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Magnesium in PDB 5xij: Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 9

Enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 9

All present enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 9:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 9, PDB code: 5xij 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) 40.36 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.848, 93.158, 91.012, 89.81, 104.52, 99.60
R / Rfree (%) 18 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 9 (pdb code 5xij). 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 9, PDB code: 5xij:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5xij

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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 9


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

b:21.4
occ:1.00
 O1G A:ANP1001 1.7 19.4 1.0
O1B A:ANP1001 1.8 21.7 1.0
O A:HOH1101 1.9 17.5 1.0
O A:HOH1104 2.1 17.6 1.0
O A:HOH1118 2.2 15.7 1.0
O A:HOH1124 2.2 21.4 1.0
PG A:ANP1001 2.9 19.9 1.0
PB A:ANP1001 3.1 21.4 1.0
O2G A:ANP1001 3.2 18.0 1.0
NH1 A:ARG470 3.5 31.9 1.0
N3B A:ANP1001 3.5 18.2 1.0
NH1 A:ARG481 3.9 25.5 1.0
O2B A:ANP1001 4.1 18.6 1.0
O3G A:ANP1001 4.1 17.6 1.0
OE1 A:GLU472 4.2 22.5 1.0
O3A A:ANP1001 4.2 20.1 1.0
OE2 A:GLU472 4.2 20.4 1.0
O A:HOH1135 4.3 39.1 1.0
N7 A:ANP1001 4.3 19.4 1.0
OE2 A:GLU418 4.4 27.9 1.0
N10 A:8731004 4.5 25.9 1.0
C8 A:ANP1001 4.5 19.0 1.0
OE1 A:GLU418 4.5 26.8 1.0
CD A:GLU472 4.7 22.5 1.0
CZ A:ARG470 4.7 28.6 1.0
C09 A:8731004 4.7 24.5 1.0
CD A:ARG470 4.8 28.9 1.0
CD A:GLU418 4.8 27.9 1.0

Magnesium binding site 2 out of 8 in 5xij

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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 9


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

b:37.3
occ:1.00
 O A:HOH1130 1.8 46.4 1.0
O A:HOH1190 2.0 41.2 1.0
O A:HOH1191 2.0 39.2 1.0
O A:HOH1199 2.2 38.2 1.0
O A:HOH1115 2.2 35.1 1.0
O2G A:ANP1001 2.5 18.0 1.0
PG A:ANP1001 3.7 19.9 1.0
O3G A:ANP1001 4.1 17.6 1.0
O2B A:ANP1001 4.1 18.6 1.0
O A:HOH1101 4.2 17.5 1.0
OE1 A:GLU532 4.2 34.6 1.0
N3B A:ANP1001 4.2 18.2 1.0
O A:HOH1123 4.3 25.3 1.0
NZ A:LYS796 4.6 57.8 1.0
PB A:ANP1001 4.8 21.4 1.0
O A:HOH1135 4.9 39.1 1.0
OE2 A:GLU532 4.9 39.2 1.0
CD A:GLU532 4.9 38.1 1.0
O1G A:ANP1001 5.0 19.4 1.0

Magnesium binding site 3 out of 8 in 5xij

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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 9


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

b:24.0
occ:1.00
 O B:HOH1112 2.0 15.2 1.0
O B:HOH1128 2.0 25.1 1.0
O B:HOH1104 2.1 16.2 1.0
O3G B:ANP1001 2.1 25.5 1.0
O B:HOH1123 2.2 22.6 1.0
O2B B:ANP1001 2.3 23.7 1.0
PG B:ANP1001 3.2 25.1 1.0
O2G B:ANP1001 3.3 30.5 1.0
PB B:ANP1001 3.6 22.0 1.0
NH1 B:ARG470 3.6 27.3 1.0
N3B B:ANP1001 4.0 21.9 1.0
OE1 B:GLU418 4.0 35.5 1.0
NH1 B:ARG481 4.1 26.7 1.0
OE1 B:GLU472 4.1 25.5 1.0
OE2 B:GLU472 4.2 28.0 1.0
OE2 B:GLU418 4.2 36.5 1.0
O1B B:ANP1001 4.3 20.5 1.0
N10 B:8731004 4.4 24.3 1.0
O1G B:ANP1001 4.4 24.1 1.0
CD B:GLU418 4.6 37.2 1.0
N7 B:ANP1001 4.6 23.2 1.0
CD B:GLU472 4.6 26.7 1.0
CD B:ARG470 4.6 22.9 1.0
CZ B:ARG470 4.6 26.9 1.0
C09 B:8731004 4.7 23.6 1.0
O3A B:ANP1001 4.8 24.0 1.0
C8 B:ANP1001 4.8 24.4 1.0
O B:HOH1129 4.9 55.8 1.0

Magnesium binding site 4 out of 8 in 5xij

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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 9


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

b:38.4
occ:1.00
 O B:HOH1161 1.9 47.0 1.0
O B:HOH1156 2.0 45.2 1.0
O B:HOH1145 2.0 40.9 1.0
O B:HOH1129 2.1 55.8 1.0
O B:HOH1101 2.3 42.6 1.0
O2G B:ANP1001 2.6 30.5 1.0
PG B:ANP1001 3.7 25.1 1.0
O1G B:ANP1001 3.9 24.1 1.0
O1B B:ANP1001 4.2 20.5 1.0
O B:HOH1104 4.3 16.2 1.0
OE1 B:GLU532 4.3 49.0 1.0
N3B B:ANP1001 4.5 21.9 1.0
PB B:ANP1001 4.9 22.0 1.0
O B:GLU532 4.9 31.8 1.0
CD B:GLU532 4.9 44.4 1.0
O3G B:ANP1001 4.9 25.5 1.0
OE2 B:GLU532 5.0 49.1 1.0

Magnesium binding site 5 out of 8 in 5xij

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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 9


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

b:23.8
occ:1.00
 O2G C:ANP1001 1.8 27.3 1.0
O2B C:ANP1001 1.9 26.8 1.0
O C:HOH1135 2.0 26.7 1.0
O C:HOH1106 2.0 23.4 1.0
O C:HOH1104 2.1 17.2 1.0
O C:HOH1102 2.1 24.0 1.0
PG C:ANP1001 2.9 23.3 1.0
PB C:ANP1001 3.1 26.3 1.0
O1G C:ANP1001 3.4 25.9 1.0
N3B C:ANP1001 3.4 23.1 1.0
NH1 C:ARG470 3.5 21.9 1.0
O1B C:ANP1001 3.8 24.8 1.0
NH1 C:ARG481 4.0 31.7 1.0
OE2 C:GLU472 4.2 23.6 1.0
O3G C:ANP1001 4.2 24.4 1.0
OE1 C:GLU472 4.2 25.3 1.0
O3A C:ANP1001 4.3 25.7 1.0
OE1 C:GLU418 4.4 29.0 1.0
OE2 C:GLU418 4.4 28.5 1.0
N10 C:8731004 4.5 27.7 1.0
N7 C:ANP1001 4.5 23.5 1.0
CD C:GLU472 4.6 24.8 1.0
C09 C:8731004 4.7 28.6 1.0
CZ C:ARG470 4.7 21.2 1.0
CD C:ARG470 4.8 21.6 1.0
CD C:GLU418 4.8 26.6 1.0
C8 C:ANP1001 5.0 23.0 1.0

Magnesium binding site 6 out of 8 in 5xij

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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 9


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

b:42.7
occ:1.00
 O C:HOH1153 1.9 52.0 1.0
O C:HOH1145 1.9 56.8 1.0
O C:HOH1118 2.1 28.6 1.0
O C:HOH1139 2.1 39.4 1.0
O C:HOH1174 2.1 33.5 1.0
O1G C:ANP1001 2.4 25.9 1.0
PG C:ANP1001 3.8 23.3 1.0
O1B C:ANP1001 4.0 24.8 1.0
O C:HOH1106 4.0 23.4 1.0
O3G C:ANP1001 4.2 24.4 1.0
OE1 C:GLU532 4.3 36.2 1.0
NZ C:LYS796 4.5 50.4 1.0
O2G C:ANP1001 4.7 27.3 1.0
N3B C:ANP1001 4.7 23.1 1.0
PB C:ANP1001 4.9 26.3 1.0

Magnesium binding site 7 out of 8 in 5xij

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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 9


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

b:22.1
occ:1.00
 O1B D:ANP1001 1.9 25.6 1.0
O D:HOH1125 2.0 20.6 1.0
O1G D:ANP1001 2.0 28.9 1.0
O D:HOH1118 2.1 24.4 1.0
O D:HOH1101 2.1 18.7 1.0
O D:HOH1115 2.3 12.9 1.0
PG D:ANP1001 3.1 26.8 1.0
O2G D:ANP1001 3.1 28.8 1.0
PB D:ANP1001 3.2 25.1 1.0
NH1 D:ARG470 3.7 29.2 1.0
N3B D:ANP1001 3.7 24.7 1.0
NZ D:LYS474 3.8 33.1 1.0
NH1 D:ARG481 4.0 31.7 1.0
OE1 D:GLU418 4.0 29.2 1.0
O2B D:ANP1001 4.2 27.7 1.0
O3A D:ANP1001 4.2 26.0 1.0
OE2 D:GLU472 4.2 31.2 1.0
OE1 D:GLU472 4.3 28.6 1.0
N10 D:8731004 4.3 26.4 1.0
O3G D:ANP1001 4.4 25.4 1.0
N7 D:ANP1001 4.4 23.1 1.0
OE2 D:GLU418 4.5 33.5 1.0
CD D:ARG470 4.7 25.8 1.0
CD D:GLU418 4.7 28.9 1.0
CD D:GLU472 4.7 27.9 1.0
CZ D:ARG470 4.7 28.6 1.0
C09 D:8731004 4.8 31.1 1.0
CE D:LYS474 4.9 32.5 1.0
C8 D:ANP1001 4.9 24.3 1.0

Magnesium binding site 8 out of 8 in 5xij

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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 9


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

b:38.5
occ:1.00
 O D:HOH1150 1.9 34.1 1.0
O D:HOH1128 2.1 26.5 1.0
O D:HOH1148 2.2 27.5 1.0
O D:HOH1167 2.2 52.3 1.0
O D:HOH1163 2.3 43.2 1.0
O2G D:ANP1001 2.8 28.8 1.0
O3G D:ANP1001 3.8 25.4 1.0
PG D:ANP1001 3.8 26.8 1.0
NZ D:LYS796 4.1 55.3 1.0
OE1 D:GLU532 4.2 57.0 1.0
N3B D:ANP1001 4.4 24.7 1.0
O D:HOH1101 4.4 18.7 1.0
OE2 D:GLU532 4.6 49.8 1.0
O2B D:ANP1001 4.6 27.7 1.0
NZ D:LYS474 4.6 33.1 1.0
CD D:GLU532 4.8 52.9 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 09:25:23 2024

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