Bromine in PDB 6d6d: The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13

The structure of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13, PDB code: 6d6d was solved by S.H.Dong, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.480, 64.200, 53.920, 90.00, 92.32, 90.00
R / Rfree (%)	22.8 / 27.4

The binding sites of Bromine atom in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13 (pdb code 6d6d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13, PDB code: 6d6d:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br300 b:13.2 occ:1.00 BR1 A:FY7300 0.0 13.2 1.0 C4 A:FY7300 1.9 12.7 1.0 C3 A:FY7300 2.8 13.2 1.0 C5 A:FY7300 2.8 12.5 1.0 NE1 A:TRP60 3.5 9.6 1.0 CG A:TYR64 3.6 7.9 1.0 CD2 A:TYR64 3.6 7.6 1.0 CB A:TYR64 3.7 8.4 1.0 CD2 A:TYR56 3.8 7.9 1.0 O19 A:FY7300 3.9 11.3 1.0 CD1 A:TRP60 3.9 9.7 1.0 O A:HOH443 4.0 16.9 1.0 CD1 A:LEU36 4.0 8.7 1.0 CA A:ARG61 4.1 10.5 1.0 CE2 A:TYR56 4.1 7.7 1.0 C2 A:FY7300 4.1 13.8 1.0 C6 A:FY7300 4.1 12.2 1.0 CG A:ARG61 4.2 11.9 1.0 CD1 A:TYR64 4.2 7.6 1.0 CE2 A:TYR64 4.2 7.3 1.0 CE2 A:TRP60 4.2 9.7 1.0 N A:ARG61 4.6 10.0 1.0 O A:TRP60 4.6 9.5 1.0 C1 A:FY7300 4.6 12.9 1.0 CB A:ARG61 4.7 11.2 1.0 CG A:TRP60 4.7 9.5 1.0 CE1 A:TYR64 4.7 7.3 1.0 CZ A:TYR64 4.8 7.2 1.0 C A:TRP60 4.8 9.7 1.0 CZ2 A:TRP60 4.8 9.8 1.0 O A:ARG61 4.9 10.3 1.0 CD2 A:TRP60 4.9 9.6 1.0 N16 A:FY7300 5.0 11.4 1.0 C A:ARG61 5.0 10.4 1.0

Bromine binding site 2 out of 4 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br300 b:18.4 occ:1.00 BR2 A:FY7300 0.0 18.4 1.0 C2 A:FY7300 1.9 13.8 1.0 C3 A:FY7300 2.8 13.2 1.0 C1 A:FY7300 2.9 12.9 1.0 O20 A:FY7300 3.1 12.1 1.0 O22 A:FY7300 3.2 12.2 1.0 C21 A:FY7300 3.3 12.0 1.0 O A:TYR47 3.7 14.7 1.0 CB A:TYR47 3.8 13.6 1.0 O A:HOH427 3.9 16.1 1.0 C4 A:FY7300 4.1 12.7 1.0 C6 A:FY7300 4.2 12.2 1.0 C A:TYR47 4.2 14.4 1.0 CD1 A:ILE52 4.2 10.8 1.0 CE1 A:TYR64 4.3 7.3 1.0 CA A:TYR47 4.4 14.1 1.0 C25 A:FY7300 4.4 11.6 1.0 N3 A:FY7300 4.4 12.1 1.0 C19 A:FY7300 4.4 11.8 1.0 CG A:TYR47 4.6 13.4 1.0 CD1 A:TYR47 4.6 13.2 1.0 O A:HOH443 4.7 16.9 1.0 C5 A:FY7300 4.7 12.5 1.0 C26 A:FY7300 4.8 11.6 1.0 CD1 A:TYR64 4.8 7.6 1.0 CG1 A:ILE52 4.9 10.6 1.0 CZ A:TYR64 4.9 7.2 1.0 OD1 A:ASP65 5.0 12.2 1.0

Bromine binding site 3 out of 4 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br300 b:18.0 occ:1.00 BR1 B:FY7300 0.0 18.0 1.0 C4 B:FY7300 1.9 19.5 1.0 C5 B:FY7300 2.8 19.2 1.0 C3 B:FY7300 2.9 21.0 1.0 NE1 B:TRP60 3.5 10.4 1.0 CG B:TYR64 3.6 14.8 1.0 CB B:TYR64 3.7 15.3 1.0 CD1 B:TRP60 3.7 10.6 1.0 CD2 B:TYR56 3.7 9.9 1.0 CD2 B:TYR64 3.8 14.7 1.0 O19 B:FY7300 3.8 17.0 1.0 O B:HOH418 3.9 19.2 1.0 CD1 B:LEU36 4.0 10.2 1.0 CA B:ARG61 4.0 12.9 1.0 CE2 B:TYR56 4.0 9.9 1.0 C6 B:FY7300 4.1 19.6 1.0 CD1 B:TYR64 4.2 14.8 1.0 C2 B:FY7300 4.2 22.5 1.0 CG B:ARG61 4.2 15.0 1.0 CE2 B:TRP60 4.3 10.5 1.0 O B:TRP60 4.4 10.9 1.0 N B:ARG61 4.4 11.8 1.0 CE2 B:TYR64 4.5 14.3 1.0 CB B:ARG61 4.6 13.7 1.0 CG B:TRP60 4.6 10.7 1.0 C B:TRP60 4.6 11.2 1.0 C1 B:FY7300 4.7 21.1 1.0 CE1 B:TYR64 4.8 14.9 1.0 CZ B:TYR64 4.9 14.6 1.0 O B:ARG61 4.9 13.4 1.0 CD2 B:TRP60 4.9 10.6 1.0 CG B:TYR56 4.9 10.2 1.0 C B:ARG61 5.0 13.3 1.0 CZ2 B:TRP60 5.0 10.6 1.0

Bromine binding site 4 out of 4 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br300 b:30.6 occ:1.00 BR2 B:FY7300 0.0 30.6 1.0 C2 B:FY7300 1.9 22.5 1.0 C3 B:FY7300 2.9 21.0 1.0 C1 B:FY7300 2.9 21.1 1.0 O20 B:FY7300 3.1 21.2 1.0 O22 B:FY7300 3.3 21.7 1.0 C21 B:FY7300 3.3 21.5 1.0 CE1 B:TYR64 4.1 14.9 1.0 C4 B:FY7300 4.2 19.5 1.0 C6 B:FY7300 4.2 19.6 1.0 C25 B:FY7300 4.3 21.6 1.0 O B:HOH418 4.4 19.2 1.0 C19 B:FY7300 4.4 22.5 1.0 N3 B:FY7300 4.4 22.9 1.0 O B:TYR47 4.5 45.5 1.0 CD1 B:TYR47 4.5 46.7 1.0 CD1 B:TYR64 4.6 14.8 1.0 CB B:TYR47 4.6 46.4 1.0 C5 B:FY7300 4.7 19.2 1.0 C26 B:FY7300 4.8 22.2 1.0 OD1 B:ASP65 4.8 21.9 1.0 CZ B:TYR64 4.9 14.6 1.0

M.C.O'reilly, S.H.Dong, F.M.Rossi, K.M.Karlen, R.S.Kumar, S.K.Nair, H.E.Blackwell. Structural and Biochemical Studies of Non-Native Agonists of the Lasr Quorum-Sensing Receptor Reveal An L3 Loop "Out" Conformation For Lasr. Cell Chem Biol V. 25 1128 2018.
ISSN: ESSN 2451-9448
PubMed: 30033130
DOI: 10.1016/J.CHEMBIOL.2018.06.007