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Bromine in PDB 6d6p: The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 19

Protein crystallography data

The structure of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 19, PDB code: 6d6p 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 (°) 56.130, 84.610, 77.170, 90.00, 101.41, 90.00
R / Rfree (%) 21.9 / 24.8

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 19 (pdb code 6d6p). 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 19, PDB code: 6d6p:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 6d6p

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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 19


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

b:32.5
occ:1.00
 BR1 A:FY1300 0.0 32.5 1.0
C2 A:FY1300 1.9 23.6 1.0
C1 A:FY1300 2.8 22.9 1.0
C3 A:FY1300 2.9 22.7 1.0
O20 A:FY1300 3.0 22.4 1.0
C21 A:FY1300 3.6 22.6 1.0
CD1 A:ILE52 4.1 17.5 1.0
C6 A:FY1300 4.1 21.3 1.0
C4 A:FY1300 4.2 21.7 1.0
O A:HOH507 4.2 24.8 1.0
CE1 A:TYR64 4.3 17.9 1.0
CE2 A:TYR47 4.3 30.6 1.0
O A:HOH492 4.3 36.5 1.0
O A:HOH421 4.5 36.7 1.0
O25 A:FY1300 4.6 23.4 1.0
C5 A:FY1300 4.7 21.2 1.0
CD2 A:LEU36 4.7 14.9 1.0
O A:HOH410 4.7 20.3 1.0
CD2 A:TYR47 4.8 29.4 1.0
CD1 A:TYR64 4.8 18.2 1.0
CZ A:TYR64 4.8 17.4 1.0
OH A:TYR64 4.9 18.1 1.0
CZ A:TYR47 5.0 30.9 1.0
CG1 A:ILE52 5.0 15.7 1.0

Bromine binding site 2 out of 8 in 6d6p

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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 19


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

b:21.0
occ:1.00
 BR2 A:FY1300 0.0 21.0 1.0
C4 A:FY1300 1.9 21.7 1.0
C3 A:FY1300 2.8 22.7 1.0
C5 A:FY1300 2.9 21.2 1.0
NE1 A:TRP60 3.4 20.1 1.0
CD1 A:TRP60 3.5 19.2 1.0
CD2 A:TYR64 3.5 18.0 1.0
CG A:TYR64 3.5 18.5 1.0
CB A:TYR64 3.6 19.0 1.0
CD2 A:TYR56 3.9 13.6 1.0
CD A:ARG61 4.0 18.9 1.0
O18 A:FY1300 4.1 20.7 1.0
O A:HOH410 4.1 20.3 1.0
CE2 A:TRP60 4.1 19.6 1.0
C2 A:FY1300 4.1 23.6 1.0
C6 A:FY1300 4.2 21.3 1.0
CA A:ARG61 4.2 18.6 1.0
O A:TRP60 4.2 18.3 1.0
CE2 A:TYR64 4.2 18.0 1.0
CD1 A:TYR64 4.2 18.2 1.0
CE2 A:TYR56 4.3 13.9 1.0
CG A:TRP60 4.3 19.2 1.0
CD2 A:LEU36 4.5 14.9 1.0
N A:ARG61 4.5 17.9 1.0
C A:TRP60 4.5 17.6 1.0
CD2 A:TRP60 4.7 19.3 1.0
C1 A:FY1300 4.7 22.9 1.0
CG A:ARG61 4.7 19.3 1.0
NE A:ARG61 4.8 19.8 1.0
CZ A:TYR64 4.8 17.4 1.0
CE1 A:TYR64 4.8 17.9 1.0
CZ2 A:TRP60 4.8 19.7 1.0
O A:ARG61 5.0 17.6 1.0
CB A:ARG61 5.0 18.8 1.0

Bromine binding site 3 out of 8 in 6d6p

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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 19


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

b:35.0
occ:1.00
 BR1 B:FY1300 0.0 35.0 1.0
C2 B:FY1300 1.9 26.4 1.0
C1 B:FY1300 2.8 25.1 1.0
C3 B:FY1300 2.8 25.2 1.0
O20 B:FY1300 3.0 25.3 1.0
C21 B:FY1300 3.5 25.8 1.0
CE1 B:TYR64 4.1 17.9 1.0
C6 B:FY1300 4.1 23.3 1.0
C4 B:FY1300 4.1 23.3 1.0
CE2 B:TYR47 4.2 41.4 1.0
CD1 B:ILE52 4.3 26.5 1.0
O B:HOH468 4.3 28.4 1.0
O B:HOH420 4.3 33.4 1.0
O B:HOH443 4.4 40.1 1.0
O25 B:FY1300 4.6 26.8 1.0
C5 B:FY1300 4.7 23.0 1.0
CZ B:TYR64 4.7 17.4 1.0
CD1 B:TYR64 4.7 18.4 1.0
OH B:TYR64 4.8 17.6 1.0
CD2 B:TYR47 4.8 41.2 1.0
CD2 B:LEU36 4.8 20.6 1.0
O B:HOH441 4.8 22.1 1.0
CZ B:TYR47 5.0 42.2 1.0

Bromine binding site 4 out of 8 in 6d6p

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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 19


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

b:23.4
occ:1.00
 BR2 B:FY1300 0.0 23.4 1.0
C4 B:FY1300 1.9 23.3 1.0
C5 B:FY1300 2.8 23.0 1.0
C3 B:FY1300 2.8 25.2 1.0
NE1 B:TRP60 3.3 20.4 1.0
CD1 B:TRP60 3.5 20.5 1.0
CD2 B:TYR64 3.5 18.1 1.0
CG B:TYR64 3.5 18.7 1.0
CB B:TYR64 3.6 19.7 1.0
CD2 B:TYR56 3.9 18.7 1.0
O B:HOH441 4.0 22.1 1.0
O18 B:FY1300 4.0 20.8 1.0
CD B:ARG61 4.0 18.9 1.0
CE2 B:TRP60 4.0 20.0 1.0
CA B:ARG61 4.1 19.2 1.0
C2 B:FY1300 4.1 26.4 1.0
C6 B:FY1300 4.1 23.3 1.0
O B:TRP60 4.2 19.2 1.0
CE2 B:TYR64 4.2 17.8 1.0
CD1 B:TYR64 4.3 18.4 1.0
CG B:TRP60 4.3 19.9 1.0
CE2 B:TYR56 4.3 18.7 1.0
CD2 B:LEU36 4.4 20.6 1.0
N B:ARG61 4.4 18.5 1.0
C B:TRP60 4.5 19.2 1.0
CD2 B:TRP60 4.6 20.1 1.0
C1 B:FY1300 4.7 25.1 1.0
NE B:ARG61 4.7 19.4 1.0
CG B:ARG61 4.7 19.0 1.0
CZ2 B:TRP60 4.8 20.3 1.0
CZ B:TYR64 4.8 17.4 1.0
CE1 B:TYR64 4.9 17.9 1.0
O B:ARG61 5.0 19.9 1.0
CB B:ARG61 5.0 19.1 1.0

Bromine binding site 5 out of 8 in 6d6p

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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 19


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

b:39.3
occ:1.00
 BR1 C:FY1300 0.0 39.3 1.0
C2 C:FY1300 1.9 30.8 1.0
C1 C:FY1300 2.8 29.4 1.0
C3 C:FY1300 2.9 28.6 1.0
O20 C:FY1300 3.0 29.2 1.0
C21 C:FY1300 3.6 28.9 1.0
CD1 C:ILE52 3.8 28.6 1.0
CE1 C:TYR64 4.1 21.6 1.0
C6 C:FY1300 4.1 27.5 1.0
C4 C:FY1300 4.2 28.1 1.0
O C:HOH430 4.3 30.5 1.0
CE2 C:TYR47 4.3 47.1 1.0
O C:HOH448 4.3 31.8 1.0
O C:HOH407 4.6 40.6 1.0
CD1 C:TYR64 4.6 22.0 1.0
O25 C:FY1300 4.6 29.7 1.0
CG1 C:ILE52 4.6 27.9 1.0
O C:HOH436 4.6 30.6 1.0
CZ C:TYR64 4.6 21.2 1.0
C5 C:FY1300 4.7 27.5 1.0
CD2 C:LEU36 4.7 22.8 1.0
OH C:TYR64 4.8 20.5 1.0
CG2 C:ILE52 4.8 27.1 1.0
CD2 C:TYR47 4.9 47.2 1.0

Bromine binding site 6 out of 8 in 6d6p

Go back to Bromine Binding Sites List in 6d6p
Bromine binding site 6 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 19


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

b:27.2
occ:1.00
 BR2 C:FY1300 0.0 27.2 1.0
C4 C:FY1300 1.9 28.1 1.0
C3 C:FY1300 2.8 28.6 1.0
C5 C:FY1300 2.9 27.5 1.0
NE1 C:TRP60 3.4 21.4 1.0
CD2 C:TYR64 3.5 21.8 1.0
CD1 C:TRP60 3.5 21.8 1.0
CG C:TYR64 3.6 21.4 1.0
CB C:TYR64 3.6 21.6 1.0
CD2 C:TYR56 3.9 21.3 1.0
CD C:ARG61 4.0 21.1 1.0
O18 C:FY1300 4.0 23.2 1.0
O C:HOH436 4.0 30.6 1.0
CE2 C:TRP60 4.1 21.6 1.0
CA C:ARG61 4.1 21.7 1.0
C2 C:FY1300 4.1 30.8 1.0
C6 C:FY1300 4.2 27.5 1.0
O C:TRP60 4.2 20.6 1.0
CE2 C:TYR64 4.2 21.1 1.0
CD1 C:TYR64 4.3 22.0 1.0
CG C:TRP60 4.3 21.6 1.0
CE2 C:TYR56 4.4 21.1 1.0
N C:ARG61 4.4 21.6 1.0
CD2 C:LEU36 4.5 22.8 1.0
C C:TRP60 4.5 21.2 1.0
CD2 C:TRP60 4.6 21.4 1.0
CG C:ARG61 4.6 21.2 1.0
C1 C:FY1300 4.7 29.4 1.0
NE C:ARG61 4.7 21.9 1.0
CZ2 C:TRP60 4.8 21.6 1.0
CZ C:TYR64 4.9 21.2 1.0
CE1 C:TYR64 4.9 21.6 1.0
CB C:ARG61 4.9 21.8 1.0

Bromine binding site 7 out of 8 in 6d6p

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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 19


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

b:41.8
occ:1.00
 BR1 D:FY1300 0.0 41.8 1.0
C2 D:FY1300 1.9 31.7 1.0
C1 D:FY1300 2.8 30.0 1.0
C3 D:FY1300 2.8 29.8 1.0
O20 D:FY1300 3.0 29.1 1.0
C21 D:FY1300 3.7 29.8 1.0
CD1 D:ILE52 4.0 32.8 1.0
CE2 D:TYR47 4.0 62.1 1.0
CE1 D:TYR64 4.1 24.9 1.0
C4 D:FY1300 4.1 28.3 1.0
C6 D:FY1300 4.1 27.6 1.0
O D:HOH451 4.5 32.3 1.0
O25 D:FY1300 4.6 31.0 1.0
CD1 D:TYR64 4.6 25.4 1.0
C5 D:FY1300 4.7 27.8 1.0
OH D:TYR47 4.7 62.4 1.0
CZ D:TYR47 4.7 62.5 1.0
CZ D:TYR64 4.7 24.6 1.0
CD2 D:TYR47 4.7 62.7 1.0
CG1 D:ILE52 4.8 32.0 1.0
CD2 D:LEU36 4.8 21.4 1.0
OH D:TYR64 4.8 23.9 1.0
O D:HOH428 4.8 26.1 1.0

Bromine binding site 8 out of 8 in 6d6p

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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 19


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

b:28.0
occ:1.00
 BR2 D:FY1300 0.0 28.0 1.0
C4 D:FY1300 1.9 28.3 1.0
C3 D:FY1300 2.8 29.8 1.0
C5 D:FY1300 2.9 27.8 1.0
NE1 D:TRP60 3.3 23.2 1.0
CD1 D:TRP60 3.5 23.3 1.0
CD2 D:TYR64 3.5 24.9 1.0
CG D:TYR64 3.5 25.1 1.0
CB D:TYR64 3.6 26.2 1.0
CD2 D:TYR56 3.9 20.2 1.0
O18 D:FY1300 4.0 26.0 1.0
O D:HOH428 4.0 26.1 1.0
CE2 D:TRP60 4.1 23.4 1.0
CD D:ARG61 4.1 22.2 1.0
C2 D:FY1300 4.1 31.7 1.0
C6 D:FY1300 4.2 27.6 1.0
CE2 D:TYR64 4.2 24.6 1.0
O D:TRP60 4.2 22.3 1.0
CD1 D:TYR64 4.2 25.4 1.0
CA D:ARG61 4.3 23.1 1.0
CG D:TRP60 4.3 22.9 1.0
CE2 D:TYR56 4.3 20.1 1.0
CD2 D:LEU36 4.4 21.4 1.0
C D:TRP60 4.5 22.3 1.0
N D:ARG61 4.5 22.7 1.0
CD2 D:TRP60 4.6 23.3 1.0
C1 D:FY1300 4.7 30.0 1.0
NE D:ARG61 4.7 22.2 1.0
CZ2 D:TRP60 4.8 22.7 1.0
CG D:ARG61 4.8 22.6 1.0
CZ D:TYR64 4.8 24.6 1.0
CE1 D:TYR64 4.8 24.9 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 01:39:39 2024

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