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Magnesium in PDB 4ydq: Crystal Structure of Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp

Enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp

All present enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp, PDB code: 4ydq was solved by V.Jain, M.Yogavel, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.82 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.026, 88.929, 86.295, 90.00, 96.71, 90.00
R / Rfree (%) 18.4 / 23.2

Other elements in 4ydq:

The structure of Crystal Structure of Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp (pdb code 4ydq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp, PDB code: 4ydq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4ydq

Go back to Magnesium Binding Sites List in 4ydq
Magnesium binding site 1 out of 2 in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp


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 Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:45.7
occ:1.00
 O1G A:ANP801 1.9 46.9 1.0
O A:HOH1070 1.9 46.5 1.0
O A:HOH1066 2.0 41.0 1.0
O2B A:ANP801 2.2 43.8 1.0
O A:HOH1065 2.3 38.3 1.0
O A:HOH940 2.4 29.8 1.0
PG A:ANP801 3.3 57.9 1.0
PB A:ANP801 3.4 41.3 1.0
N3B A:ANP801 3.8 0.6 1.0
NZ A:LYS394 3.9 51.0 1.0
O1B A:ANP801 4.0 44.9 1.0
NH1 A:ARG390 4.0 27.9 1.0
O3G A:ANP801 4.1 40.0 1.0
OE1 A:GLU338 4.1 39.1 1.0
N1 A:HFG802 4.1 32.0 0.9
NH1 A:ARG401 4.3 33.5 1.0
OE2 A:GLU392 4.4 30.6 1.0
O2G A:ANP801 4.4 44.3 1.0
OE2 A:GLU338 4.4 43.8 1.0
OE1 A:GLU392 4.5 37.9 1.0
C2 A:HFG802 4.5 35.4 0.9
O3A A:ANP801 4.6 40.7 1.0
N7 A:ANP801 4.7 30.6 1.0
CD A:GLU338 4.7 41.8 1.0
CE A:LYS394 4.9 51.5 1.0
CD A:ARG390 4.9 29.1 1.0
CD A:GLU392 4.9 35.1 1.0
CE1 A:PHE335 4.9 41.3 1.0

Magnesium binding site 2 out of 2 in 4ydq

Go back to Magnesium Binding Sites List in 4ydq
Magnesium binding site 2 out of 2 in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp


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 Prolyl-Trna Synthetase (Prs) From Plasmodium Falciparum in Complex with Halofuginone and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:56.1
occ:1.00
 O2G B:ANP801 2.1 62.5 0.9
O B:HOH1012 2.3 44.6 1.0
O B:HOH1023 2.5 62.8 1.0
N1 B:HFG802 3.3 36.9 0.9
OE1 B:GLU338 3.5 56.2 1.0
PG B:ANP801 3.7 76.3 0.9
O2B B:ANP801 3.8 46.8 0.9
NH1 B:ARG390 3.8 31.6 1.0
CD B:ARG390 4.0 40.0 1.0
C2 B:HFG802 4.0 39.1 0.9
OE2 B:GLU338 4.3 71.1 1.0
O B:HOH1034 4.3 48.2 0.8
CD B:GLU338 4.3 69.5 1.0
C9 B:HFG802 4.4 37.9 0.9
C8 B:HFG802 4.5 38.0 0.9
N3B B:ANP801 4.5 50.3 0.9
O1G B:ANP801 4.5 73.9 0.9
PB B:ANP801 4.6 42.3 0.9
O3G B:ANP801 4.6 70.5 0.9
CZ B:ARG390 4.6 37.9 1.0
OE1 B:GLU392 4.7 75.0 1.0
NE B:ARG390 4.7 31.3 1.0
O3A B:ANP801 4.7 44.2 0.9
N7 B:ANP801 4.9 39.8 0.9
NH1 B:ARG401 5.0 53.6 1.0
CG B:ARG390 5.0 40.0 1.0

Reference:

V.Jain, M.Yogavel, Y.Oshima, H.Kikuchi, B.Touquet, M.A.Hakimi, A.Sharma. Structure of Prolyl-Trna Synthetase-Halofuginone Complex Provides Basis For Development of Drugs Against Malaria and Toxoplasmosis Structure V. 23 819 2015.
ISSN: ISSN 0969-2126
PubMed: 25817387
DOI: 10.1016/J.STR.2015.02.011
Page generated: Tue Aug 12 04:10:20 2025

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