Atomistry » Magnesium » PDB 5xfa-5xlg » 5xih
Atomistry »
  Magnesium »
    PDB 5xfa-5xlg »
      5xih »

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

Go back to Magnesium Binding Sites List in 5xih
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

Go back to Magnesium Binding Sites List in 5xih
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

Go back to Magnesium Binding Sites List in 5xih
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

Go back to Magnesium Binding Sites List in 5xih
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

Go back to Magnesium Binding Sites List in 5xih
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

Go back to Magnesium Binding Sites List in 5xih
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

Go back to Magnesium Binding Sites List in 5xih
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

Go back to Magnesium Binding Sites List in 5xih
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: Tue Aug 12 23:35:41 2025

Last articles

Na in 3LJQ
Na in 3LJW
Na in 3LDE
Na in 3LHC
Na in 3LD4
Na in 3LBG
Na in 3KZW
Na in 3L88
Na in 3LA1
Na in 3L9G
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy