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Magnesium in PDB 5xig: Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 1

Enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 1

All present enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 1:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 1, PDB code: 5xig 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) 43.81 / 2.41
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.762, 90.379, 93.209, 89.90, 99.58, 104.22
R / Rfree (%) 18.2 / 24.5

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 5xig

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:20.6
occ:1.00
 O1G A:ANP1001 1.6 19.3 1.0
O1B A:ANP1001 1.8 21.5 1.0
O A:HOH1110 2.3 19.4 1.0
O A:HOH1125 2.3 19.6 1.0
O A:HOH1159 2.3 20.1 1.0
O A:HOH1208 2.4 23.0 1.0
PG A:ANP1001 2.9 19.5 1.0
PB A:ANP1001 3.0 20.4 1.0
N3B A:ANP1001 3.4 19.1 1.0
O2G A:ANP1001 3.4 20.9 1.0
NH1 A:ARG470 3.7 30.4 1.0
NH1 A:ARG481 3.9 28.4 1.0
O2B A:ANP1001 3.9 19.7 1.0
O3G A:ANP1001 4.1 18.7 1.0
O A:HOH1221 4.1 40.4 1.0
O3A A:ANP1001 4.2 22.3 1.0
OE1 A:GLU472 4.2 20.5 1.0
OE2 A:GLU472 4.3 25.3 1.0
N7 A:ANP1001 4.4 18.4 1.0
OE2 A:GLU418 4.4 32.5 1.0
OE1 A:GLU418 4.5 28.6 1.0
N1 A:87F1004 4.6 25.8 1.0
CD A:GLU472 4.8 23.1 1.0
C8 A:ANP1001 4.8 20.3 1.0
CD A:ARG470 4.9 27.3 1.0
CD A:GLU418 4.9 30.4 1.0
CZ A:ARG470 4.9 27.8 1.0
C7 A:87F1004 4.9 23.3 1.0
CZ A:ARG481 5.0 28.4 1.0

Magnesium binding site 2 out of 8 in 5xig

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:30.8
occ:1.00
 O2G A:ANP1001 1.9 20.9 1.0
O A:HOH1223 2.3 36.3 1.0
O A:HOH1132 2.4 46.6 1.0
O A:HOH1158 2.4 30.4 1.0
O A:HOH1228 2.5 33.2 1.0
O A:HOH1234 2.6 32.1 1.0
PG A:ANP1001 3.3 19.5 1.0
O3G A:ANP1001 3.8 18.7 1.0
N3B A:ANP1001 4.0 19.1 1.0
O2B A:ANP1001 4.2 19.7 1.0
O A:HOH1208 4.3 23.0 1.0
O1G A:ANP1001 4.4 19.3 1.0
OE1 A:GLU532 4.4 29.2 1.0
NZ A:LYS796 4.5 45.2 1.0
PB A:ANP1001 4.7 20.4 1.0
O A:HOH1221 4.9 40.4 1.0

Magnesium binding site 3 out of 8 in 5xig

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:21.2
occ:1.00
 O1B B:ANP1001 1.9 24.5 1.0
O2G B:ANP1001 2.0 24.5 1.0
O B:HOH1101 2.2 13.3 1.0
O B:HOH1109 2.3 13.9 1.0
O B:HOH1102 2.5 18.9 1.0
O B:HOH1116 2.5 15.3 1.0
PG B:ANP1001 3.2 25.1 1.0
PB B:ANP1001 3.2 25.5 1.0
O1G B:ANP1001 3.4 22.9 1.0
NH1 B:ARG470 3.6 28.2 1.0
N3B B:ANP1001 3.7 24.8 1.0
NH1 B:ARG481 3.9 27.6 1.0
NZ B:LYS474 3.9 33.6 1.0
O2B B:ANP1001 4.1 29.2 1.0
OE1 B:GLU418 4.2 29.4 1.0
OE2 B:GLU472 4.2 27.1 1.0
O3A B:ANP1001 4.3 25.5 1.0
N1 B:87F1004 4.3 27.1 1.0
OE2 B:GLU418 4.3 32.6 1.0
OE1 B:GLU472 4.4 26.9 1.0
O3G B:ANP1001 4.4 22.6 1.0
N7 B:ANP1001 4.5 26.3 1.0
C7 B:87F1004 4.5 27.2 1.0
CD B:GLU418 4.7 30.7 1.0
CD B:ARG470 4.7 27.8 1.0
CZ B:ARG470 4.7 28.3 1.0
CD B:GLU472 4.7 25.9 1.0
CE B:LYS474 4.9 32.6 1.0
C8 B:ANP1001 5.0 26.4 1.0

Magnesium binding site 4 out of 8 in 5xig

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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 1


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

b:32.2
occ:1.00
 O B:HOH1173 2.1 44.0 1.0
O B:HOH1179 2.1 38.9 1.0
O B:HOH1137 2.3 30.1 1.0
O1G B:ANP1001 2.3 22.9 1.0
O B:HOH1160 2.3 28.0 1.0
O B:HOH1167 2.4 29.9 1.0
PG B:ANP1001 3.6 25.1 1.0
O B:HOH1116 3.8 15.3 1.0
O3G B:ANP1001 4.0 22.6 1.0
N3B B:ANP1001 4.2 24.8 1.0
NZ B:LYS474 4.3 33.6 1.0
NZ B:LYS796 4.3 45.6 1.0
OE1 B:GLU532 4.6 41.0 1.0
O2B B:ANP1001 4.7 29.2 1.0
OE2 B:GLU532 4.7 43.3 1.0
O2G B:ANP1001 4.8 24.5 1.0
PB B:ANP1001 5.0 25.5 1.0

Magnesium binding site 5 out of 8 in 5xig

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:24.5
occ:1.00
 O1B C:ANP1001 1.7 28.2 1.0
O1G C:ANP1001 1.8 25.2 1.0
O C:HOH1135 2.0 22.6 1.0
O C:HOH1115 2.1 20.0 1.0
O C:HOH1145 2.1 26.2 1.0
O C:HOH1102 2.2 16.8 1.0
PG C:ANP1001 3.0 25.1 1.0
PB C:ANP1001 3.0 28.4 1.0
O2G C:ANP1001 3.3 25.0 1.0
N3B C:ANP1001 3.5 23.8 1.0
NH1 C:ARG470 3.5 20.2 1.0
NH1 C:ARG481 3.9 31.3 1.0
O3A C:ANP1001 4.0 26.8 1.0
O2B C:ANP1001 4.0 27.6 1.0
O3G C:ANP1001 4.2 22.4 1.0
OE1 C:GLU472 4.3 27.2 1.0
N7 C:ANP1001 4.3 28.6 1.0
OE2 C:GLU472 4.3 29.3 1.0
OE1 C:GLU418 4.5 32.4 1.0
N1 C:87F1004 4.6 30.3 1.0
CD C:ARG470 4.6 19.7 1.0
OE2 C:GLU418 4.6 33.2 1.0
CZ C:ARG470 4.7 18.9 1.0
C8 C:ANP1001 4.7 27.4 1.0
CD C:GLU472 4.8 26.3 1.0
C7 C:87F1004 4.8 28.3 1.0

Magnesium binding site 6 out of 8 in 5xig

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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 1


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

b:51.7
occ:1.00
 O C:HOH1178 1.7 74.3 1.0
O C:HOH1140 1.8 36.7 1.0
O C:HOH1177 2.1 38.2 1.0
O C:HOH1147 2.2 48.3 1.0
O2G C:ANP1001 2.2 25.0 1.0
O C:HOH1185 2.3 42.6 1.0
PG C:ANP1001 3.6 25.1 1.0
O C:HOH1102 3.7 16.8 1.0
O3G C:ANP1001 4.1 22.4 1.0
O2B C:ANP1001 4.2 27.6 1.0
O C:HOH1125 4.2 35.0 1.0
N3B C:ANP1001 4.3 23.8 1.0
O1G C:ANP1001 4.7 25.2 1.0
PB C:ANP1001 4.7 28.4 1.0
OE1 C:GLU532 4.8 40.1 1.0
NZ C:LYS796 4.9 64.1 1.0
O1B C:ANP1001 5.0 28.2 1.0

Magnesium binding site 7 out of 8 in 5xig

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:20.4
occ:1.00
 O2G D:ANP1001 1.8 31.0 1.0
O1B D:ANP1001 1.8 23.7 1.0
O D:HOH1131 2.2 19.4 1.0
O D:HOH1165 2.4 23.2 1.0
O D:HOH1102 2.4 17.0 1.0
O D:HOH1120 2.5 17.9 1.0
PG D:ANP1001 2.9 27.0 1.0
PB D:ANP1001 3.1 24.0 1.0
O1G D:ANP1001 3.2 27.3 1.0
N3B D:ANP1001 3.5 23.1 1.0
NH1 D:ARG470 3.9 26.9 1.0
O2B D:ANP1001 4.0 23.4 1.0
NH1 D:ARG481 4.1 28.1 1.0
O3A D:ANP1001 4.1 23.9 1.0
O3G D:ANP1001 4.2 22.7 1.0
OE2 D:GLU418 4.3 34.6 1.0
OE1 D:GLU472 4.4 19.8 1.0
OE1 D:GLU418 4.5 31.8 1.0
OE2 D:GLU472 4.5 23.9 1.0
N1 D:87F1004 4.5 23.9 1.0
N7 D:ANP1001 4.5 23.8 1.0
C7 D:87F1004 4.8 25.5 1.0
CD D:GLU418 4.9 36.5 1.0
CD D:GLU472 4.9 25.1 1.0
O D:HOH1155 4.9 42.1 1.0
CD D:ARG470 4.9 24.4 1.0
C8 D:ANP1001 5.0 24.5 1.0

Magnesium binding site 8 out of 8 in 5xig

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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 1


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

b:35.7
occ:1.00
 O D:HOH1112 2.1 43.3 1.0
O D:HOH1139 2.1 36.7 1.0
O1G D:ANP1001 2.2 27.3 1.0
O D:HOH1155 2.2 42.1 1.0
O D:HOH1105 2.3 34.5 1.0
O D:HOH1166 2.6 32.9 1.0
PG D:ANP1001 3.6 27.0 1.0
O D:HOH1165 4.1 23.2 1.0
O2B D:ANP1001 4.2 23.4 1.0
N3B D:ANP1001 4.2 23.1 1.0
O3G D:ANP1001 4.2 22.7 1.0
OE1 D:GLU532 4.4 46.3 1.0
O D:HOH1119 4.5 31.0 1.0
NZ D:LYS796 4.5 60.3 1.0
PB D:ANP1001 4.7 24.0 1.0
O2G D:ANP1001 4.7 31.0 1.0
OE2 D:GLU532 4.8 39.8 1.0
CD D:GLU532 4.9 40.5 1.0
O D:GLU532 5.0 42.6 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 09:24:00 2024

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