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Bromine 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:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 2 binding sites of Bromine 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 Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 4ydq

Go back to Bromine Binding Sites List in 4ydq
Bromine 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 Bromine with other atoms in the Br 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:Br802

b:53.2
occ:0.91
 BR1 A:HFG802 0.0 53.2 0.9
C7 A:HFG802 1.9 38.0 0.9
C8 A:HFG802 2.9 29.8 0.9
C6 A:HFG802 2.9 36.1 0.9
CL1 A:HFG802 3.3 44.2 0.9
O A:PHE335 3.3 44.4 1.0
CB A:PRO358 3.5 26.5 1.0
CG2 A:VAL339 3.5 31.5 1.0
CG A:PRO358 3.7 28.2 1.0
CB A:PHE335 3.8 46.5 1.0
CB A:GLU338 3.8 37.2 1.0
N A:VAL339 3.8 32.8 1.0
C A:GLU338 3.9 32.0 1.0
C A:PHE335 4.1 48.5 1.0
C9 A:HFG802 4.1 36.1 0.9
CA A:VAL339 4.2 31.7 1.0
O A:GLU338 4.2 33.9 1.0
C5 A:HFG802 4.2 35.2 0.9
CA A:GLU338 4.3 34.3 1.0
OE1 A:GLU338 4.5 39.1 1.0
CA A:PHE335 4.5 54.2 1.0
CB A:VAL339 4.5 31.2 1.0
CG A:PHE335 4.7 48.0 1.0
C10 A:HFG802 4.7 34.5 0.9
N A:GLU338 4.7 41.8 1.0
CG A:ARG390 4.8 27.2 1.0
CA A:PRO358 5.0 24.9 1.0

Bromine binding site 2 out of 2 in 4ydq

Go back to Bromine Binding Sites List in 4ydq
Bromine 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 Bromine with other atoms in the Br 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:Br802

b:77.9
occ:0.88
 BR1 B:HFG802 0.0 77.9 0.9
C7 B:HFG802 1.9 48.0 0.9
C8 B:HFG802 2.9 38.0 0.9
C6 B:HFG802 2.9 43.8 0.9
CL1 B:HFG802 3.2 43.6 0.9
O B:PHE335 3.3 72.5 1.0
CG2 B:VAL339 3.6 44.6 1.0
CB B:PRO358 3.7 32.6 1.0
CB B:GLU338 3.8 61.3 1.0
CG B:PRO358 4.0 32.4 1.0
C9 B:HFG802 4.1 37.9 0.9
C5 B:HFG802 4.1 38.2 0.9
N B:VAL339 4.1 45.1 1.0
C B:PHE335 4.2 82.0 1.0
CB B:PHE335 4.2 83.0 1.0
C B:GLU338 4.2 50.7 1.0
CB B:VAL339 4.4 46.5 1.0
CA B:GLU338 4.4 56.7 1.0
CA B:VAL339 4.6 39.0 1.0
CA B:PHE335 4.6 86.1 1.0
C10 B:HFG802 4.6 38.7 0.9
O B:GLU338 4.6 48.6 1.0
OE1 B:GLU338 4.7 56.2 1.0
N B:GLU338 4.8 59.4 1.0
CG B:ARG390 4.8 40.0 1.0
CG B:GLU338 4.9 61.5 1.0
CD1 B:PHE335 5.0 72.0 1.0
CD B:GLU338 5.0 69.5 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: Wed Jul 10 23:05:17 2024

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