 24.6 1.0

Magnesium binding site 8 out of 8 in 5xii

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Magnesium binding site 8 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:23.2
occ:1.00
 O1B D:ANP1001 1.9 21.9 1.0
O D:HOH1179 2.0 23.5 1.0
O D:HOH1132 2.0 20.9 1.0
O2G D:ANP1001 2.0 24.6 1.0
O D:HOH1101 2.1 24.5 1.0
O D:HOH1134 2.2 21.1 1.0
PG D:ANP1001 3.0 23.6 1.0
O1G D:ANP1001 3.0 28.4 1.0
PB D:ANP1001 3.3 22.1 1.0
NH1 D:ARG470 3.7 16.2 1.0
N3B D:ANP1001 3.7 21.3 1.0
NH1 D:ARG481 4.0 23.8 1.0
OE2 D:GLU472 4.2 25.8 1.0
O2B D:ANP1001 4.2 22.0 1.0
O D:HOH1200 4.2 37.7 1.0
O3A D:ANP1001 4.3 24.3 1.0
OE2 D:GLU418 4.3 30.1 1.0
O3G D:ANP1001 4.3 24.1 1.0
N09 D:86X1004 4.3 24.8 0.5
OE1 D:GLU472 4.4 25.8 1.0
O D:HOH1149 4.4 37.8 1.0
OE1 D:GLU418 4.4 26.8 1.0
N7 D:ANP1001 4.5 23.8 1.0
N09 D:86X1004 4.6 27.7 0.5
C10 D:86X1004 4.7 24.4 0.5
CD D:ARG470 4.7 16.8 1.0
CD D:GLU472 4.7 24.8 1.0
C10 D:86X1004 4.8 26.9 0.5
CD D:GLU418 4.8 28.3 1.0
O D:HOH1254 4.8 38.8 1.0
CZ D:ARG470 4.8 18.4 1.0
C8 D:ANP1001 5.0 24.2 1.0

Reference:

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
Page generated: Mon Sep 30 09:25:22 2024

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