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

Enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5

All present enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5, PDB code: 5xih 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) 47.06 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.710, 90.763, 93.034, 89.71, 80.58, 75.77
R / Rfree (%) 17.6 / 22.6

Other elements in 5xih:

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5 also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Chlorine (Cl) 8 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 5 (pdb code 5xih). 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 5, PDB code: 5xih:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5xih

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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 5


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

b:32.2
occ:1.00
 O A:HOH1258 1.9 45.2 1.0
O A:HOH1206 2.0 23.7 0.5
O A:HOH1269 2.1 37.3 1.0
O A:HOH1225 2.1 35.0 1.0
O A:HOH1134 2.2 39.7 1.0
O2G A:ANP1001 2.3 20.0 1.0
PG A:ANP1001 3.6 20.2 1.0
O A:HOH1164 3.7 42.5 1.0
O A:HOH1101 3.9 20.3 1.0
O A:HOH1130 3.9 31.6 1.0
O1G A:ANP1001 4.0 19.3 1.0
N3B A:ANP1001 4.1 19.8 1.0
O1B A:ANP1001 4.3 21.6 1.0
OE1 A:GLU532 4.4 25.8 1.0
NZ A:LYS796 4.4 49.5 1.0
PB A:ANP1001 4.7 20.5 1.0
O3G A:ANP1001 4.7 18.2 1.0
O A:HOH1247 4.8 35.0 1.0

Magnesium binding site 2 out of 8 in 5xih

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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 5


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

b:21.9
occ:1.00
 O3G A:ANP1001 1.9 18.2 1.0
O2B A:ANP1001 2.0 19.9 1.0
O A:HOH1142 2.0 18.4 1.0
O A:HOH1181 2.1 12.3 1.0
O A:HOH1114 2.1 19.3 1.0
O A:HOH1101 2.1 20.3 1.0
PG A:ANP1001 3.1 20.2 1.0
PB A:ANP1001 3.3 20.5 1.0
O2G A:ANP1001 3.4 20.0 1.0
N3B A:ANP1001 3.7 19.8 1.0
NH1 A:ARG470 3.8 18.8 1.0
O A:HOH1247 3.9 35.0 1.0
NH1 A:ARG481 4.0 20.4 1.0
O A:HOH1112 4.1 40.3 1.0
OE1 A:GLU472 4.1 19.1 1.0
OE2 A:GLU418 4.2 25.3 1.0
O1B A:ANP1001 4.3 21.6 1.0
OE2 A:GLU472 4.3 22.6 1.0
O3A A:ANP1001 4.3 20.9 1.0
O1G A:ANP1001 4.3 19.3 1.0
OE1 A:GLU418 4.3 23.6 1.0
N08 A:86U1004 4.4 13.8 0.5
N7 A:ANP1001 4.5 16.5 1.0
N08 A:86U1004 4.6 28.4 0.5
CD A:GLU472 4.7 20.3 1.0
CD A:GLU418 4.7 25.1 1.0
CD A:ARG470 4.8 19.1 1.0
C09 A:86U1004 4.8 12.7 0.5
C09 A:86U1004 4.9 27.2 0.5
C8 A:ANP1001 5.0 16.8 1.0
CZ A:ARG470 5.0 20.4 1.0

Magnesium binding site 3 out of 8 in 5xih

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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 5


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

b:41.4
occ:1.00
 O B:HOH1201 1.7 41.3 1.0
O B:HOH1191 1.8 25.6 0.5
O B:HOH1204 2.0 46.9 1.0
O B:HOH1119 2.1 36.7 0.5
O B:HOH1193 2.2 28.9 0.5
O2G B:ANP1001 2.3 25.6 1.0
PG B:ANP1001 3.6 25.1 1.0
O1G B:ANP1001 3.9 23.8 1.0
O B:HOH1102 4.0 18.6 1.0
O B:HOH1132 4.1 31.8 1.0
N3B B:ANP1001 4.2 23.0 1.0
OE1 B:GLU532 4.2 39.0 1.0
NZ B:LYS796 4.3 56.5 1.0
O1B B:ANP1001 4.4 21.6 1.0
O B:HOH1198 4.8 41.5 1.0
O3G B:ANP1001 4.8 25.8 1.0
PB B:ANP1001 4.8 23.4 1.0
CD B:GLU532 5.0 40.4 1.0

Magnesium binding site 4 out of 8 in 5xih

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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 5


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

b:25.7
occ:1.00
 O3G B:ANP1001 1.8 25.8 1.0
O B:HOH1159 2.0 25.8 1.0
O2B B:ANP1001 2.0 21.0 1.0
O B:HOH1102 2.1 18.6 1.0
O B:HOH1105 2.1 21.1 1.0
O B:HOH1135 2.2 18.3 1.0
PG B:ANP1001 3.0 25.1 1.0
O2G B:ANP1001 3.1 25.6 1.0
PB B:ANP1001 3.3 23.4 1.0
N3B B:ANP1001 3.7 23.0 1.0
O B:HOH1171 3.9 38.5 1.0
NH1 B:ARG481 4.0 20.2 1.0
NH1 B:ARG470 4.0 19.3 1.0
O B:HOH1198 4.1 41.5 1.0
OE2 B:GLU418 4.2 31.2 1.0
O1G B:ANP1001 4.2 23.8 1.0
OE1 B:GLU472 4.2 23.9 1.0
O1B B:ANP1001 4.2 21.6 1.0
O3A B:ANP1001 4.3 23.6 1.0
OE1 B:GLU418 4.3 24.5 1.0
OE2 B:GLU472 4.3 23.0 1.0
N08 B:86U1004 4.4 19.1 0.5
N7 B:ANP1001 4.5 21.7 1.0
C09 B:86U1004 4.7 19.1 0.5
CD B:GLU418 4.7 27.5 1.0
CD B:GLU472 4.8 22.7 1.0
N08 B:86U1004 4.8 23.4 0.5
CD B:ARG470 4.9 19.5 1.0

Magnesium binding site 5 out of 8 in 5xih

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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 5


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

b:39.3
occ:1.00
 O C:HOH1114 1.7 54.0 1.0
O C:HOH1238 1.9 44.8 1.0
O C:HOH1102 1.9 50.8 1.0
O C:HOH1232 2.0 57.4 1.0
O2G C:ANP1001 2.4 26.2 1.0
O C:HOH1258 3.4 46.2 1.0
PG C:ANP1001 3.6 22.4 1.0
O1G C:ANP1001 3.8 21.7 1.0
O C:HOH1136 3.9 32.2 1.0
OE1 C:GLU532 4.0 34.1 1.0
O C:HOH1106 4.3 21.4 1.0
NZ C:LYS796 4.3 50.6 1.0
N3B C:ANP1001 4.4 20.5 1.0
O1B C:ANP1001 4.6 20.4 1.0
OE2 C:GLU532 4.6 35.8 1.0
CD C:GLU532 4.7 34.1 1.0
O C:HOH1213 4.7 40.5 1.0
O3G C:ANP1001 4.8 21.0 1.0

Magnesium binding site 6 out of 8 in 5xih

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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 5


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

b:22.1
occ:1.00
 O3G C:ANP1001 1.9 21.0 1.0
O2B C:ANP1001 2.0 19.0 1.0
O C:HOH1144 2.0 16.5 1.0
O C:HOH1162 2.1 23.3 1.0
O C:HOH1106 2.1 21.4 1.0
O C:HOH1116 2.2 18.0 1.0
PG C:ANP1001 3.1 22.4 1.0
PB C:ANP1001 3.3 19.9 1.0
O2G C:ANP1001 3.4 26.2 1.0
N3B C:ANP1001 3.7 20.5 1.0
NH1 C:ARG470 3.7 13.4 1.0
NH1 C:ARG481 3.9 22.4 1.0
O C:HOH1213 4.0 40.5 1.0
OE2 C:GLU472 4.1 22.6 1.0
O3A C:ANP1001 4.1 21.4 1.0
OE2 C:GLU418 4.2 23.7 1.0
OE1 C:GLU472 4.2 24.4 1.0
OE1 C:GLU418 4.3 20.1 1.0
O1G C:ANP1001 4.3 21.7 1.0
O C:HOH1185 4.3 39.6 1.0
N08 C:86U1004 4.4 23.6 0.5
O1B C:ANP1001 4.4 20.4 1.0
N08 C:86U1004 4.4 16.4 0.5
N7 C:ANP1001 4.5 20.8 1.0
CD C:GLU472 4.6 22.2 1.0
CD C:GLU418 4.7 22.3 1.0
CD C:ARG470 4.7 14.3 1.0
C09 C:86U1004 4.8 16.1 0.5
C09 C:86U1004 4.9 24.4 0.5
CZ C:ARG470 4.9 15.4 1.0

Magnesium binding site 7 out of 8 in 5xih

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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 5


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

b:42.1
occ:1.00
 O D:HOH1155 1.4 61.5 1.0
O D:HOH1201 2.0 47.0 1.0
O D:HOH1215 2.1 38.8 1.0
O D:HOH1226 2.1 40.8 1.0
O D:HOH1227 2.2 50.0 1.0
O2G D:ANP1001 2.3 25.9 1.0
PG D:ANP1001 3.6 24.3 1.0
O1G D:ANP1001 3.9 27.2 1.0
O D:HOH1101 4.0 24.2 1.0
NZ D:LYS474 4.0 27.8 1.0
N3B D:ANP1001 4.2 22.2 1.0
OE1 D:GLU532 4.5 35.7 1.0
O3G D:ANP1001 4.8 24.1 1.0
O1B D:ANP1001 4.8 23.6 1.0
PB D:ANP1001 5.0 23.7 1.0
OE2 D:GLU532 5.0 39.6 1.0

Magnesium binding site 8 out of 8 in 5xih

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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 5


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

b:23.6
occ:1.00
 O2B D:ANP1001 1.9 21.1 1.0
O D:HOH1129 2.0 22.2 1.0
O D:HOH1141 2.0 20.4 1.0
O D:HOH1123 2.1 14.0 1.0
O3G D:ANP1001 2.1 24.1 1.0
O D:HOH1101 2.2 24.2 1.0
PG D:ANP1001 3.2 24.3 1.0
PB D:ANP1001 3.2 23.7 1.0
O2G D:ANP1001 3.4 25.9 1.0
N3B D:ANP1001 3.7 22.2 1.0
NH1 D:ARG470 3.9 17.5 1.0
NZ D:LYS474 3.9 27.8 1.0
NH1 D:ARG481 4.0 23.0 1.0
O3A D:ANP1001 4.0 22.8 1.0
OE1 D:GLU418 4.1 25.0 1.0
OE2 D:GLU418 4.1 27.0 1.0
OE1 D:GLU472 4.2 22.9 1.0
OE2 D:GLU472 4.3 20.7 1.0
O1B D:ANP1001 4.3 23.6 1.0
N08 D:86U1004 4.4 17.9 0.5
N7 D:ANP1001 4.5 19.9 1.0
N08 D:86U1004 4.5 26.8 0.5
O1G D:ANP1001 4.5 27.2 1.0
CD D:GLU418 4.6 25.5 1.0
CE D:LYS474 4.6 29.2 1.0
CD D:GLU472 4.7 22.1 1.0
CD D:ARG470 4.7 17.5 1.0
C09 D:86U1004 4.7 18.0 0.5
C8 D:ANP1001 4.9 19.8 1.0
CZ D:ARG470 5.0 17.9 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 09:24:25 2024

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