Bromine in PDB 5zqu: Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn

The structure of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn, PDB code: 5zqu was solved by Y.Miyashita, N.Numoto, S.Arulmozhiraja, S.Nakano, N.Matsuo, K.Shimizu, H.Kakuta, S.Ito, T.Ikura, N.Ito, H.Tokiwa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.52 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.571, 100.492, 111.010, 90.00, 99.27, 90.00
R / Rfree (%)	22.2 / 27

Pages:

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

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn (pdb code 5zqu). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 11 binding sites of Bromine where determined in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn, PDB code: 5zqu:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Br503 b:45.2 occ:0.75 O B:HOH606 3.1 39.5 1.0 O A:HOH610 3.1 46.7 1.0 O A:HOH620 3.2 56.9 1.0 NH1 A:ARG393 3.5 54.5 1.0 CD A:ARG393 3.5 41.3 1.0 NH2 B:ARG421 3.5 38.2 1.0 CG A:PRO378 4.1 43.0 1.0 CB B:LEU420 4.2 40.0 1.0 CZ A:ARG393 4.3 42.5 1.0 NE A:ARG393 4.3 42.3 1.0 OE2 A:GLU390 4.4 56.7 1.0 CD1 B:LEU420 4.5 43.0 1.0 CZ B:ARG421 4.5 39.3 1.0 O B:LEU420 4.6 34.8 1.0 CD A:PRO378 4.6 40.3 1.0 CG A:GLU390 4.6 51.4 1.0 NE B:ARG421 4.7 37.9 1.0 CG A:ARG393 4.7 44.0 1.0 CG B:LEU420 5.0 44.3 1.0 CD A:GLU390 5.0 55.4 1.0

Bromine binding site 2 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Br504 b:46.2 occ:0.75 O A:HOH605 3.2 34.5 1.0 NH1 B:ARG393 3.4 37.1 1.0 NH2 A:ARG421 3.5 36.7 1.0 CD B:ARG393 3.6 41.1 1.0 CB A:LEU420 4.0 36.8 1.0 CG B:PRO378 4.2 45.6 1.0 CZ B:ARG393 4.3 40.8 1.0 CD1 A:LEU420 4.4 41.0 1.0 NE B:ARG393 4.4 42.8 1.0 O A:LEU420 4.4 37.1 1.0 CZ A:ARG421 4.5 41.4 1.0 NE A:ARG421 4.6 38.8 1.0 OE2 B:GLU390 4.7 72.6 1.0 CD B:PRO378 4.7 45.6 1.0 CG B:ARG393 4.8 48.9 1.0 CG A:LEU420 4.8 38.2 1.0 C A:LEU420 5.0 38.4 1.0 CG B:GLU390 5.0 59.7 1.0

Bromine binding site 3 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Br505 b:69.0 occ:0.75 CG1 A:ILE345 3.8 62.5 1.0 NH2 A:ARG348 3.9 77.9 1.0 CB A:ALA344 4.0 59.5 1.0 NZ A:LYS431 4.1 70.4 1.0 N A:ILE345 4.1 53.4 1.0 CD A:ARG348 4.1 64.4 1.0 C A:ALA344 4.2 54.2 1.0 CA A:ILE345 4.3 55.8 1.0 CD A:LYS431 4.4 62.9 1.0 CG A:LYS431 4.4 53.5 1.0 CE1 A:HIS435 4.5 74.1 1.0 O A:ALA344 4.5 54.2 1.0 O A:HOH630 4.6 59.9 1.0 CB A:ILE345 4.6 67.2 1.0 CB A:LYS431 4.6 52.4 1.0 CD1 A:ILE345 4.8 67.0 1.0 CA A:ALA344 4.8 57.4 1.0 CE A:LYS431 4.8 73.0 1.0 CZ A:ARG348 4.9 84.2 1.0 ND1 A:HIS435 4.9 73.1 1.0 NE A:ARG348 5.0 85.0 1.0 O A:HOH604 5.0 42.7 1.0

Bromine binding site 4 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Br506 b:74.1 occ:0.75 O A:HOH614 3.3 49.5 1.0 NH1 A:ARG348 3.5 76.6 1.0 CB A:SER427 3.8 36.2 1.0 O B:HOH619 3.8 43.6 1.0 OG A:SER427 3.8 41.5 1.0 NH1 B:ARG426 3.9 35.6 1.0 CD B:ARG426 4.1 35.1 1.0 CZ A:ARG348 4.2 84.2 1.0 NZ A:LYS431 4.3 70.4 1.0 CZ B:ARG426 4.4 41.9 1.0 NE B:ARG426 4.4 41.0 1.0 NE A:ARG348 4.6 85.0 1.0 CD2 B:LEU430 4.7 41.3 1.0 NH2 A:ARG348 4.9 77.9 1.0 CD1 B:LEU430 4.9 39.4 1.0

Bromine binding site 5 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ B:Br502 b:62.9 occ:0.75 NH1 B:ARG371 3.2 44.8 1.0 CD B:ARG371 3.5 43.0 1.0 CA B:GLY368 3.7 35.4 1.0 NE1 B:TRP282 3.8 43.3 1.0 N B:GLY368 4.0 37.1 1.0 CD2 B:LEU367 4.1 41.7 1.0 CZ B:ARG371 4.1 46.1 1.0 CG B:LEU367 4.2 40.2 1.0 NE B:ARG371 4.3 52.9 1.0 C B:LEU367 4.5 41.7 1.0 CD1 B:TRP282 4.5 42.7 1.0 CE2 B:TRP282 4.5 42.3 1.0 O B:LEU367 4.6 42.7 1.0 CG B:ARG371 4.6 38.4 1.0 CZ2 B:TRP282 4.8 42.3 1.0 CB B:LEU367 4.9 42.0 1.0 O B:LYS364 4.9 47.0 1.0 CB B:ARG371 4.9 36.8 1.0 C B:GLY368 5.0 39.1 1.0

Bromine binding site 6 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ B:Br503 b:69.1 occ:0.75 CD B:ARG348 3.6 60.3 1.0 CG1 B:ILE345 3.8 80.2 1.0 CB B:ALA344 3.9 59.7 1.0 N B:ILE345 4.1 58.7 1.0 C B:ALA344 4.2 59.5 1.0 CA B:ILE345 4.3 62.8 1.0 CG B:LYS431 4.3 61.9 1.0 CD B:LYS431 4.4 66.5 1.0 O B:ALA344 4.4 58.1 1.0 CE1 B:HIS435 4.5 78.7 1.0 CB B:LYS431 4.6 50.9 1.0 CB B:ILE345 4.6 63.1 1.0 NE B:ARG348 4.6 66.8 1.0 CG B:ARG348 4.6 58.1 1.0 CA B:ALA344 4.7 67.0 1.0 CE B:LYS431 4.8 64.5 1.0 CD1 B:ILE345 4.8 0.8 1.0 ND1 B:HIS435 4.9 78.1 1.0 O B:HOH622 4.9 64.3 1.0

Bromine binding site 7 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ B:Br504 b:77.1 occ:0.75 NH2 B:ARG371 3.2 43.6 1.0 NH1 B:ARG371 3.8 44.8 1.0 CZ B:ARG371 3.9 46.1 1.0 OG B:SER312 4.0 52.2 1.0 CG2 B:THR278 4.2 46.2 1.0 CA B:LEU279 4.2 47.1 1.0 CD1 B:LEU279 4.2 44.0 1.0 O B:THR278 4.3 46.4 1.0 CB B:TRP282 4.4 45.6 1.0 N B:LEU279 4.5 45.8 1.0 C B:THR278 4.5 47.5 1.0 CB B:LEU279 4.6 55.8 1.0 CG B:TRP282 4.7 45.8 1.0 CB B:SER312 4.9 50.1 1.0 CD2 B:LEU309 5.0 50.0 1.0

Bromine binding site 8 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ C:Br502 b:55.4 occ:0.75 O D:HOH605 3.1 38.3 1.0 O D:HOH610 3.2 54.1 1.0 NH1 C:ARG393 3.4 51.6 1.0 NH2 D:ARG421 3.6 44.4 1.0 CD C:ARG393 3.6 55.3 1.0 CB D:LEU420 4.1 50.0 1.0 CG C:PRO378 4.1 55.3 1.0 CZ C:ARG393 4.2 52.8 1.0 NE C:ARG393 4.3 61.0 1.0 CD1 D:LEU420 4.4 52.3 1.0 O D:LEU420 4.5 48.5 1.0 CZ D:ARG421 4.5 44.8 1.0 OE2 C:GLU390 4.6 67.7 1.0 CD C:PRO378 4.6 53.4 1.0 NE D:ARG421 4.6 44.3 1.0 CG C:ARG393 4.8 55.4 1.0 CG C:GLU390 4.8 57.8 1.0 CG D:LEU420 4.9 51.1 1.0

Bromine binding site 9 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ C:Br503 b:73.2 occ:0.75 NE C:ARG348 3.6 80.9 1.0 CE C:LYS431 3.6 78.5 1.0 CG1 C:ILE345 3.8 71.7 1.0 CB C:ALA344 4.1 64.7 1.0 N C:ILE345 4.1 67.6 1.0 C C:ALA344 4.2 67.9 1.0 CA C:ILE345 4.3 67.1 1.0 CD C:ARG348 4.3 82.7 1.0 CG C:LYS431 4.4 61.8 1.0 O C:ALA344 4.4 68.9 1.0 NH2 C:ARG348 4.4 0.9 1.0 CZ C:ARG348 4.5 93.6 1.0 CG C:ARG348 4.5 77.1 1.0 CB C:LYS431 4.5 53.6 1.0 NZ C:LYS431 4.6 77.9 1.0 CE1 C:HIS435 4.6 81.0 1.0 CB C:ILE345 4.6 66.5 1.0 CD C:LYS431 4.6 74.0 1.0 O C:HOH602 4.6 62.0 1.0 CD1 C:ILE345 4.8 84.8 1.0 CA C:ALA344 4.8 67.9 1.0

Bromine binding site 10 out of 11 in the Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of Tetrameric Rxralpha-Lbd Complexed with Partial Agonist Cbt-Pmn within 5.0Å range: probe atom residue distance (Å) B Occ D:Br503 b:60.2 occ:0.75 NH2 C:ARG421 3.5 50.2 1.0 NH1 D:ARG393 3.6 55.3 1.0 CD D:ARG393 3.7 57.5 1.0 CG D:PRO378 4.0 58.8 1.0 CB C:LEU420 4.2 52.7 1.0 OE2 D:GLU390 4.3 77.3 1.0 CZ D:ARG393 4.4 56.9 1.0 CZ C:ARG421 4.5 57.5 1.0 NE D:ARG393 4.5 70.2 1.0 O C:LEU420 4.5 51.6 1.0 NE C:ARG421 4.5 51.2 1.0 CD1 C:LEU420 4.5 55.2 1.0 CG D:GLU390 4.6 69.2 1.0 CD D:PRO378 4.6 58.6 1.0 CG D:ARG393 4.9 56.3 1.0 CD D:GLU390 4.9 71.9 1.0 NZ C:LYS417 5.0 88.2 1.0

Y.Miyashita, N.Numoto, S.Arulmozhiraja, S.Nakano, N.Matsuo, K.Shimizu, O.Shibahara, M.Fujihara, H.Kakuta, S.Ito, T.Ikura, N.Ito, H.Tokiwa. Dual Conformation of the Ligand Induces the Partial Agonistic Activity of Retinoid X Receptor Alpha (Rxr Alpha ). Febs Lett. V. 593 242 2019.
ISSN: ISSN 1873-3468
PubMed: 30565665
DOI: 10.1002/1873-3468.13301