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Bromine in PDB 6wqt: Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123

Enzymatic activity of Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123

All present enzymatic activity of Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123:
6.1.1.10;

Protein crystallography data

The structure of Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123, PDB code: 6wqt was solved by G.F.Mercaldi, C.E.Benedetti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.24 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.335, 84.478, 96.268, 90, 90, 90
R / Rfree (%) 20.2 / 23.1

Other elements in 6wqt:

The structure of Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123 (pdb code 6wqt). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123, PDB code: 6wqt:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 6wqt

Go back to Bromine Binding Sites List in 6wqt
Bromine binding site 1 out of 2 in the Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br602

b:56.3
occ:1.00
BR1 A:U81602 0.0 56.3 1.0
C6 A:U81602 1.9 54.0 1.0
C5 A:U81602 2.9 42.5 1.0
C7 A:U81602 2.9 45.4 1.0
CE3 A:TRP253 3.3 37.1 1.0
CZ3 A:TRP253 3.4 42.5 1.0
CZ A:PHE298 3.8 39.4 1.0
CG2 A:VAL252 3.8 42.6 1.0
CE2 A:PHE298 3.9 43.7 1.0
CE1 A:PHE298 3.9 40.1 1.0
CD2 A:PHE298 4.0 37.3 1.0
CD1 A:PHE298 4.1 38.5 1.0
CG A:PHE298 4.1 34.5 1.0
C4 A:U81602 4.2 43.0 1.0
C8 A:U81602 4.2 44.4 1.0
CG1 A:VAL252 4.4 44.0 1.0
O A:VAL252 4.5 31.5 1.0
CA A:TRP253 4.5 33.3 1.0
CD2 A:TRP253 4.6 37.9 1.0
C A:VAL252 4.6 29.2 1.0
CH2 A:TRP253 4.7 43.1 1.0
C3 A:U81602 4.7 40.5 1.0
CB A:ALA256 4.7 27.5 1.0
CB A:VAL252 4.7 37.7 1.0
N A:TRP253 4.7 31.2 1.0
CB A:PHE298 5.0 32.3 1.0

Bromine binding site 2 out of 2 in 6wqt

Go back to Bromine Binding Sites List in 6wqt
Bromine binding site 2 out of 2 in the Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Xanthomonas Citri Methionyl-Trna Synthetase in Complex with REP3123 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br602

b:42.4
occ:1.00
BR2 A:U81602 0.0 42.4 1.0
C4 A:U81602 1.9 43.0 1.0
C5 A:U81602 2.9 42.5 1.0
C3 A:U81602 2.9 40.5 1.0
O1 A:U81602 3.0 39.3 1.0
OH A:TYR260 3.1 27.0 1.0
N A:LEU11 3.6 26.3 1.0
CZ A:TYR260 3.8 28.6 1.0
CE1 A:HIS299 3.8 28.2 1.0
NE2 A:HIS299 3.9 22.8 1.0
CA A:ALA10 4.0 25.4 1.0
CG A:LEU11 4.1 27.5 1.0
C6 A:U81602 4.2 54.0 1.0
CB A:ALA10 4.2 24.9 1.0
C8 A:U81602 4.2 44.4 1.0
CE1 A:TYR260 4.3 25.5 1.0
C A:ALA10 4.3 24.4 1.0
CB A:LEU11 4.4 24.9 1.0
C2 A:U81602 4.5 39.8 1.0
CD1 A:ILE295 4.5 32.6 1.0
CE2 A:TYR260 4.5 26.0 1.0
CA A:LEU11 4.6 26.7 1.0
C7 A:U81602 4.7 45.4 1.0
O A:LEU11 5.0 28.2 1.0
CD1 A:LEU11 5.0 28.2 1.0

Reference:

G.F.Mercaldi, M.De Oliveira Andrade, J.De Lima Zanella, A.T.Cordeiro, C.E.Benedetti. Molecular Basis For Diaryldiamine Selectivity and Competition with Trna in A Type-2METHIONYL-Trna Synthetase From A Gram-Negative Bacterium J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Sat Jul 10 09:52:11 2021

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