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Bromine in PDB 4yre: Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145)

Enzymatic activity of Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145)

All present enzymatic activity of Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145):
6.1.1.21;

Protein crystallography data

The structure of Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145), PDB code: 4yre was solved by C.-Y.Koh, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.76 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.849, 118.609, 93.516, 90.00, 91.32, 90.00
R / Rfree (%) 20 / 22.6

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145) (pdb code 4yre). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145), PDB code: 4yre:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 4yre

Go back to Bromine Binding Sites List in 4yre
Bromine binding site 1 out of 4 in the Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145)


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 T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br502

b:35.5
occ:0.85
 BR A:4HR502 0.0 35.5 0.8
C A:4HR502 0.5 27.4 0.1
O A:4HR502 1.0 27.0 0.1
C1 A:4HR502 1.8 27.8 0.1
C6 A:4HR502 1.9 34.4 0.8
C2 A:4HR502 2.6 27.9 0.1
C5 A:4HR502 2.8 34.7 0.8
C1 A:4HR502 2.9 34.8 0.8
C6 A:4HR502 3.0 28.1 0.1
C A:4HR502 3.2 36.1 0.8
NH1 A:ARG165 3.3 42.7 1.0
N A:GLU167 3.4 25.4 1.0
O A:GLU167 3.5 22.7 1.0
NE A:ARG156 3.5 35.2 1.0
C A:GLU167 3.6 22.4 1.0
BR A:4HR502 3.6 28.8 0.1
CB A:HIS168 3.8 21.1 1.0
CG A:HIS168 3.9 21.0 1.0
CB A:ARG165 3.9 37.4 1.0
O A:ARG165 3.9 33.9 1.0
C A:ARG166 3.9 27.1 1.0
N A:HIS168 3.9 21.2 1.0
CA A:GLU167 3.9 23.7 1.0
CD A:ARG156 4.0 34.4 1.0
CZ A:ARG156 4.0 35.7 1.0
C3 A:4HR502 4.0 28.2 0.1
C A:ARG165 4.1 34.3 1.0
CD2 A:HIS168 4.1 21.2 1.0
C4 A:4HR502 4.1 35.3 0.8
C2 A:4HR502 4.1 35.8 0.8
CZ A:ARG165 4.2 41.7 1.0
C5 A:4HR502 4.2 28.2 0.1
CG A:ARG156 4.2 33.8 1.0
NH1 A:ARG156 4.3 36.2 1.0
N A:ARG166 4.3 31.5 1.0
CA A:ARG166 4.4 30.0 1.0
CA A:HIS168 4.5 20.4 1.0
O A:ARG166 4.5 26.0 1.0
ND1 A:HIS168 4.5 21.5 1.0
C4 A:4HR502 4.6 28.2 0.1
O A:4HR502 4.6 37.4 0.8
NH2 A:ARG156 4.6 36.2 1.0
C3 A:4HR502 4.6 35.3 0.8
CA A:ARG165 4.7 37.1 1.0
NE2 A:HIS168 4.8 21.4 1.0
NE A:ARG165 4.8 41.1 1.0
CD A:ARG165 4.8 39.7 1.0
NH2 A:ARG165 4.9 42.5 1.0
O A:CYS154 5.0 21.2 1.0

Bromine binding site 2 out of 4 in 4yre

Go back to Bromine Binding Sites List in 4yre
Bromine binding site 2 out of 4 in the Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145)


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 T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br502

b:28.8
occ:0.15
 BR A:4HR502 0.0 28.8 0.1
C4 A:4HR502 0.6 35.3 0.8
C5 A:4HR502 0.9 34.7 0.8
C3 A:4HR502 1.8 35.3 0.8
C6 A:4HR502 1.9 28.1 0.1
C6 A:4HR502 2.0 34.4 0.8
C2 A:4HR502 2.6 35.8 0.8
C1 A:4HR502 2.7 34.8 0.8
C5 A:4HR502 2.8 28.2 0.1
C1 A:4HR502 2.9 27.8 0.1
C A:4HR502 3.2 27.4 0.1
CD2 A:HIS168 3.4 21.2 1.0
C A:TRP155 3.4 28.6 1.0
O A:TRP155 3.5 29.5 1.0
NE2 A:HIS168 3.5 21.4 1.0
O A:CYS154 3.5 21.2 1.0
N A:TRP155 3.6 23.9 1.0
C A:CYS154 3.6 21.9 1.0
BR A:4HR502 3.6 35.5 0.8
CA A:TRP155 3.8 26.1 1.0
N A:ARG156 3.9 31.0 1.0
CB A:ARG156 4.0 33.6 1.0
O A:PRO125 4.1 20.9 1.0
O A:HOH612 4.1 27.9 1.0
C4 A:4HR502 4.1 28.2 0.1
C2 A:4HR502 4.1 27.9 0.1
CG A:ARG156 4.1 33.8 1.0
CB A:CYS154 4.2 19.9 1.0
C A:4HR502 4.2 36.1 0.8
CD A:ARG156 4.3 34.4 1.0
CG A:HIS168 4.3 21.0 1.0
CE1 A:HIS168 4.5 21.2 1.0
CA A:CYS154 4.5 20.3 1.0
CA A:ARG156 4.6 33.5 1.0
O A:4HR502 4.6 27.0 0.1
C3 A:4HR502 4.6 28.2 0.1
O A:ARG166 4.8 26.0 1.0
N A:HIS168 4.8 21.2 1.0
C A:PRO125 4.9 21.1 1.0
CA A:PRO125 4.9 22.8 1.0
ND1 A:HIS168 4.9 21.5 1.0

Bromine binding site 3 out of 4 in 4yre

Go back to Bromine Binding Sites List in 4yre
Bromine binding site 3 out of 4 in the Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br502

b:31.9
occ:0.85
 BR B:4HR502 0.0 31.9 0.8
C B:4HR502 0.5 25.9 0.1
O B:4HR502 0.9 25.8 0.1
C1 B:4HR502 1.7 26.2 0.1
C6 B:4HR502 1.9 32.7 0.8
C2 B:4HR502 2.4 26.1 0.1
C5 B:4HR502 2.8 32.7 0.8
C1 B:4HR502 2.9 32.2 0.8
C6 B:4HR502 2.9 26.3 0.1
C B:4HR502 3.2 33.2 0.8
NH2 B:ARG165 3.3 37.6 1.0
C B:GLU167 3.5 21.5 1.0
N B:GLU167 3.5 23.9 1.0
O B:GLU167 3.5 21.3 1.0
NE B:ARG156 3.6 35.6 1.0
BR B:4HR502 3.7 27.0 0.1
C3 B:4HR502 3.8 26.4 0.1
CB B:HIS168 3.8 20.6 1.0
CA B:GLU167 3.8 22.6 1.0
N B:HIS168 3.9 20.5 1.0
CG B:HIS168 3.9 20.8 1.0
O B:ARG165 3.9 32.4 1.0
CB B:ARG165 3.9 34.1 1.0
C B:ARG166 3.9 25.7 1.0
CD B:ARG156 4.0 34.3 1.0
CD2 B:HIS168 4.1 21.1 1.0
CZ B:ARG156 4.1 37.4 1.0
C B:ARG165 4.1 31.9 1.0
C4 B:4HR502 4.1 33.2 0.8
C5 B:4HR502 4.1 26.4 0.1
C2 B:4HR502 4.1 33.1 0.8
CZ B:ARG165 4.1 37.7 1.0
CG B:ARG156 4.2 33.6 1.0
N B:ARG166 4.4 29.2 1.0
NH2 B:ARG156 4.4 38.1 1.0
CA B:ARG166 4.4 28.2 1.0
CA B:HIS168 4.5 19.8 1.0
C4 B:4HR502 4.5 26.3 0.1
O B:ARG166 4.5 25.0 1.0
ND1 B:HIS168 4.5 21.0 1.0
O B:4HR502 4.6 35.0 0.8
C3 B:4HR502 4.6 33.1 0.8
CA B:ARG165 4.7 33.8 1.0
NH1 B:ARG156 4.8 38.5 1.0
NE2 B:HIS168 4.8 21.1 1.0
NH1 B:ARG165 4.8 38.2 1.0
NE B:ARG165 4.8 37.2 1.0
CD B:ARG165 4.9 35.4 1.0
O B:CYS154 4.9 21.3 1.0

Bromine binding site 4 out of 4 in 4yre

Go back to Bromine Binding Sites List in 4yre
Bromine binding site 4 out of 4 in the Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of T. Cruzi Histidyl-Trna Synthetase in Complex with (2-Bromophenyl)Methanol (Chem 145) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br502

b:27.0
occ:0.15
 BR B:4HR502 0.0 27.0 0.1
C4 B:4HR502 0.7 33.2 0.8
C5 B:4HR502 1.0 32.7 0.8
C6 B:4HR502 1.9 26.3 0.1
C3 B:4HR502 1.9 33.1 0.8
C6 B:4HR502 2.1 32.7 0.8
C2 B:4HR502 2.7 33.1 0.8
C1 B:4HR502 2.8 32.2 0.8
C5 B:4HR502 2.8 26.4 0.1
C1 B:4HR502 2.9 26.2 0.1
C B:4HR502 3.2 25.9 0.1
C B:TRP155 3.4 27.1 1.0
O B:TRP155 3.4 26.8 1.0
CD2 B:HIS168 3.4 21.1 1.0
O B:CYS154 3.5 21.3 1.0
N B:TRP155 3.5 22.9 1.0
C B:CYS154 3.5 21.8 1.0
NE2 B:HIS168 3.5 21.1 1.0
CA B:TRP155 3.7 24.6 1.0
BR B:4HR502 3.7 31.9 0.8
N B:ARG156 3.9 29.7 1.0
O B:PRO125 4.0 19.4 1.0
O B:HOH605 4.1 21.9 1.0
CB B:ARG156 4.1 32.8 1.0
CB B:CYS154 4.1 20.1 1.0
C4 B:4HR502 4.1 26.3 0.1
C2 B:4HR502 4.1 26.1 0.1
CG B:ARG156 4.2 33.6 1.0
C B:4HR502 4.3 33.2 0.8
CG B:HIS168 4.4 20.8 1.0
CD B:ARG156 4.4 34.3 1.0
CA B:CYS154 4.4 20.3 1.0
CE1 B:HIS168 4.5 20.9 1.0
CA B:ARG156 4.6 32.4 1.0
O B:4HR502 4.6 25.8 0.1
C3 B:4HR502 4.6 26.4 0.1
C B:PRO125 4.8 19.9 1.0
CA B:PRO125 4.8 21.4 1.0
O B:ARG166 4.8 25.0 1.0
N B:HIS168 4.8 20.5 1.0
ND1 B:HIS168 5.0 21.0 1.0
O B:HOH695 5.0 31.6 1.0

Reference:

C.Y.Koh, L.K.Siddaramaiah, R.M.Ranade, J.Nguyen, T.Jian, Z.Zhang, J.R.Gillespie, F.S.Buckner, C.L.Verlinde, E.Fan, W.G.Hol. A Binding Hotspot in Trypanosoma Cruzi Histidyl-Trna Synthetase Revealed By Fragment-Based Crystallographic Cocktail Screens. Acta Crystallogr. D Biol. V. 71 1684 2015CRYSTALLOGR..
ISSN: ESSN 1399-0047
PubMed: 26249349
DOI: 10.1107/S1399004715007683
Page generated: Wed Jul 10 23:06:34 2024

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