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Bromine in PDB 6d6n: The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 16

Protein crystallography data

The structure of The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 16, PDB code: 6d6n 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) 75.46 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.297, 84.455, 76.907, 90.00, 101.12, 90.00
R / Rfree (%) 19.2 / 24.3

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 16 (pdb code 6d6n). 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 16, PDB code: 6d6n:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 6d6n

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br201

b:24.1
occ:1.00
 BR1 A:FXJ201 0.0 24.1 1.0
C07 A:FXJ201 1.7 20.4 1.0
C09 A:FXJ201 2.7 25.3 1.0
C06 A:FXJ201 2.8 20.2 1.0
NE1 A:TRP60 3.3 23.8 1.0
CD1 A:TRP60 3.4 23.2 1.0
CG A:TYR64 3.6 21.5 1.0
CB A:TYR64 3.6 19.4 1.0
CD2 A:TYR64 3.7 22.6 1.0
CD2 A:TYR56 3.8 16.2 1.0
C10 A:FXJ201 3.9 21.1 1.0
O27 A:FXJ201 4.0 23.4 1.0
CD A:ARG61 4.0 20.6 1.0
CE2 A:TRP60 4.0 21.9 1.0
C05 A:FXJ201 4.1 19.6 1.0
O A:TRP60 4.1 22.6 1.0
CA A:ARG61 4.1 20.8 1.0
CG A:TRP60 4.2 21.7 1.0
O A:HOH313 4.2 26.2 1.0
CE2 A:TYR56 4.2 17.5 1.0
CD1 A:TYR64 4.3 19.6 1.0
N A:ARG61 4.3 20.3 1.0
CE2 A:TYR64 4.4 21.1 1.0
C A:TRP60 4.4 21.0 1.0
C12 A:FXJ201 4.5 24.6 1.0
CD2 A:TRP60 4.5 24.1 1.0
CD2 A:LEU36 4.5 20.7 1.0
CG A:ARG61 4.6 20.8 1.0
CZ2 A:TRP60 4.8 23.2 1.0
NE A:ARG61 4.8 20.1 1.0
CE1 A:TYR64 4.9 19.9 1.0
CB A:ARG61 4.9 21.0 1.0
CZ A:TYR64 4.9 21.0 1.0
CG A:TYR56 5.0 15.1 1.0

Bromine binding site 2 out of 8 in 6d6n

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br201

b:39.6
occ:1.00
 BR2 A:FXJ201 0.0 39.6 1.0
C10 A:FXJ201 2.0 21.1 1.0
C12 A:FXJ201 2.8 24.6 1.0
C09 A:FXJ201 2.9 25.3 1.0
O13 A:FXJ201 3.0 23.0 1.0
C14 A:FXJ201 3.4 32.7 1.0
O23 A:FXJ201 3.7 35.6 1.0
O A:HOH328 3.9 51.2 1.0
CD1 A:ILE52 4.0 23.8 1.0
C15 A:FXJ201 4.0 34.5 1.0
CE1 A:TYR64 4.1 19.9 1.0
C05 A:FXJ201 4.1 19.6 1.0
C07 A:FXJ201 4.2 20.4 1.0
O A:HOH313 4.2 26.2 1.0
C22 A:FXJ201 4.5 36.2 1.0
CD1 A:TYR64 4.5 19.6 1.0
OD1 A:ASP65 4.6 41.3 1.0
C06 A:FXJ201 4.7 20.2 1.0
CD2 A:LEU36 4.7 20.7 1.0
CZ A:TYR64 4.8 21.0 1.0
CE2 A:TYR47 4.8 26.4 1.0
C16 A:FXJ201 4.9 33.7 1.0
CD2 A:TYR47 4.9 25.7 1.0
CG1 A:ILE52 4.9 19.4 1.0
OH A:TYR64 5.0 20.9 1.0
CG2 A:ILE52 5.0 20.7 1.0

Bromine binding site 3 out of 8 in 6d6n

Go back to Bromine Binding Sites List in 6d6n
Bromine binding site 3 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br201

b:25.9
occ:1.00
 BR1 B:FXJ201 0.0 25.9 1.0
C07 B:FXJ201 1.9 26.1 1.0
C09 B:FXJ201 2.8 25.4 1.0
C06 B:FXJ201 2.8 24.3 1.0
NE1 B:TRP60 3.4 23.1 1.0
CD1 B:TRP60 3.5 26.6 1.0
CG B:TYR64 3.6 23.1 1.0
CB B:TYR64 3.6 24.0 1.0
CD2 B:TYR64 3.6 26.9 1.0
CD2 B:TYR56 3.8 21.8 1.0
O28 B:FXJ201 4.0 24.8 1.0
CE2 B:TRP60 4.0 24.8 1.0
C10 B:FXJ201 4.1 26.5 1.0
CD B:ARG61 4.1 22.4 1.0
O B:TRP60 4.1 20.4 1.0
CA B:ARG61 4.1 19.6 1.0
C05 B:FXJ201 4.2 26.0 1.0
CG B:TRP60 4.2 25.1 1.0
CE2 B:TYR56 4.2 22.8 1.0
N B:ARG61 4.2 20.0 1.0
CD1 B:TYR64 4.3 21.6 1.0
C B:TRP60 4.3 20.0 1.0
CD2 B:LEU36 4.3 25.1 1.0
O B:HOH326 4.3 26.4 1.0
CE2 B:TYR64 4.4 24.7 1.0
CD2 B:TRP60 4.5 22.9 1.0
C12 B:FXJ201 4.6 26.4 1.0
CG B:ARG61 4.7 22.0 1.0
CZ2 B:TRP60 4.7 23.7 1.0
NE B:ARG61 4.9 21.7 1.0
CB B:ARG61 4.9 21.7 1.0
CG B:TYR56 4.9 22.1 1.0
CE1 B:TYR64 4.9 21.8 1.0
CZ B:TYR64 5.0 22.6 1.0

Bromine binding site 4 out of 8 in 6d6n

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br201

b:37.7
occ:1.00
 BR2 B:FXJ201 0.0 37.7 1.0
C10 B:FXJ201 1.9 26.5 1.0
C12 B:FXJ201 2.8 26.4 1.0
C09 B:FXJ201 2.8 25.4 1.0
O13 B:FXJ201 2.9 26.9 1.0
C14 B:FXJ201 3.3 29.4 1.0
CD1 B:ILE52 3.7 33.7 1.0
O23 B:FXJ201 3.8 36.6 1.0
C15 B:FXJ201 3.9 34.0 1.0
CE1 B:TYR64 4.0 21.8 1.0
O B:HOH355 4.0 36.1 1.0
C07 B:FXJ201 4.1 26.1 1.0
C05 B:FXJ201 4.1 26.0 1.0
C22 B:FXJ201 4.1 31.0 1.0
O B:HOH326 4.3 26.4 1.0
CD1 B:TYR64 4.4 21.6 1.0
C06 B:FXJ201 4.6 24.3 1.0
CG2 B:ILE52 4.7 28.0 1.0
CZ B:TYR64 4.7 22.6 1.0
CE2 B:TYR47 4.7 35.9 1.0
OD1 B:ASP65 4.7 37.7 1.0
CG1 B:ILE52 4.7 31.3 1.0
CD2 B:LEU36 4.8 25.1 1.0
C16 B:FXJ201 4.9 34.3 1.0
OH B:TYR64 4.9 22.1 1.0

Bromine binding site 5 out of 8 in 6d6n

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br202

b:24.9
occ:1.00
 BR1 C:FXJ202 0.0 24.9 1.0
C07 C:FXJ202 1.9 24.4 1.0
C06 C:FXJ202 2.8 21.5 1.0
C09 C:FXJ202 2.9 24.9 1.0
NE1 C:TRP60 3.4 22.5 1.0
CD1 C:TRP60 3.5 23.9 1.0
CD2 C:TYR64 3.6 23.6 1.0
CB C:TYR64 3.6 27.1 1.0
CG C:TYR64 3.6 22.5 1.0
CD2 C:TYR56 3.8 21.2 1.0
CE2 C:TRP60 4.0 22.1 1.0
CD C:ARG61 4.0 24.3 1.0
O27 C:FXJ202 4.0 23.4 1.0
O C:TRP60 4.1 22.3 1.0
C10 C:FXJ202 4.1 25.7 1.0
CA C:ARG61 4.1 22.0 1.0
O C:HOH329 4.2 26.1 1.0
C05 C:FXJ202 4.2 21.6 1.0
CG C:TRP60 4.2 22.9 1.0
N C:ARG61 4.3 21.2 1.0
CE2 C:TYR56 4.3 21.8 1.0
CD1 C:TYR64 4.3 23.6 1.0
CE2 C:TYR64 4.3 20.8 1.0
C C:TRP60 4.3 23.5 1.0
CD2 C:LEU36 4.4 27.9 1.0
CD2 C:TRP60 4.5 22.5 1.0
C12 C:FXJ202 4.6 25.4 1.0
CG C:ARG61 4.7 24.4 1.0
CZ2 C:TRP60 4.7 21.0 1.0
NE C:ARG61 4.8 22.9 1.0
CZ C:TYR64 4.9 22.9 1.0
CE1 C:TYR64 4.9 23.2 1.0
CB C:ARG61 4.9 21.8 1.0
CG C:TYR56 5.0 22.6 1.0
C C:ARG61 5.0 24.0 1.0
O C:ARG61 5.0 27.8 1.0

Bromine binding site 6 out of 8 in 6d6n

Go back to Bromine Binding Sites List in 6d6n
Bromine binding site 6 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br202

b:39.7
occ:1.00
 BR2 C:FXJ202 0.0 39.7 1.0
C10 C:FXJ202 1.9 25.7 1.0
C09 C:FXJ202 2.7 24.9 1.0
C12 C:FXJ202 2.8 25.4 1.0
O13 C:FXJ202 2.9 26.9 1.0
C14 C:FXJ202 3.3 32.7 1.0
O23 C:FXJ202 3.7 37.0 1.0
C15 C:FXJ202 3.9 35.7 1.0
CE1 C:TYR64 4.0 23.2 1.0
O C:HOH362 4.1 43.9 1.0
C07 C:FXJ202 4.1 24.4 1.0
C05 C:FXJ202 4.1 21.6 1.0
CD1 C:ILE52 4.1 30.1 1.0
C16 C:FXJ202 4.4 39.0 1.0
O C:HOH329 4.4 26.1 1.0
CD1 C:TYR64 4.5 23.6 1.0
C06 C:FXJ202 4.6 21.5 1.0
CZ C:TYR64 4.7 22.9 1.0
CE2 C:TYR47 4.7 37.7 1.0
OD1 C:ASP65 4.7 36.0 1.0
C22 C:FXJ202 4.8 36.3 1.0
OH C:TYR64 4.9 20.3 1.0
CG1 C:ILE52 4.9 32.2 1.0
CD2 C:LEU36 4.9 27.9 1.0
CG2 C:ILE52 5.0 32.1 1.0
CD2 C:TYR47 5.0 36.8 1.0

Bromine binding site 7 out of 8 in 6d6n

Go back to Bromine Binding Sites List in 6d6n
Bromine binding site 7 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br201

b:27.0
occ:1.00
 BR1 D:FXJ201 0.0 27.0 1.0
C07 D:FXJ201 1.8 27.1 1.0
C06 D:FXJ201 2.8 24.2 1.0
C09 D:FXJ201 2.8 28.7 1.0
NE1 D:TRP60 3.3 26.9 1.0
CD1 D:TRP60 3.5 28.9 1.0
CB D:TYR64 3.6 27.8 1.0
CG D:TYR64 3.6 23.8 1.0
CD2 D:TYR64 3.6 24.9 1.0
CD2 D:TYR56 3.8 20.1 1.0
CD D:ARG61 4.0 23.6 1.0
O27 D:FXJ201 4.0 25.4 1.0
CE2 D:TRP60 4.0 26.7 1.0
C10 D:FXJ201 4.0 33.1 1.0
O D:TRP60 4.1 25.2 1.0
C05 D:FXJ201 4.1 26.9 1.0
CA D:ARG61 4.1 24.0 1.0
CE2 D:TYR56 4.2 20.1 1.0
CG D:TRP60 4.3 26.2 1.0
CD1 D:TYR64 4.3 24.9 1.0
O D:HOH321 4.3 24.5 1.0
CD2 D:LEU36 4.3 25.5 1.0
CE2 D:TYR64 4.3 23.8 1.0
N D:ARG61 4.4 24.8 1.0
C D:TRP60 4.4 24.5 1.0
CD2 D:TRP60 4.6 29.7 1.0
C12 D:FXJ201 4.6 28.5 1.0
NE D:ARG61 4.7 22.4 1.0
CZ2 D:TRP60 4.7 28.9 1.0
CG D:ARG61 4.8 23.7 1.0
CG D:TYR56 4.9 19.7 1.0
CE1 D:TYR64 4.9 24.9 1.0
CB D:ARG61 5.0 22.5 1.0
CZ D:TYR64 5.0 25.6 1.0

Bromine binding site 8 out of 8 in 6d6n

Go back to Bromine Binding Sites List in 6d6n
Bromine binding site 8 out of 8 in the The Structure of Ligand Binding Domain of Lasr in Complex with Tp-1 Homolog, Compound 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br201

b:44.0
occ:1.00
 BR2 D:FXJ201 0.0 44.0 1.0
C10 D:FXJ201 1.9 33.1 1.0
C09 D:FXJ201 2.8 28.7 1.0
C12 D:FXJ201 2.8 28.5 1.0
O13 D:FXJ201 3.0 29.4 1.0
C14 D:FXJ201 3.2 39.7 1.0
O23 D:FXJ201 3.3 43.9 1.0
CD1 D:ILE52 3.7 37.5 1.0
CE1 D:TYR64 3.9 24.9 1.0
C07 D:FXJ201 4.1 27.1 1.0
C15 D:FXJ201 4.1 39.9 1.0
C05 D:FXJ201 4.2 26.9 1.0
CD1 D:TYR64 4.4 24.9 1.0
O D:HOH321 4.4 24.5 1.0
CG1 D:ILE52 4.6 37.9 1.0
CZ D:TYR64 4.6 25.6 1.0
C06 D:FXJ201 4.6 24.2 1.0
C16 D:FXJ201 4.6 44.7 1.0
OD1 D:ASP65 4.8 48.1 1.0
OH D:TYR64 4.8 25.1 1.0
CD2 D:LEU36 4.9 25.5 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 01:39:08 2024

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