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Bromine in PDB 6d6o: The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17

Protein crystallography data

The structure of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17, PDB code: 6d6o 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 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.020, 84.280, 76.640, 90.00, 101.24, 90.00
R / Rfree (%) 22.3 / 25.9

Bromine 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 17 (pdb code 6d6o). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17, PDB code: 6d6o:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 6d6o

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Bromine binding site 1 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br300

b:37.8
occ:1.00
 BR1 A:FX7300 0.0 37.8 1.0
C2 A:FX7300 1.9 27.4 1.0
C3 A:FX7300 2.8 26.7 1.0
C1 A:FX7300 2.9 27.2 1.0
O20 A:FX7300 3.1 27.9 1.0
O A:HOH466 3.2 64.1 1.0
O22 A:FX7300 3.4 30.5 1.0
C21 A:FX7300 3.5 31.1 1.0
CD1 A:ILE52 3.8 18.2 1.0
C4 A:FX7300 4.1 24.3 1.0
C6 A:FX7300 4.2 24.2 1.0
CE1 A:TYR64 4.2 18.4 1.0
O A:HOH490 4.2 45.2 1.0
O A:HOH421 4.3 23.1 1.0
C25 A:FX7300 4.6 33.0 1.0
CD1 A:TYR64 4.6 18.7 1.0
C5 A:FX7300 4.7 23.4 1.0
CD2 A:LEU36 4.7 15.3 1.0
C30 A:FX7300 4.7 35.4 1.0
CE2 A:TYR47 4.7 31.3 1.0
CG1 A:ILE52 4.8 16.8 1.0
CD2 A:TYR47 4.8 29.8 1.0
OD1 A:ASP65 4.8 34.8 1.0
CZ A:TYR64 4.9 18.6 1.0
CG2 A:ILE52 4.9 16.0 1.0

Bromine binding site 2 out of 8 in 6d6o

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Bromine binding site 2 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br300

b:24.6
occ:1.00
 BR2 A:FX7300 0.0 24.6 1.0
C4 A:FX7300 1.9 24.3 1.0
C3 A:FX7300 2.8 26.7 1.0
C5 A:FX7300 2.9 23.4 1.0
NE1 A:TRP60 3.4 20.8 1.0
CD1 A:TRP60 3.5 20.3 1.0
CG A:TYR64 3.5 19.1 1.0
CB A:TYR64 3.6 19.4 1.0
CD2 A:TYR64 3.6 18.8 1.0
CD2 A:TYR56 3.8 15.9 1.0
O18 A:FX7300 3.9 22.6 1.0
CD A:ARG61 4.0 19.0 1.0
C2 A:FX7300 4.1 27.4 1.0
CE2 A:TRP60 4.1 20.4 1.0
CA A:ARG61 4.1 19.1 1.0
O A:TRP60 4.1 18.2 1.0
C6 A:FX7300 4.1 24.2 1.0
O A:HOH421 4.1 23.1 1.0
CD1 A:TYR64 4.2 18.7 1.0
CE2 A:TYR56 4.2 16.4 1.0
CG A:TRP60 4.3 19.7 1.0
CE2 A:TYR64 4.3 18.9 1.0
N A:ARG61 4.4 18.4 1.0
C A:TRP60 4.4 18.3 1.0
CD2 A:LEU36 4.4 15.3 1.0
CD2 A:TRP60 4.6 20.3 1.0
C1 A:FX7300 4.6 27.2 1.0
CG A:ARG61 4.6 18.6 1.0
NE A:ARG61 4.8 19.7 1.0
CE1 A:TYR64 4.8 18.4 1.0
CZ2 A:TRP60 4.8 20.5 1.0
CZ A:TYR64 4.9 18.6 1.0
CB A:ARG61 4.9 18.7 1.0
CG A:TYR56 4.9 15.7 1.0
O A:ARG61 5.0 18.6 1.0

Bromine binding site 3 out of 8 in 6d6o

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Bromine binding site 3 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br300

b:40.6
occ:1.00
 BR1 B:FX7300 0.0 40.6 1.0
C2 B:FX7300 1.9 29.8 1.0
C3 B:FX7300 2.8 28.1 1.0
C1 B:FX7300 2.9 28.3 1.0
O20 B:FX7300 3.1 28.6 1.0
C21 B:FX7300 3.4 29.7 1.0
O22 B:FX7300 3.6 29.9 1.0
C30 B:FX7300 3.9 32.9 1.0
CD1 B:ILE52 3.9 31.6 1.0
C4 B:FX7300 4.1 25.8 1.0
CE1 B:TYR64 4.1 20.1 1.0
C6 B:FX7300 4.2 25.4 1.0
C25 B:FX7300 4.3 31.3 1.0
CE2 B:TYR47 4.3 44.5 1.0
O B:HOH431 4.4 23.9 1.0
O B:HOH411 4.4 37.1 1.0
CD1 B:TYR64 4.6 20.5 1.0
CG1 B:ILE52 4.6 32.3 1.0
C5 B:FX7300 4.7 25.5 1.0
CD2 B:TYR47 4.7 44.9 1.0
CD2 B:LEU36 4.7 22.5 1.0
CG2 B:ILE52 4.8 31.2 1.0
CZ B:TYR64 4.8 19.6 1.0
OD1 B:ASP65 4.9 32.5 1.0

Bromine binding site 4 out of 8 in 6d6o

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Bromine binding site 4 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br300

b:25.0
occ:1.00
 BR2 B:FX7300 0.0 25.0 1.0
C4 B:FX7300 1.9 25.8 1.0
C3 B:FX7300 2.8 28.1 1.0
C5 B:FX7300 2.8 25.5 1.0
NE1 B:TRP60 3.2 20.9 1.0
CD1 B:TRP60 3.4 21.0 1.0
CG B:TYR64 3.6 20.4 1.0
CB B:TYR64 3.6 21.3 1.0
CD2 B:TYR64 3.6 19.9 1.0
CD2 B:TYR56 3.8 21.2 1.0
O18 B:FX7300 3.9 22.6 1.0
CE2 B:TRP60 3.9 20.8 1.0
CD B:ARG61 4.0 21.5 1.0
CA B:ARG61 4.1 21.7 1.0
C2 B:FX7300 4.1 29.8 1.0
O B:TRP60 4.1 21.0 1.0
O B:HOH431 4.1 23.9 1.0
C6 B:FX7300 4.1 25.4 1.0
CG B:TRP60 4.2 20.5 1.0
CD1 B:TYR64 4.2 20.5 1.0
CE2 B:TYR56 4.2 21.7 1.0
CE2 B:TYR64 4.3 19.3 1.0
N B:ARG61 4.3 21.4 1.0
CD2 B:LEU36 4.4 22.5 1.0
C B:TRP60 4.4 21.2 1.0
CD2 B:TRP60 4.5 20.5 1.0
C1 B:FX7300 4.6 28.3 1.0
CG B:ARG61 4.7 21.6 1.0
CZ2 B:TRP60 4.7 20.9 1.0
NE B:ARG61 4.7 22.1 1.0
CE1 B:TYR64 4.9 20.1 1.0
CZ B:TYR64 4.9 19.6 1.0
CB B:ARG61 4.9 21.5 1.0
O B:ARG61 4.9 22.3 1.0
CG B:TYR56 5.0 21.5 1.0
C B:ARG61 5.0 22.5 1.0
N16 B:FX7300 5.0 21.8 1.0

Bromine binding site 5 out of 8 in 6d6o

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Bromine binding site 5 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br300

b:37.9
occ:1.00
 BR1 C:FX7300 0.0 37.9 1.0
C2 C:FX7300 1.9 29.8 1.0
C1 C:FX7300 2.8 28.4 1.0
C3 C:FX7300 2.8 27.9 1.0
O20 C:FX7300 3.0 28.7 1.0
C21 C:FX7300 3.4 29.8 1.0
O22 C:FX7300 3.5 31.0 1.0
CD1 C:ILE52 3.7 26.8 1.0
O C:HOH448 3.9 33.6 1.0
CE1 C:TYR64 4.0 21.3 1.0
C30 C:FX7300 4.1 32.3 1.0
C6 C:FX7300 4.1 26.5 1.0
C4 C:FX7300 4.1 26.8 1.0
C25 C:FX7300 4.4 31.1 1.0
O C:HOH422 4.4 26.8 1.0
CE2 C:TYR47 4.4 45.4 1.0
CD1 C:TYR64 4.4 21.4 1.0
CG1 C:ILE52 4.4 26.1 1.0
CG2 C:ILE52 4.6 25.8 1.0
C5 C:FX7300 4.7 26.4 1.0
CZ C:TYR64 4.7 21.3 1.0
CD2 C:LEU36 4.7 20.4 1.0
CD2 C:TYR47 4.8 46.2 1.0
OH C:TYR64 4.9 20.6 1.0
OD1 C:ASP65 4.9 31.1 1.0

Bromine binding site 6 out of 8 in 6d6o

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Bromine binding site 6 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br300

b:25.7
occ:1.00
 BR2 C:FX7300 0.0 25.7 1.0
C4 C:FX7300 1.9 26.8 1.0
C3 C:FX7300 2.8 27.9 1.0
C5 C:FX7300 2.9 26.4 1.0
NE1 C:TRP60 3.3 21.7 1.0
CD1 C:TRP60 3.4 22.1 1.0
CG C:TYR64 3.6 21.3 1.0
CD2 C:TYR64 3.6 21.6 1.0
CB C:TYR64 3.6 21.5 1.0
CD2 C:TYR56 3.8 21.2 1.0
O18 C:FX7300 3.8 23.8 1.0
CE2 C:TRP60 3.9 21.8 1.0
CD C:ARG61 4.0 20.9 1.0
O C:TRP60 4.1 20.2 1.0
CA C:ARG61 4.1 21.3 1.0
C2 C:FX7300 4.1 29.8 1.0
CG C:TRP60 4.1 21.3 1.0
O C:HOH422 4.2 26.8 1.0
C6 C:FX7300 4.2 26.5 1.0
CE2 C:TYR56 4.2 21.2 1.0
CD1 C:TYR64 4.3 21.4 1.0
CE2 C:TYR64 4.3 21.0 1.0
N C:ARG61 4.3 21.4 1.0
C C:TRP60 4.3 20.6 1.0
CD2 C:LEU36 4.4 20.4 1.0
CD2 C:TRP60 4.4 21.7 1.0
CG C:ARG61 4.6 21.3 1.0
C1 C:FX7300 4.7 28.4 1.0
CZ2 C:TRP60 4.7 22.4 1.0
NE C:ARG61 4.8 21.1 1.0
CE1 C:TYR64 4.9 21.3 1.0
CG C:TYR56 4.9 21.5 1.0
CZ C:TYR64 4.9 21.3 1.0
CB C:ARG61 4.9 21.8 1.0
N16 C:FX7300 5.0 24.2 1.0

Bromine binding site 7 out of 8 in 6d6o

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Bromine binding site 7 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br300

b:44.0
occ:1.00
 BR1 D:FX7300 0.0 44.0 1.0
C2 D:FX7300 1.9 33.8 1.0
C3 D:FX7300 2.8 31.1 1.0
C1 D:FX7300 2.9 32.3 1.0
O20 D:FX7300 3.1 32.9 1.0
C21 D:FX7300 3.5 35.2 1.0
O22 D:FX7300 3.6 36.2 1.0
CD1 D:ILE52 3.7 31.1 1.0
CE1 D:TYR64 4.1 26.6 1.0
C4 D:FX7300 4.1 29.6 1.0
C6 D:FX7300 4.2 29.4 1.0
C30 D:FX7300 4.2 38.7 1.0
CG1 D:ILE52 4.3 30.7 1.0
O D:HOH415 4.4 27.2 1.0
C25 D:FX7300 4.4 36.9 1.0
CD1 D:TYR64 4.5 27.1 1.0
CG2 D:ILE52 4.6 30.2 1.0
C5 D:FX7300 4.7 29.1 1.0
CD2 D:LEU36 4.7 21.4 1.0
C29 D:FX7300 4.7 39.9 1.0
CZ D:TYR64 4.8 26.5 1.0
OD1 D:ASP65 4.9 42.0 1.0
OH D:TYR64 5.0 25.9 1.0

Bromine binding site 8 out of 8 in 6d6o

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Bromine binding site 8 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br300

b:28.8
occ:1.00
 BR2 D:FX7300 0.0 28.8 1.0
C4 D:FX7300 1.9 29.6 1.0
C3 D:FX7300 2.8 31.1 1.0
C5 D:FX7300 2.9 29.1 1.0
NE1 D:TRP60 3.3 23.9 1.0
CD1 D:TRP60 3.5 23.9 1.0
CG D:TYR64 3.6 26.8 1.0
CD2 D:TYR64 3.6 26.9 1.0
CB D:TYR64 3.6 27.8 1.0
CD2 D:TYR56 3.7 20.1 1.0
O18 D:FX7300 4.0 26.4 1.0
CD D:ARG61 4.0 22.7 1.0
CE2 D:TRP60 4.0 23.8 1.0
C2 D:FX7300 4.1 33.8 1.0
O D:TRP60 4.1 24.6 1.0
CA D:ARG61 4.1 23.4 1.0
C6 D:FX7300 4.2 29.4 1.0
O D:HOH415 4.2 27.2 1.0
CE2 D:TYR56 4.2 19.9 1.0
CG D:TRP60 4.2 23.9 1.0
CD1 D:TYR64 4.3 27.1 1.0
CE2 D:TYR64 4.3 26.4 1.0
N D:ARG61 4.4 23.5 1.0
CD2 D:LEU36 4.4 21.4 1.0
C D:TRP60 4.4 23.9 1.0
CD2 D:TRP60 4.5 23.8 1.0
C1 D:FX7300 4.6 32.3 1.0
NE D:ARG61 4.7 22.8 1.0
CG D:ARG61 4.7 23.1 1.0
CZ2 D:TRP60 4.8 23.1 1.0
CZ D:TYR64 4.9 26.5 1.0
CG D:TYR56 4.9 20.2 1.0
CE1 D:TYR64 4.9 26.6 1.0
CB D:ARG61 5.0 23.3 1.0

Reference:

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
Page generated: Thu Jul 11 01:39:38 2024

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