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Magnesium in PDB 5xiq: Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone

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

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

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone, PDB code: 5xiq 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) 40.32 / 2.19
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.852, 90.898, 92.869, 89.86, 80.92, 75.82
R / Rfree (%) 16.5 / 20.7

Other elements in 5xiq:

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

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone (pdb code 5xiq). 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 Halofuginone, PDB code: 5xiq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5xiq

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

b:32.2
occ:1.00
 O3G A:ANP1001 1.6 31.0 1.0
O A:HOH1120 2.0 28.3 1.0
O A:HOH1103 2.1 33.3 1.0
O A:HOH1110 2.1 31.6 1.0
O A:HOH1159 2.1 33.3 1.0
O2B A:ANP1001 2.2 32.0 1.0
PG A:ANP1001 3.0 35.7 1.0
PB A:ANP1001 3.3 32.2 1.0
O2G A:ANP1001 3.5 36.6 1.0
N3B A:ANP1001 3.6 34.8 1.0
NH1 A:ARG470 3.8 29.5 1.0
O A:HOH1165 3.9 45.3 1.0
O A:HOH1204 3.9 51.5 1.0
OE1 A:GLU472 4.0 33.1 1.0
NH1 A:ARG481 4.0 32.8 1.0
O1G A:ANP1001 4.0 35.6 1.0
O1B A:ANP1001 4.1 28.4 1.0
OE2 A:GLU472 4.1 42.1 1.0
OE2 A:GLU418 4.3 47.5 1.0
OE1 A:GLU418 4.3 38.2 1.0
N7 A:ANP1001 4.4 27.6 1.0
N1 A:HFG1002 4.5 30.4 1.0
CD A:GLU472 4.5 36.6 1.0
O3A A:ANP1001 4.6 31.7 1.0
CD A:GLU418 4.7 37.2 1.0
CD A:ARG470 4.8 29.0 1.0
C2 A:HFG1002 4.9 31.7 1.0
C8 A:ANP1001 4.9 27.5 1.0
CZ A:ARG470 5.0 30.3 1.0

Magnesium binding site 2 out of 8 in 5xiq

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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 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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:51.0
occ:1.00
 O A:HOH1179 1.8 54.2 1.0
O A:HOH1138 1.9 44.7 1.0
O A:HOH1155 2.0 36.2 1.0
O A:HOH1173 2.0 52.9 1.0
O A:HOH1153 2.0 41.9 1.0
O2G A:ANP1001 2.2 36.6 1.0
PG A:ANP1001 3.5 35.7 1.0
O A:HOH1139 3.9 41.1 1.0
N3B A:ANP1001 4.0 34.8 1.0
O1G A:ANP1001 4.1 35.6 1.0
NZ A:LYS796 4.1 69.2 1.0
OE1 A:GLU532 4.2 43.2 1.0
O1B A:ANP1001 4.2 28.4 1.0
O A:HOH1103 4.2 33.3 1.0
O A:HOH1102 4.6 44.6 1.0
O3G A:ANP1001 4.6 31.0 1.0
PB A:ANP1001 4.6 32.2 1.0
O A:HOH1204 4.9 51.5 1.0

Magnesium binding site 3 out of 8 in 5xiq

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

b:36.5
occ:1.00
 O1B B:ANP1001 2.0 35.2 1.0
O B:HOH1109 2.0 29.6 1.0
O3G B:ANP1001 2.1 37.8 1.0
O B:HOH1126 2.1 28.5 1.0
O B:HOH1102 2.2 33.7 1.0
O B:HOH1116 2.3 28.9 1.0
O2G B:ANP1001 3.1 42.0 1.0
PG B:ANP1001 3.1 39.9 1.0
PB B:ANP1001 3.3 35.7 1.0
O B:HOH1169 3.7 53.0 1.0
N3B B:ANP1001 3.8 37.1 1.0
O2B B:ANP1001 4.0 36.3 1.0
NH1 B:ARG470 4.0 30.4 1.0
NH1 B:ARG481 4.0 32.1 1.0
OE2 B:GLU418 4.1 46.9 1.0
OE1 B:GLU472 4.2 41.0 1.0
OE1 B:GLU418 4.3 40.1 1.0
OE2 B:GLU472 4.3 36.3 1.0
O1G B:ANP1001 4.3 41.8 1.0
O3A B:ANP1001 4.5 36.2 1.0
N1 B:HFG1002 4.5 30.6 1.0
N7 B:ANP1001 4.6 33.7 1.0
CD B:GLU418 4.7 47.9 1.0
CD B:GLU472 4.7 36.1 1.0
C2 B:HFG1002 4.8 35.5 1.0
CD B:ARG470 5.0 33.2 1.0

Magnesium binding site 4 out of 8 in 5xiq

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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 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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:56.5
occ:1.00
 O B:HOH1149 1.8 48.4 1.0
O B:HOH1165 1.8 48.6 1.0
O B:HOH1138 1.9 61.3 1.0
O B:HOH1160 2.0 45.0 1.0
O2G B:ANP1001 2.7 42.0 1.0
PG B:ANP1001 3.6 39.9 1.0
OE1 B:GLU532 3.7 59.8 1.0
O1G B:ANP1001 3.7 41.8 1.0
NZ B:LYS796 3.7 67.5 1.0
N3B B:ANP1001 4.1 37.1 1.0
O B:HOH1102 4.5 33.7 1.0
O2B B:ANP1001 4.5 36.3 1.0
CD B:GLU532 4.7 59.2 1.0
PB B:ANP1001 4.8 35.7 1.0

Magnesium binding site 5 out of 8 in 5xiq

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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 Halofuginone


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 Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:37.6
occ:1.00
 O C:HOH1114 2.0 28.6 1.0
O C:HOH1130 2.0 29.3 1.0
O3G C:ANP1001 2.0 31.2 1.0
O2B C:ANP1001 2.0 28.6 1.0
O C:HOH1101 2.2 35.9 1.0
O C:HOH1117 2.2 37.2 1.0
PG C:ANP1001 3.1 36.7 1.0
O2G C:ANP1001 3.3 35.1 1.0
PB C:ANP1001 3.3 31.1 1.0
NH1 C:ARG470 3.7 30.6 1.0
N3B C:ANP1001 3.8 34.9 1.0
OE2 C:GLU472 4.0 34.8 1.0
NH1 C:ARG481 4.1 40.7 1.0
O1B C:ANP1001 4.1 35.8 1.0
O C:HOH1189 4.1 53.1 1.0
O C:HOH1165 4.2 56.8 1.0
OE1 C:GLU472 4.2 33.9 1.0
OE2 C:GLU418 4.2 39.8 1.0
N1 C:HFG1002 4.3 32.5 1.0
OE1 C:GLU418 4.3 43.6 1.0
O1G C:ANP1001 4.4 31.2 1.0
O3A C:ANP1001 4.5 30.6 1.0
N7 C:ANP1001 4.5 32.3 1.0
CD C:GLU472 4.6 34.5 1.0
C2 C:HFG1002 4.6 31.6 1.0
CD C:ARG470 4.7 31.8 1.0
CD C:GLU418 4.7 42.2 1.0
CZ C:ARG470 4.8 34.8 1.0
C8 C:ANP1001 5.0 31.0 1.0

Magnesium binding site 6 out of 8 in 5xiq

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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 Halofuginone


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 Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1004

b:44.9
occ:1.00
 O C:HOH1164 1.7 64.8 1.0
O C:HOH1194 1.9 43.0 1.0
O C:HOH1171 1.9 24.0 0.5
O C:HOH1133 2.1 53.1 1.0
O C:HOH1169 2.1 49.1 1.0
O2G C:ANP1001 2.5 35.1 1.0
O C:HOH1171 3.1 41.9 0.5
PG C:ANP1001 3.6 36.7 1.0
O1G C:ANP1001 3.9 31.2 1.0
O C:HOH1101 4.1 35.9 1.0
N3B C:ANP1001 4.1 34.9 1.0
NZ C:LYS796 4.1 57.5 1.0
OE1 C:GLU532 4.1 46.2 1.0
O C:HOH1166 4.3 42.0 1.0
O1B C:ANP1001 4.5 35.8 1.0
O C:HOH1189 4.7 53.1 1.0
PB C:ANP1001 4.8 31.1 1.0
O3G C:ANP1001 4.9 31.2 1.0
CD C:GLU532 5.0 47.1 1.0
OE2 C:GLU532 5.0 47.9 1.0

Magnesium binding site 7 out of 8 in 5xiq

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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 Halofuginone


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 Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:29.9
occ:1.00
 O2B D:ANP1001 2.0 30.3 1.0
O D:HOH1110 2.1 24.4 1.0
O D:HOH1108 2.1 28.1 1.0
O D:HOH1105 2.1 25.4 1.0
O3G D:ANP1001 2.1 33.8 1.0
O D:HOH1120 2.1 33.0 1.0
PG D:ANP1001 3.2 36.8 1.0
PB D:ANP1001 3.3 33.0 1.0
O2G D:ANP1001 3.4 30.8 1.0
N3B D:ANP1001 3.6 29.2 1.0
NZ D:LYS474 3.9 43.1 1.0
NH1 D:ARG481 3.9 37.0 1.0
NH1 D:ARG470 3.9 32.8 1.0
O3A D:ANP1001 4.0 32.6 1.0
OE1 D:GLU418 4.1 36.1 1.0
OE2 D:GLU418 4.2 37.1 1.0
OE1 D:GLU472 4.2 31.6 1.0
N1 D:HFG1002 4.3 29.0 1.0
OE2 D:GLU472 4.3 36.6 1.0
O1B D:ANP1001 4.4 34.6 1.0
O1G D:ANP1001 4.5 33.2 1.0
N7 D:ANP1001 4.5 32.6 1.0
CD D:GLU418 4.6 35.8 1.0
C2 D:HFG1002 4.7 34.0 1.0
CD D:GLU472 4.7 31.4 1.0
CD D:ARG470 4.8 33.2 1.0
CE D:LYS474 4.8 41.3 1.0
CZ D:ARG470 4.9 32.3 1.0

Magnesium binding site 8 out of 8 in 5xiq

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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 Halofuginone


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 Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1004

b:50.4
occ:1.00
 O D:HOH1129 1.6 53.1 1.0
O D:HOH1167 1.7 42.0 1.0
O D:HOH1157 1.9 46.4 1.0
O D:HOH1170 2.0 48.2 1.0
O D:HOH1123 2.0 38.6 1.0
O2G D:ANP1001 2.3 30.8 1.0
PG D:ANP1001 3.6 36.8 1.0
O1G D:ANP1001 3.8 33.2 1.0
O D:HOH1105 4.1 25.4 1.0
OE1 D:GLU532 4.4 49.6 1.0
N3B D:ANP1001 4.4 29.2 1.0
O1B D:ANP1001 4.5 34.6 1.0
NZ D:LYS474 4.5 43.1 1.0
NZ D:LYS796 4.5 80.2 1.0
O3G D:ANP1001 4.7 33.8 1.0
PB D:ANP1001 4.8 33.0 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 09:28:39 2024

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