Bromine in PDB 6d6m: The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15

The structure of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15, PDB code: 6d6m 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 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.290, 84.590, 77.200, 90.00, 100.95, 90.00
R / Rfree (%)	21.2 / 24.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Bromine atom in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15 (pdb code 6d6m). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 12 binding sites of Bromine where determined in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15, PDB code: 6d6m:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


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 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br300 b:28.4 occ:1.00 BR2 A:TX7300 0.0 28.4 1.0 C4 A:TX7300 1.9 28.9 1.0 C3 A:TX7300 2.8 29.8 1.0 C5 A:TX7300 2.8 27.6 1.0 NE1 A:TRP60 3.4 23.6 1.0 CG A:TYR64 3.6 25.7 1.0 CD1 A:TRP60 3.6 24.6 1.0 CB A:TYR64 3.6 25.2 1.0 CD2 A:TYR64 3.6 25.8 1.0 CD2 A:TYR56 3.8 21.8 1.0 O19 A:TX7300 3.8 25.5 1.0 CD A:ARG61 4.0 24.6 1.0 CE2 A:TRP60 4.1 24.6 1.0 C2 A:TX7300 4.1 32.0 1.0 C6 A:TX7300 4.1 28.4 1.0 O A:TRP60 4.2 24.4 1.0 O A:HOH423 4.2 30.1 1.0 CA A:ARG61 4.2 25.0 1.0 CE2 A:TYR56 4.2 21.6 1.0 CD1 A:TYR64 4.3 24.8 1.0 CE2 A:TYR64 4.3 24.5 1.0 CG A:TRP60 4.4 24.1 1.0 CD2 A:LEU36 4.4 19.4 1.0 N A:ARG61 4.4 24.0 1.0 C A:TRP60 4.5 24.1 1.0 CD2 A:TRP60 4.6 24.8 1.0 C1 A:TX7300 4.7 30.3 1.0 NE A:ARG61 4.7 25.9 1.0 CG A:ARG61 4.7 24.6 1.0 CZ2 A:TRP60 4.8 24.4 1.0 CE1 A:TYR64 4.9 24.2 1.0 CZ A:TYR64 4.9 24.0 1.0 CG A:TYR56 5.0 22.3 1.0 O A:ARG61 5.0 24.5 1.0 CB A:ARG61 5.0 24.9 1.0

Bromine binding site 2 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


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 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br300 b:40.0 occ:1.00 BR A:TX7300 0.0 40.0 1.0 C2 A:TX7300 1.9 32.0 1.0 C1 A:TX7300 2.9 30.3 1.0 C3 A:TX7300 2.9 29.8 1.0 O20 A:TX7300 3.1 30.5 1.0 C21 A:TX7300 3.4 34.9 1.0 O22 A:TX7300 3.7 35.1 1.0 O A:HOH480 3.9 42.6 1.0 CD1 A:ILE52 4.0 27.2 1.0 CE1 A:TYR64 4.2 24.2 1.0 C4 A:TX7300 4.2 28.9 1.0 C6 A:TX7300 4.2 28.4 1.0 C26 A:TX7300 4.3 38.2 1.0 O A:HOH423 4.3 30.1 1.0 C25 A:TX7300 4.3 35.8 1.0 CE2 A:TYR47 4.5 34.1 1.0 CD1 A:TYR64 4.6 24.8 1.0 C5 A:TX7300 4.7 27.6 1.0 CD2 A:TYR47 4.8 34.0 1.0 CG1 A:ILE52 4.8 24.3 1.0 CD2 A:LEU36 4.9 19.4 1.0 CZ A:TYR64 4.9 24.0 1.0 OD1 A:ASP65 4.9 38.4 1.0

Bromine binding site 3 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


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 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br300 b:43.5 occ:1.00 BR1 A:TX7300 0.0 43.5 1.0 C28 A:TX7300 1.9 39.6 1.0 C29 A:TX7300 2.8 38.0 1.0 C27 A:TX7300 2.9 37.8 1.0 CG A:LEU125 3.6 21.6 1.0 CD2 A:LEU125 3.8 21.0 1.0 CD1 A:LEU125 3.9 20.1 1.0 CB A:CYS79 4.0 23.1 1.0 C30 A:TX7300 4.1 36.5 1.0 C26 A:TX7300 4.1 38.2 1.0 O A:VAL76 4.2 23.6 1.0 CG2 A:THR80 4.4 24.6 1.0 CD1 A:LEU40 4.5 27.4 1.0 CG1 A:VAL76 4.5 25.7 1.0 CA A:GLY126 4.6 19.6 1.0 C25 A:TX7300 4.6 35.8 1.0 O A:GLY126 4.7 18.6 1.0 N A:GLY126 4.7 19.5 1.0 C A:GLY126 4.8 18.6 1.0 C A:LEU125 4.9 19.3 1.0 N A:THR80 4.9 25.2 1.0 CB A:LEU125 5.0 20.2 1.0 O A:LEU125 5.0 18.8 1.0 SG A:CYS79 5.0 23.7 1.0

Bromine binding site 4 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


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 15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br300 b:29.3 occ:1.00 BR2 B:TX7300 0.0 29.3 1.0 C4 B:TX7300 1.9 30.8 1.0 C3 B:TX7300 2.8 32.9 1.0 C5 B:TX7300 2.8 29.3 1.0 NE1 B:TRP60 3.3 27.8 1.0 CD1 B:TRP60 3.5 27.5 1.0 CB B:TYR64 3.6 27.8 1.0 CD2 B:TYR64 3.6 24.3 1.0 CG B:TYR64 3.6 24.4 1.0 CD2 B:TYR56 3.8 24.0 1.0 O19 B:TX7300 3.8 25.2 1.0 CD B:ARG61 4.0 27.6 1.0 CE2 B:TRP60 4.0 25.9 1.0 C2 B:TX7300 4.1 33.5 1.0 C6 B:TX7300 4.1 29.4 1.0 O B:HOH430 4.1 25.3 1.0 CA B:ARG61 4.2 27.0 1.0 CE2 B:TYR56 4.2 23.3 1.0 O B:TRP60 4.2 24.6 1.0 CD2 B:LEU36 4.2 26.0 1.0 CD1 B:TYR64 4.3 24.1 1.0 CG B:TRP60 4.3 26.6 1.0 CE2 B:TYR64 4.3 23.8 1.0 N B:ARG61 4.4 26.4 1.0 C B:TRP60 4.5 26.8 1.0 CD2 B:TRP60 4.6 26.6 1.0 C1 B:TX7300 4.7 32.3 1.0 CG B:ARG61 4.7 27.2 1.0 CZ2 B:TRP60 4.7 26.1 1.0 NE B:ARG61 4.8 26.2 1.0 CE1 B:TYR64 4.9 24.0 1.0 CZ B:TYR64 4.9 24.3 1.0 CG B:TYR56 5.0 24.6 1.0 CB B:ARG61 5.0 26.8 1.0

Bromine binding site 5 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br300 b:40.4 occ:1.00 BR B:TX7300 0.0 40.4 1.0 C2 B:TX7300 1.9 33.5 1.0 C3 B:TX7300 2.9 32.9 1.0 C1 B:TX7300 2.9 32.3 1.0 O20 B:TX7300 3.1 32.0 1.0 C21 B:TX7300 3.4 36.9 1.0 O22 B:TX7300 3.6 36.8 1.0 O B:HOH413 4.0 41.7 1.0 C4 B:TX7300 4.1 30.8 1.0 CE1 B:TYR64 4.2 24.0 1.0 CD1 B:ILE52 4.2 32.4 1.0 C6 B:TX7300 4.2 29.4 1.0 C26 B:TX7300 4.3 43.2 1.0 C25 B:TX7300 4.3 40.4 1.0 O B:HOH430 4.5 25.3 1.0 CD1 B:TYR64 4.6 24.1 1.0 C5 B:TX7300 4.7 29.3 1.0 CE2 B:TYR47 4.7 42.3 1.0 CD2 B:LEU36 4.8 26.0 1.0 CZ B:TYR64 4.8 24.3 1.0 CG1 B:ILE52 4.9 33.0 1.0 OD1 B:ASP65 4.9 41.1 1.0 CD2 B:TYR47 4.9 43.5 1.0

Bromine binding site 6 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br300 b:56.4 occ:1.00 BR1 B:TX7300 0.0 56.4 1.0 C28 B:TX7300 1.9 49.7 1.0 C29 B:TX7300 2.8 46.7 1.0 C27 B:TX7300 2.9 47.5 1.0 CG B:LEU125 3.5 25.1 1.0 CD2 B:LEU125 3.6 25.2 1.0 CD1 B:LEU125 3.9 24.6 1.0 C30 B:TX7300 4.1 43.3 1.0 C26 B:TX7300 4.2 43.2 1.0 CB B:CYS79 4.3 21.2 1.0 CG1 B:VAL76 4.3 26.7 1.0 O B:VAL76 4.3 24.4 1.0 CG2 B:THR80 4.4 24.9 1.0 C25 B:TX7300 4.6 40.4 1.0 O B:GLY126 4.6 20.4 1.0 CA B:GLY126 4.8 22.5 1.0 N B:GLY126 4.8 22.6 1.0 CD1 B:LEU40 4.8 34.1 1.0 C B:GLY126 4.9 21.6 1.0 CB B:LEU125 4.9 24.5 1.0 C B:LEU125 5.0 23.6 1.0

Bromine binding site 7 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br300 b:32.7 occ:1.00 BR2 C:TX7300 0.0 32.7 1.0 C4 C:TX7300 1.9 33.0 1.0 C5 C:TX7300 2.8 31.7 1.0 C3 C:TX7300 2.8 33.4 1.0 NE1 C:TRP60 3.4 28.6 1.0 CG C:TYR64 3.5 29.0 1.0 CB C:TYR64 3.6 29.7 1.0 CD1 C:TRP60 3.6 30.2 1.0 CD2 C:TYR64 3.6 29.4 1.0 CD2 C:TYR56 3.8 28.5 1.0 O19 C:TX7300 3.8 30.3 1.0 CE2 C:TRP60 4.0 28.6 1.0 C2 C:TX7300 4.1 35.6 1.0 O C:TRP60 4.1 27.9 1.0 C6 C:TX7300 4.1 32.5 1.0 CD C:ARG61 4.1 26.7 1.0 O C:HOH417 4.2 27.0 1.0 CD1 C:TYR64 4.2 28.4 1.0 CA C:ARG61 4.2 27.5 1.0 CE2 C:TYR56 4.2 29.0 1.0 CG C:TRP60 4.3 29.1 1.0 CE2 C:TYR64 4.3 28.6 1.0 N C:ARG61 4.4 27.4 1.0 C C:TRP60 4.4 27.4 1.0 CD2 C:TRP60 4.5 28.6 1.0 CD2 C:LEU36 4.6 29.7 1.0 C1 C:TX7300 4.7 34.8 1.0 CZ2 C:TRP60 4.7 27.9 1.0 CG C:ARG61 4.8 26.9 1.0 CE1 C:TYR64 4.8 26.9 1.0 NE C:ARG61 4.8 26.5 1.0 CZ C:TYR64 4.9 28.1 1.0 CG C:TYR56 4.9 28.7 1.0

Bromine binding site 8 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br300 b:44.0 occ:1.00 BR C:TX7300 0.0 44.0 1.0 C2 C:TX7300 1.9 35.6 1.0 C1 C:TX7300 2.8 34.8 1.0 C3 C:TX7300 2.9 33.4 1.0 O20 C:TX7300 3.1 37.5 1.0 C21 C:TX7300 3.4 40.2 1.0 O22 C:TX7300 3.5 42.2 1.0 O C:HOH421 4.1 38.5 1.0 C4 C:TX7300 4.1 33.0 1.0 CD1 C:ILE52 4.2 41.1 1.0 C6 C:TX7300 4.2 32.5 1.0 CE1 C:TYR64 4.3 26.9 1.0 C25 C:TX7300 4.4 43.1 1.0 C26 C:TX7300 4.4 42.2 1.0 O C:HOH417 4.4 27.0 1.0 CE2 C:TYR47 4.6 52.9 1.0 CG2 C:ILE52 4.6 38.6 1.0 CD2 C:LEU36 4.7 29.7 1.0 C5 C:TX7300 4.7 31.7 1.0 CD1 C:TYR64 4.7 28.4 1.0 CG1 C:ILE52 4.8 39.4 1.0 OD1 C:ASP65 4.9 33.6 1.0 O C:HOH414 5.0 34.7 1.0

Bromine binding site 9 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br300 b:52.0 occ:1.00 BR1 C:TX7300 0.0 52.0 1.0 C28 C:TX7300 1.9 48.4 1.0 C29 C:TX7300 2.8 47.3 1.0 C27 C:TX7300 2.8 45.1 1.0 CG C:LEU125 3.6 33.4 1.0 CD1 C:LEU125 3.8 33.1 1.0 CD2 C:LEU125 4.0 33.7 1.0 C30 C:TX7300 4.1 44.1 1.0 C26 C:TX7300 4.1 42.2 1.0 CB C:CYS79 4.2 27.8 1.0 CG2 C:THR80 4.3 31.4 1.0 CG1 C:VAL76 4.4 27.2 1.0 O C:VAL76 4.4 32.5 1.0 CA C:GLY126 4.5 27.0 1.0 O C:HOH454 4.5 0.9 1.0 C25 C:TX7300 4.6 43.1 1.0 CD1 C:LEU40 4.6 40.0 1.0 N C:GLY126 4.6 28.6 1.0 O C:GLY126 4.8 25.8 1.0 C C:GLY126 4.9 26.1 1.0 C C:LEU125 4.9 28.8 1.0 CB C:LEU125 4.9 32.5 1.0

Bromine binding site 10 out of 12 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ D:Br300 b:33.9 occ:1.00 BR2 D:TX7300 0.0 33.9 1.0 C4 D:TX7300 1.9 36.8 1.0 C3 D:TX7300 2.8 37.5 1.0 C5 D:TX7300 2.8 34.3 1.0 NE1 D:TRP60 3.4 29.9 1.0 CG D:TYR64 3.6 33.0 1.0 CD1 D:TRP60 3.6 30.5 1.0 CB D:TYR64 3.6 34.2 1.0 CD2 D:TYR64 3.6 33.7 1.0 CD2 D:TYR56 3.7 26.5 1.0 O19 D:TX7300 3.8 31.4 1.0 CD D:ARG61 4.0 26.8 1.0 CE2 D:TRP60 4.1 29.7 1.0 C2 D:TX7300 4.1 39.7 1.0 C6 D:TX7300 4.1 34.4 1.0 CE2 D:TYR56 4.1 26.0 1.0 O D:TRP60 4.2 27.4 1.0 CA D:ARG61 4.2 28.5 1.0 O D:HOH426 4.2 27.7 1.0 CD1 D:TYR64 4.3 34.4 1.0 CG D:TRP60 4.3 30.2 1.0 CE2 D:TYR64 4.3 32.7 1.0 N D:ARG61 4.4 28.6 1.0 C D:TRP60 4.4 28.5 1.0 CD2 D:LEU36 4.5 27.0 1.0 CD2 D:TRP60 4.6 30.4 1.0 C1 D:TX7300 4.7 37.7 1.0 NE D:ARG61 4.7 26.6 1.0 CG D:ARG61 4.7 26.9 1.0 CZ2 D:TRP60 4.8 29.4 1.0 CG D:TYR56 4.8 26.1 1.0 CE1 D:TYR64 4.9 33.9 1.0 CZ D:TYR64 4.9 33.2 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