Bromine in PDB 6d6b: The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11

Protein crystallography data

The structure of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11, PDB code: 6d6b 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) 42.23 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.276, 84.467, 156.203, 90.00, 95.69, 90.00
R / Rfree (%) 17.9 / 21

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

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 11 (pdb code 6d6b). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 16 binding sites of Bromine where determined in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11, PDB code: 6d6b:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 16 in 6d6b

Go back to Bromine Binding Sites List in 6d6b
Bromine binding site 1 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:23.9
occ:1.00
 BR1 A:FXS300 0.0 23.9 1.0
C2 A:FXS300 1.9 15.4 1.0
C3 A:FXS300 2.9 14.7 1.0
C1 A:FXS300 2.9 13.8 1.0
O20 A:FXS300 3.0 15.9 1.0
O3 A:FXS300 3.2 34.2 1.0
C21 A:FXS300 3.6 20.2 1.0
O A:HOH406 3.8 21.6 1.0
O22 A:FXS300 3.8 24.0 1.0
O A:TYR47 3.8 21.0 1.0
CE1 A:TYR64 3.9 9.2 1.0
C4 A:FXS300 4.2 14.3 1.0
C6 A:FXS300 4.2 13.2 1.0
CD1 A:ILE52 4.3 21.2 1.0
CB A:TYR47 4.4 19.4 1.0
N1 A:FXS300 4.4 26.0 1.0
CD1 A:TYR47 4.5 18.8 1.0
CD1 A:TYR64 4.5 9.2 1.0
C25 A:FXS300 4.5 20.1 1.0
C A:TYR47 4.6 23.4 1.0
CZ A:TYR64 4.6 8.7 1.0
O A:HOH452 4.7 21.4 1.0
OH A:TYR64 4.7 9.3 1.0
CB A:ALA50 4.7 15.8 1.0
C5 A:FXS300 4.7 13.7 1.0
C26 A:FXS300 4.8 22.9 1.0
CA A:TYR47 4.9 20.0 1.0
OD1 A:ASP65 4.9 29.7 1.0
CG1 A:ILE52 4.9 18.9 1.0
CG A:TYR47 4.9 18.9 1.0

Bromine binding site 2 out of 16 in 6d6b

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Bromine binding site 2 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:15.6
occ:1.00
 BR2 A:FXS300 0.0 15.6 1.0
C4 A:FXS300 1.9 14.3 1.0
C5 A:FXS300 2.8 13.7 1.0
C3 A:FXS300 2.9 14.7 1.0
CD2 A:TYR64 3.6 8.5 1.0
CG A:TYR64 3.6 9.0 1.0
NE1 A:TRP60 3.7 12.4 1.0
CB A:TYR64 3.7 9.6 1.0
CD1 A:LEU36 3.8 12.3 1.0
O19 A:FXS300 3.9 12.9 1.0
CD2 A:TYR56 3.9 8.0 1.0
CD1 A:TRP60 3.9 12.9 1.0
CA A:ARG61 4.0 12.6 1.0
O A:HOH452 4.1 21.4 1.0
CG A:ARG61 4.1 18.8 1.0
C6 A:FXS300 4.1 13.2 1.0
C2 A:FXS300 4.2 15.4 1.0
CE2 A:TYR64 4.2 8.6 1.0
CD1 A:TYR64 4.3 9.2 1.0
CE2 A:TYR56 4.3 8.3 1.0
CB A:ARG61 4.5 14.9 1.0
N A:ARG61 4.5 11.1 1.0
CE2 A:TRP60 4.5 12.1 1.0
O A:TRP60 4.6 10.5 1.0
C1 A:FXS300 4.7 13.8 1.0
C A:TRP60 4.8 11.4 1.0
CZ A:TYR64 4.8 8.7 1.0
CE1 A:TYR64 4.8 9.2 1.0
CG A:TRP60 4.8 11.8 1.0
O A:ARG61 4.9 10.9 1.0
C A:ARG61 4.9 12.2 1.0

Bromine binding site 3 out of 16 in 6d6b

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Bromine binding site 3 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:24.8
occ:1.00
 BR1 B:FXS300 0.0 24.8 1.0
C2 B:FXS300 1.9 17.2 1.0
C3 B:FXS300 2.9 15.2 1.0
C1 B:FXS300 2.9 16.2 1.0
O20 B:FXS300 3.0 17.9 1.0
O3 B:FXS300 3.1 33.7 1.0
C21 B:FXS300 3.5 23.1 1.0
O22 B:FXS300 3.5 30.1 1.0
O B:TYR47 3.8 26.9 1.0
CE1 B:TYR64 4.0 10.9 1.0
C4 B:FXS300 4.2 14.1 1.0
C6 B:FXS300 4.2 12.6 1.0
CD1 B:ILE52 4.4 24.5 1.0
N1 B:FXS300 4.4 26.4 1.0
CB B:TYR47 4.4 23.1 1.0
C25 B:FXS300 4.5 22.4 1.0
C B:TYR47 4.5 26.2 1.0
CD1 B:TYR47 4.5 22.7 1.0
CD1 B:TYR64 4.5 11.4 1.0
CB B:ALA50 4.6 18.0 1.0
CZ B:TYR64 4.7 11.1 1.0
O B:HOH448 4.7 22.7 1.0
C5 B:FXS300 4.7 12.5 1.0
CA B:TYR47 4.8 23.6 1.0
OH B:TYR64 4.8 11.4 1.0
C26 B:FXS300 4.8 22.8 1.0
OD1 B:ASP65 4.9 31.8 1.0
CG B:TYR47 5.0 21.6 1.0
CG1 B:ILE52 5.0 20.0 1.0

Bromine binding site 4 out of 16 in 6d6b

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Bromine binding site 4 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:17.4
occ:1.00
 BR2 B:FXS300 0.0 17.4 1.0
C4 B:FXS300 1.9 14.1 1.0
C5 B:FXS300 2.8 12.5 1.0
C3 B:FXS300 2.8 15.2 1.0
CD2 B:TYR64 3.5 11.0 1.0
CG B:TYR64 3.6 11.4 1.0
NE1 B:TRP60 3.6 11.0 1.0
CB B:TYR64 3.7 11.2 1.0
CD1 B:LEU36 3.8 12.2 1.0
CD1 B:TRP60 3.9 12.2 1.0
CD2 B:TYR56 3.9 10.0 1.0
O19 B:FXS300 3.9 12.9 1.0
CA B:ARG61 4.0 13.6 1.0
CG B:ARG61 4.0 18.2 1.0
O B:HOH448 4.1 22.7 1.0
C6 B:FXS300 4.1 12.6 1.0
C2 B:FXS300 4.1 17.2 1.0
CE2 B:TYR64 4.2 10.5 1.0
CE2 B:TYR56 4.2 9.5 1.0
CD1 B:TYR64 4.3 11.4 1.0
CB B:ARG61 4.4 14.6 1.0
CE2 B:TRP60 4.4 11.3 1.0
N B:ARG61 4.5 12.2 1.0
O B:TRP60 4.6 11.8 1.0
C1 B:FXS300 4.6 16.2 1.0
CG B:TRP60 4.8 11.4 1.0
C B:TRP60 4.8 11.0 1.0
CZ B:TYR64 4.8 11.1 1.0
CE1 B:TYR64 4.8 10.9 1.0
O B:ARG61 4.9 13.8 1.0
C B:ARG61 5.0 13.6 1.0

Bromine binding site 5 out of 16 in 6d6b

Go back to Bromine Binding Sites List in 6d6b
Bromine binding site 5 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:27.7
occ:1.00
 BR1 C:FXS300 0.0 27.7 1.0
C2 C:FXS300 1.9 18.3 1.0
C3 C:FXS300 2.9 15.9 1.0
C1 C:FXS300 2.9 15.4 1.0
O20 C:FXS300 3.0 17.4 1.0
O3 C:FXS300 3.2 34.4 1.0
C21 C:FXS300 3.5 25.1 1.0
O C:HOH408 3.7 26.3 1.0
O C:TYR47 3.8 25.6 1.0
O22 C:FXS300 3.8 28.8 1.0
CE1 C:TYR64 4.0 10.4 1.0
CD1 C:ILE52 4.0 20.8 1.0
C4 C:FXS300 4.1 14.4 1.0
C6 C:FXS300 4.2 13.6 1.0
CB C:TYR47 4.2 24.1 1.0
N1 C:FXS300 4.4 25.6 1.0
C25 C:FXS300 4.5 19.9 1.0
CD2 C:TYR47 4.5 23.2 1.0
C C:TYR47 4.5 25.1 1.0
CD1 C:TYR64 4.5 10.3 1.0
CZ C:TYR64 4.6 10.5 1.0
O C:HOH457 4.6 26.2 1.0
OH C:TYR64 4.7 10.7 1.0
C5 C:FXS300 4.7 14.0 1.0
CA C:TYR47 4.8 23.4 1.0
CG1 C:ILE52 4.8 17.8 1.0
CB C:ALA50 4.8 17.6 1.0
OD1 C:ASP65 4.8 30.2 1.0
C26 C:FXS300 4.9 22.7 1.0
CG C:TYR47 4.9 21.8 1.0

Bromine binding site 6 out of 16 in 6d6b

Go back to Bromine Binding Sites List in 6d6b
Bromine binding site 6 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:17.6
occ:1.00
 BR2 C:FXS300 0.0 17.6 1.0
C4 C:FXS300 1.9 14.4 1.0
C5 C:FXS300 2.8 14.0 1.0
C3 C:FXS300 2.9 15.9 1.0
CD2 C:TYR64 3.6 9.4 1.0
CG C:TYR64 3.6 10.1 1.0
NE1 C:TRP60 3.7 12.3 1.0
CB C:TYR64 3.8 11.1 1.0
O19 C:FXS300 3.8 15.6 1.0
CD1 C:LEU36 3.9 13.6 1.0
CD2 C:TYR56 3.9 9.9 1.0
O C:HOH457 3.9 26.2 1.0
CD1 C:TRP60 3.9 11.9 1.0
CA C:ARG61 4.0 11.3 1.0
CG C:ARG61 4.0 15.1 1.0
C6 C:FXS300 4.1 13.6 1.0
C2 C:FXS300 4.1 18.3 1.0
CE2 C:TYR64 4.2 9.3 1.0
CD1 C:TYR64 4.3 10.3 1.0
CE2 C:TYR56 4.3 10.2 1.0
CE2 C:TRP60 4.4 12.0 1.0
CB C:ARG61 4.5 14.0 1.0
N C:ARG61 4.5 10.5 1.0
O C:TRP60 4.6 10.4 1.0
C1 C:FXS300 4.6 15.4 1.0
CZ C:TYR64 4.7 10.5 1.0
C C:TRP60 4.7 11.7 1.0
CE1 C:TYR64 4.8 10.4 1.0
CG C:TRP60 4.8 11.8 1.0
O C:ARG61 4.9 12.4 1.0
C C:ARG61 5.0 12.8 1.0
N16 C:FXS300 5.0 13.4 1.0

Bromine binding site 7 out of 16 in 6d6b

Go back to Bromine Binding Sites List in 6d6b
Bromine binding site 7 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:28.1
occ:1.00
 BR1 D:FXS300 0.0 28.1 1.0
C2 D:FXS300 1.9 19.2 1.0
C3 D:FXS300 2.9 17.1 1.0
C1 D:FXS300 2.9 17.9 1.0
O20 D:FXS300 3.1 18.9 1.0
O3 D:FXS300 3.1 40.1 1.0
C21 D:FXS300 3.5 25.9 1.0
O22 D:FXS300 3.5 33.2 1.0
O D:HOH404 3.6 21.0 1.0
O D:TYR47 3.7 28.7 1.0
CE1 D:TYR64 4.1 11.8 1.0
C4 D:FXS300 4.2 15.5 1.0
C6 D:FXS300 4.2 15.4 1.0
CD1 D:ILE52 4.3 22.1 1.0
N1 D:FXS300 4.4 28.6 1.0
CB D:TYR47 4.4 23.1 1.0
C D:TYR47 4.5 27.8 1.0
C25 D:FXS300 4.5 22.3 1.0
CD1 D:TYR47 4.6 21.2 1.0
CD1 D:TYR64 4.6 11.4 1.0
O D:HOH461 4.7 25.1 1.0
C5 D:FXS300 4.8 16.4 1.0
OD1 D:ASP65 4.8 28.0 1.0
CA D:TYR47 4.8 24.8 1.0
CB D:ALA50 4.8 17.5 1.0
CG1 D:ILE52 4.8 19.5 1.0
C26 D:FXS300 4.8 26.1 1.0
CZ D:TYR64 4.9 10.3 1.0
OH D:TYR64 5.0 10.0 1.0
CG D:TYR47 5.0 21.9 1.0

Bromine binding site 8 out of 16 in 6d6b

Go back to Bromine Binding Sites List in 6d6b
Bromine binding site 8 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:18.5
occ:1.00
 BR2 D:FXS300 0.0 18.5 1.0
C4 D:FXS300 1.9 15.5 1.0
C5 D:FXS300 2.8 16.4 1.0
C3 D:FXS300 2.9 17.1 1.0
CG D:TYR64 3.6 12.4 1.0
CD2 D:TYR64 3.6 11.0 1.0
CB D:TYR64 3.7 12.6 1.0
NE1 D:TRP60 3.7 16.0 1.0
O19 D:FXS300 3.8 19.5 1.0
CD1 D:LEU36 3.9 16.4 1.0
CD2 D:TYR56 3.9 11.8 1.0
CD1 D:TRP60 3.9 16.1 1.0
CA D:ARG61 3.9 13.9 1.0
CG D:ARG61 4.0 17.7 1.0
O D:HOH461 4.1 25.1 1.0
C6 D:FXS300 4.1 15.4 1.0
C2 D:FXS300 4.2 19.2 1.0
CD1 D:TYR64 4.2 11.4 1.0
CE2 D:TYR56 4.3 11.3 1.0
CE2 D:TYR64 4.3 11.0 1.0
CB D:ARG61 4.4 16.2 1.0
N D:ARG61 4.5 12.2 1.0
CE2 D:TRP60 4.5 16.6 1.0
O D:TRP60 4.5 12.7 1.0
C1 D:FXS300 4.6 17.9 1.0
C D:TRP60 4.7 14.2 1.0
CG D:TRP60 4.7 15.1 1.0
CE1 D:TYR64 4.8 11.8 1.0
CZ D:TYR64 4.8 10.3 1.0
O D:ARG61 4.9 15.2 1.0
C D:ARG61 5.0 14.6 1.0

Bromine binding site 9 out of 16 in 6d6b

Go back to Bromine Binding Sites List in 6d6b
Bromine binding site 9 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:24.4
occ:1.00
 BR1 E:FXS300 0.0 24.4 1.0
C2 E:FXS300 1.9 17.9 1.0
C3 E:FXS300 2.9 16.1 1.0
C1 E:FXS300 2.9 16.1 1.0
O20 E:FXS300 3.1 17.2 1.0
O3 E:FXS300 3.3 33.6 1.0
C21 E:FXS300 3.5 22.8 1.0
O22 E:FXS300 3.6 28.1 1.0
O E:TYR47 3.7 19.6 1.0
O E:HOH414 3.7 21.0 1.0
CE1 E:TYR64 4.2 9.6 1.0
C4 E:FXS300 4.2 15.2 1.0
CB E:TYR47 4.3 17.9 1.0
C6 E:FXS300 4.3 14.2 1.0
C E:TYR47 4.4 21.2 1.0
CD1 E:ILE52 4.5 20.3 1.0
C25 E:FXS300 4.5 19.6 1.0
N1 E:FXS300 4.5 24.0 1.0
O E:HOH428 4.6 24.9 1.0
CD1 E:TYR64 4.6 9.6 1.0
CA E:TYR47 4.7 18.3 1.0
CD1 E:TYR47 4.7 19.2 1.0
C5 E:FXS300 4.8 13.8 1.0
CB E:ALA50 4.8 18.6 1.0
CZ E:TYR64 4.8 8.7 1.0
OD1 E:ASP65 4.8 29.2 1.0
C26 E:FXS300 4.9 21.8 1.0
CG E:TYR47 4.9 18.3 1.0
OH E:TYR64 5.0 8.7 1.0

Bromine binding site 10 out of 16 in 6d6b

Go back to Bromine Binding Sites List in 6d6b
Bromine binding site 10 out of 16 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 11


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

b:15.9
occ:1.00
 BR2 E:FXS300 0.0 15.9 1.0
C4 E:FXS300 1.9 15.2 1.0
C5 E:FXS300 2.8 13.8 1.0
C3 E:FXS300 2.9 16.1 1.0
CD2 E:TYR64 3.6 9.2 1.0
CG E:TYR64 3.6 10.1 1.0
NE1 E:TRP60 3.7 10.8 1.0
CB E:TYR64 3.7 10.1 1.0
CD1 E:LEU36 3.8 12.3 1.0
O19 E:FXS300 3.9 13.2 1.0
CD2 E:TYR56 3.9 6.6 1.0
CD1 E:TRP60 3.9 10.4 1.0
CG E:ARG61 4.0 15.7 1.0
CA E:ARG61 4.0 10.4 1.0
O E:HOH428 4.0 24.9 1.0
C6 E:FXS300 4.1 14.2 1.0
C2 E:FXS300 4.2 17.9 1.0
CD1 E:TYR64 4.2 9.6 1.0
CE2 E:TYR56 4.2 7.2 1.0
CE2 E:TYR64 4.2 8.2 1.0
CB E:ARG61 4.5 13.6 1.0
N E:ARG61 4.5 9.1 1.0
CE2 E:TRP60 4.5 11.0 1.0
O E:TRP60 4.5 8.4 1.0
C1 E:FXS300 4.7 16.1 1.0
C E:TRP60 4.8 8.7 1.0
CZ E:TYR64 4.8 8.7 1.0
CE1 E:TYR64 4.8 9.6 1.0
O E:ARG61 4.8 10.3 1.0
CG E:TRP60 4.8 10.7 1.0
C E:ARG61 4.9 10.4 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: Sat Dec 12 02:32:52 2020

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