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Magnesium in PDB 5xik: Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Tetrahydro Quinazolinone Febrifugine

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

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

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Tetrahydro Quinazolinone Febrifugine, PDB code: 5xik 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) 43.76 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.644, 90.140, 93.201, 89.46, 80.34, 76.07
R / Rfree (%) 18.5 / 24.4

Other elements in 5xik:

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

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 Tetrahydro Quinazolinone Febrifugine (pdb code 5xik). 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 Tetrahydro Quinazolinone Febrifugine, PDB code: 5xik:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5xik

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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 Tetrahydro Quinazolinone Febrifugine


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 Tetrahydro Quinazolinone Febrifugine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:24.8
occ:1.00
 O3G A:ANP1001 1.7 21.0 1.0
O A:HOH1112 2.0 24.4 1.0
O A:HOH1113 2.0 25.9 1.0
O A:HOH1103 2.2 16.0 1.0
O A:HOH1106 2.2 20.8 1.0
O2B A:ANP1001 2.3 21.8 1.0
PG A:ANP1001 3.1 21.2 1.0
PB A:ANP1001 3.6 20.9 1.0
NH1 A:ARG470 3.6 31.7 1.0
O2G A:ANP1001 3.6 19.7 1.0
N3B A:ANP1001 3.8 19.7 1.0
OE2 A:GLU472 4.1 26.7 1.0
OE1 A:GLU472 4.1 24.1 1.0
OE2 A:GLU418 4.1 36.5 1.0
OE1 A:GLU418 4.2 33.1 1.0
O1G A:ANP1001 4.2 18.7 1.0
NH1 A:ARG481 4.3 27.7 1.0
O3A A:ANP1001 4.3 24.3 1.0
N10 A:87C1004 4.4 30.2 1.0
CD A:GLU472 4.6 26.1 1.0
CD A:GLU418 4.6 30.8 1.0
N7 A:ANP1001 4.7 23.2 1.0
O1B A:ANP1001 4.7 18.9 1.0
C09 A:87C1004 4.7 28.2 1.0
CD A:ARG470 4.7 28.8 1.0
CZ A:ARG470 4.8 28.7 1.0

Magnesium binding site 2 out of 8 in 5xik

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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 Tetrahydro Quinazolinone Febrifugine


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 Tetrahydro Quinazolinone Febrifugine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:30.2
occ:1.00
 O A:HOH1151 1.6 34.0 1.0
O A:HOH1101 1.9 26.3 1.0
O A:HOH1120 2.0 32.0 1.0
O2G A:ANP1001 2.2 19.7 1.0
O A:HOH1150 2.2 34.4 1.0
O A:HOH1149 2.9 45.2 1.0
PG A:ANP1001 3.6 21.2 1.0
O1G A:ANP1001 4.0 18.7 1.0
O A:HOH1103 4.1 16.0 1.0
OE1 A:GLU532 4.1 38.2 1.0
O1B A:ANP1001 4.2 18.9 1.0
N3B A:ANP1001 4.3 19.7 1.0
NZ A:LYS796 4.3 48.6 1.0
PB A:ANP1001 4.6 20.9 1.0
O3G A:ANP1001 4.6 21.0 1.0
O2B A:ANP1001 4.8 21.8 1.0
CD A:GLU532 4.9 39.3 1.0

Magnesium binding site 3 out of 8 in 5xik

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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 Tetrahydro Quinazolinone Febrifugine


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 Tetrahydro Quinazolinone Febrifugine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:28.1
occ:1.00
 O3G B:ANP1001 1.8 26.5 1.0
O B:HOH1117 1.8 16.6 1.0
O B:HOH1101 1.9 14.7 1.0
O B:HOH1114 2.0 21.6 1.0
O2B B:ANP1001 2.0 25.9 1.0
O B:HOH1108 2.2 20.4 1.0
PG B:ANP1001 3.1 28.0 1.0
PB B:ANP1001 3.2 27.0 1.0
N3B B:ANP1001 3.5 26.3 1.0
O2G B:ANP1001 3.6 28.6 1.0
NH1 B:ARG470 3.7 29.7 1.0
O3A B:ANP1001 4.0 27.3 1.0
OE1 B:GLU418 4.1 34.6 1.0
OE2 B:GLU472 4.1 27.1 1.0
OE1 B:GLU472 4.2 28.7 1.0
O B:HOH1132 4.2 44.5 1.0
O1G B:ANP1001 4.2 25.0 1.0
NH1 B:ARG481 4.3 23.0 1.0
OE2 B:GLU418 4.3 36.1 1.0
O1B B:ANP1001 4.3 24.7 1.0
N10 B:87C1004 4.3 26.0 1.0
N7 B:ANP1001 4.5 23.1 1.0
CD B:GLU472 4.6 32.2 1.0
C09 B:87C1004 4.6 25.1 1.0
CD B:GLU418 4.6 35.3 1.0
CD B:ARG470 4.7 25.7 1.0
CZ B:ARG470 4.7 27.2 1.0

Magnesium binding site 4 out of 8 in 5xik

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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 Tetrahydro Quinazolinone Febrifugine


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 Tetrahydro Quinazolinone Febrifugine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:32.9
occ:1.00
 O B:HOH1116 1.7 35.5 1.0
O B:HOH1104 1.9 38.0 1.0
O B:HOH1111 2.0 34.5 1.0
O B:HOH1128 2.1 38.3 1.0
O B:HOH1136 2.3 31.6 1.0
O2G B:ANP1001 2.3 28.6 1.0
PG B:ANP1001 3.8 28.0 1.0
OE1 B:GLU532 3.9 37.7 1.0
NZ B:LYS796 4.2 62.1 1.0
O B:HOH1101 4.3 14.7 1.0
O1G B:ANP1001 4.3 25.0 1.0
O B:HOH1110 4.5 31.4 1.0
O1B B:ANP1001 4.5 24.7 1.0
N3B B:ANP1001 4.6 26.3 1.0
O3G B:ANP1001 4.8 26.5 1.0
PB B:ANP1001 4.9 27.0 1.0
CD B:GLU532 5.0 46.6 1.0

Magnesium binding site 5 out of 8 in 5xik

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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 Tetrahydro Quinazolinone Febrifugine


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 Tetrahydro Quinazolinone Febrifugine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:24.0
occ:1.00
 O2B C:ANP1001 1.8 21.7 1.0
O3G C:ANP1001 1.8 26.3 1.0
O C:HOH1106 1.9 23.4 1.0
O C:HOH1117 2.0 18.8 1.0
O C:HOH1102 2.1 29.0 1.0
O C:HOH1105 2.3 14.9 1.0
PG C:ANP1001 3.1 26.5 1.0
PB C:ANP1001 3.1 24.0 1.0
N3B C:ANP1001 3.6 22.3 1.0
O2G C:ANP1001 3.6 29.5 1.0
NZ C:LYS474 3.8 29.9 1.0
NH1 C:ARG470 3.9 27.5 1.0
NH1 C:ARG481 3.9 26.5 1.0
O1B C:ANP1001 4.0 22.4 1.0
OE2 C:GLU472 4.1 25.5 1.0
O3A C:ANP1001 4.2 23.8 1.0
OE1 C:GLU418 4.2 40.7 1.0
O1G C:ANP1001 4.3 25.8 1.0
OE2 C:GLU418 4.3 39.6 1.0
OE1 C:GLU472 4.4 25.3 1.0
N10 C:87C1004 4.4 23.2 1.0
N7 C:ANP1001 4.5 26.1 1.0
CE C:LYS474 4.7 29.8 1.0
CD C:GLU472 4.7 27.3 1.0
C09 C:87C1004 4.7 22.6 1.0
CD C:GLU418 4.7 39.1 1.0
CZ C:ARG470 5.0 26.2 1.0
CD C:ARG470 5.0 26.0 1.0

Magnesium binding site 6 out of 8 in 5xik

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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 Tetrahydro Quinazolinone Febrifugine


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 Tetrahydro Quinazolinone Febrifugine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:43.1
occ:1.00
 O C:HOH1120 1.8 40.7 1.0
O C:HOH1140 1.9 48.1 1.0
O C:HOH1113 2.2 32.1 1.0
O C:HOH1133 2.2 32.5 1.0
O C:HOH1128 2.3 38.2 1.0
O2G C:ANP1001 2.3 29.5 1.0
PG C:ANP1001 3.8 26.5 1.0
OE1 C:GLU532 4.1 51.0 1.0
O C:HOH1109 4.1 14.0 0.5
NZ C:LYS796 4.3 49.6 1.0
O C:HOH1117 4.3 18.8 1.0
O1G C:ANP1001 4.4 25.8 1.0
N3B C:ANP1001 4.4 22.3 1.0
NZ C:LYS474 4.5 29.9 1.0
O C:HOH1109 4.7 11.1 0.5
O1B C:ANP1001 4.7 22.4 1.0
O3G C:ANP1001 4.8 26.3 1.0
CD C:GLU532 5.0 54.3 1.0

Magnesium binding site 7 out of 8 in 5xik

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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 Tetrahydro Quinazolinone Febrifugine


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 Tetrahydro Quinazolinone Febrifugine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:24.6
occ:1.00
 O3G D:ANP1001 1.7 25.2 1.0
O2B D:ANP1001 1.9 26.0 1.0
O D:HOH1101 2.1 24.5 1.0
O D:HOH1116 2.1 30.3 1.0
O D:HOH1109 2.1 18.6 1.0
O D:HOH1103 2.2 16.2 1.0
PG D:ANP1001 3.0 26.4 1.0
PB D:ANP1001 3.2 24.7 1.0
O2G D:ANP1001 3.4 25.2 1.0
N3B D:ANP1001 3.5 24.6 1.0
NH1 D:ARG470 3.7 18.5 1.0
NH1 D:ARG481 3.9 24.8 1.0
O D:HOH1130 4.0 34.9 1.0
O1B D:ANP1001 4.1 27.4 1.0
O1G D:ANP1001 4.1 24.2 1.0
O3A D:ANP1001 4.2 26.9 1.0
OE1 D:GLU418 4.3 35.4 1.0
OE2 D:GLU472 4.3 25.4 1.0
N10 D:87C1004 4.3 35.0 1.0
OE2 D:GLU418 4.3 35.0 1.0
OE1 D:GLU472 4.3 25.4 1.0
C09 D:87C1004 4.5 35.9 1.0
N7 D:ANP1001 4.6 27.2 1.0
CD D:GLU418 4.7 32.7 1.0
CD D:GLU472 4.8 26.8 1.0
CZ D:ARG470 4.8 18.9 1.0
CD D:ARG470 4.8 20.9 1.0

Magnesium binding site 8 out of 8 in 5xik

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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 Tetrahydro Quinazolinone Febrifugine


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 Tetrahydro Quinazolinone Febrifugine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:30.8
occ:1.00
 O D:HOH1112 1.9 29.4 1.0
O D:HOH1128 2.0 56.9 1.0
O D:HOH1137 2.1 56.0 1.0
O2G D:ANP1001 2.1 25.2 1.0
O D:HOH1139 2.1 43.6 1.0
O D:HOH1129 2.1 43.4 1.0
PG D:ANP1001 3.5 26.4 1.0
O D:HOH1101 3.7 24.5 1.0
O1G D:ANP1001 4.0 24.2 1.0
N3B D:ANP1001 4.1 24.6 1.0
O1B D:ANP1001 4.3 27.4 1.0
OE1 D:GLU532 4.5 47.9 1.0
O3G D:ANP1001 4.6 25.2 1.0
O D:HOH1130 4.6 34.9 1.0
PB D:ANP1001 4.7 24.7 1.0
OE2 D:GLU532 5.0 55.3 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 09:27:05 2024

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