Bromine in PDB 5y9s: Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator

The structure of Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator, PDB code: 5y9s was solved by Y.Jang, S.Hong, I.Jo, J.Ahn, N.C.Ha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.77 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.669, 221.895, 57.875, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.4

The binding sites of Bromine atom in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator (pdb code 5y9s). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator, PDB code: 5y9s:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator


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 VV2_1132, A Lysr Family Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Br401 b:80.3 occ:1.00 OG1 A:THR152 3.4 50.4 1.0 ND1 A:HIS138 3.6 35.1 1.0 CD2 A:LEU102 3.8 39.1 1.0 CB A:THR152 3.8 39.2 1.0 CB A:ILE135 4.0 39.6 1.0 CA A:ILE135 4.0 37.6 1.0 CG1 A:ILE135 4.1 44.2 1.0 CD1 A:LEU150 4.2 29.0 1.0 CE1 A:HIS138 4.2 33.8 1.0 CD1 A:ILE135 4.3 52.1 1.0 N A:ILE135 4.5 36.6 1.0 CG A:LEU102 4.6 53.7 1.0 CG A:HIS138 4.6 32.4 1.0 CG2 A:THR152 4.7 33.8 1.0 O A:LEU133 4.8 40.5 1.0 CD2 A:LEU150 4.9 21.0 1.0 CB A:HIS138 5.0 26.9 1.0

Bromine binding site 2 out of 9 in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator


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 VV2_1132, A Lysr Family Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Br402 b:0.8 occ:1.00 CD1 A:LEU207 3.5 44.6 1.0 CG A:LEU207 3.5 37.3 1.0 N A:LEU207 3.6 55.0 1.0 OG1 A:THR104 3.8 39.5 1.0 CB A:LEU207 3.9 35.4 1.0 CB A:PHE206 4.1 55.0 1.0 N A:PHE206 4.1 49.1 1.0 CD1 A:LEU102 4.2 56.3 1.0 CA A:LEU207 4.4 42.2 1.0 CA A:PHE206 4.5 51.9 1.0 O A:THR229 4.5 56.1 1.0 C A:PHE206 4.5 49.2 1.0 CB A:THR205 4.6 55.7 1.0 CE2 A:TYR153 4.7 53.2 1.0 CD2 A:LEU207 4.9 33.1 1.0 CD2 A:TYR153 4.9 51.7 1.0 OG1 A:THR205 4.9 58.4 1.0 CB A:THR104 4.9 49.5 1.0

Bromine binding site 3 out of 9 in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator


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 VV2_1132, A Lysr Family Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ B:Br401 b:77.7 occ:1.00 NE1 B:TRP46 3.4 19.9 1.0 N B:LEU5 3.5 20.7 1.0 CA B:PRO4 3.9 23.3 1.0 CE2 D:PHE7 3.9 36.2 1.0 CZ2 B:TRP46 4.0 22.3 1.0 CZ D:PHE7 4.0 27.3 1.0 O B:ASN3 4.0 53.9 1.0 CE2 B:TRP46 4.1 23.0 1.0 CG1 D:VAL79 4.1 12.6 1.0 C B:PRO4 4.2 26.8 1.0 CB B:LEU5 4.2 13.0 1.0 CD2 D:PHE7 4.3 44.5 1.0 CE1 D:PHE7 4.4 30.5 1.0 CA B:LEU5 4.5 18.6 1.0 CD1 B:TRP46 4.6 25.5 1.0 CG D:PHE7 4.7 41.4 1.0 CB B:PRO4 4.7 20.2 1.0 CD1 D:PHE7 4.8 33.6 1.0 C B:ASN3 4.8 40.3 1.0 N B:PRO4 4.8 32.7 1.0

Bromine binding site 4 out of 9 in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator


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 VV2_1132, A Lysr Family Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ C:Br401 b:93.4 occ:1.00 CE A:MET141 3.8 43.6 1.0 O C:GLU44 3.8 15.0 1.0 N C:PRO50 3.9 15.0 1.0 C C:VAL49 4.0 20.8 1.0 CB C:GLU44 4.0 12.4 1.0 C C:GLU44 4.0 13.0 1.0 O C:HOH509 4.1 19.7 1.0 CD C:PRO50 4.2 17.4 1.0 O C:VAL49 4.3 18.1 1.0 CA C:VAL49 4.3 16.7 1.0 N C:VAL45 4.3 11.9 1.0 CA C:PRO50 4.4 14.2 1.0 N C:VAL49 4.5 15.3 1.0 C C:GLY48 4.5 18.6 1.0 O C:GLY48 4.5 19.5 1.0 CA C:GLU44 4.6 16.1 1.0 CA C:VAL45 4.6 11.9 1.0 CB C:PRO50 4.7 18.3 1.0

Bromine binding site 5 out of 9 in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator


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 VV2_1132, A Lysr Family Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ C:Br402 b:35.6 occ:1.00 O C:HOH510 3.2 30.9 1.0 N C:THR104 3.6 23.6 1.0 N C:SER231 3.7 24.7 1.0 CG2 C:THR104 3.7 17.0 1.0 CB C:THR104 3.9 30.2 1.0 CA C:LEU230 4.1 24.3 1.0 CB C:HIS103 4.1 14.8 1.0 N C:HIS103 4.2 26.8 1.0 CB C:SER231 4.3 26.0 1.0 O C:THR229 4.3 30.3 1.0 CA C:THR104 4.3 21.0 1.0 OG C:SER231 4.4 43.8 1.0 C C:LEU230 4.4 23.7 1.0 CD2 C:LEU230 4.5 22.4 1.0 CA C:HIS103 4.5 29.5 1.0 C C:HIS103 4.5 25.9 1.0 CA C:SER231 4.6 20.5 1.0 CB C:LEU102 4.6 30.2 1.0 CB C:LEU230 4.6 21.5 1.0 CD2 C:LEU102 4.7 27.6 1.0 ND1 C:HIS103 4.8 22.7 1.0 C C:LEU102 4.9 18.4 1.0 O C:HOH519 4.9 23.2 1.0 CG C:HIS103 4.9 19.4 1.0

Bromine binding site 6 out of 9 in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator


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 VV2_1132, A Lysr Family Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ C:Br403 b:71.8 occ:1.00 N C:GLY134 3.2 10.6 1.0 OG C:SER131 3.4 41.6 1.0 CZ C:PHE206 3.4 63.8 1.0 CA C:GLY134 3.6 18.9 1.0 N C:VAL132 3.6 21.6 1.0 C C:SER131 3.7 23.1 1.0 O C:SER131 3.9 19.1 1.0 C C:VAL132 3.9 20.3 1.0 CA C:VAL132 3.9 18.6 1.0 N C:LEU133 3.9 19.4 1.0 C C:GLY134 3.9 29.4 1.0 CB C:SER131 4.0 22.6 1.0 CE1 C:PHE206 4.0 66.8 1.0 N C:ILE135 4.3 25.3 1.0 CD2 C:HIS138 4.3 12.6 1.0 CA C:SER131 4.3 24.0 1.0 C C:LEU133 4.4 19.9 1.0 O C:VAL132 4.4 18.2 1.0 O C:GLY134 4.5 32.6 1.0 CE2 C:PHE206 4.5 67.7 1.0 NE2 C:HIS138 4.5 17.1 1.0 CA C:LEU133 4.8 14.8 1.0 CA C:ILE135 5.0 24.6 1.0

Bromine binding site 7 out of 9 in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator


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 VV2_1132, A Lysr Family Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ C:Br404 b:94.8 occ:1.00 N C:LEU5 3.4 19.6 1.0 NE1 C:TRP46 3.7 18.9 1.0 CZ A:PHE7 3.8 39.2 1.0 CG1 A:VAL79 3.8 23.4 1.0 O A:HOH542 3.8 28.4 1.0 CE2 A:PHE7 3.9 42.5 1.0 CA C:PRO4 3.9 28.1 1.0 CZ2 C:TRP46 4.0 20.2 1.0 CE1 A:PHE7 4.0 39.7 1.0 C C:PRO4 4.1 17.3 1.0 CD2 A:PHE7 4.1 49.9 1.0 CB C:LEU5 4.2 24.5 1.0 CE2 C:TRP46 4.2 17.4 1.0 CD1 A:PHE7 4.2 49.6 1.0 O C:ASN3 4.2 48.6 1.0 CG A:PHE7 4.3 48.5 1.0 CA C:LEU5 4.4 15.9 1.0 CB C:PRO4 4.6 29.0 1.0 N C:PRO4 5.0 31.6 1.0 CD1 C:TRP46 5.0 20.2 1.0

Bromine binding site 8 out of 9 in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator


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 VV2_1132, A Lysr Family Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ D:Br401 b:41.9 occ:1.00 O D:HOH514 2.9 20.1 1.0 CG D:LEU207 3.6 28.7 1.0 N D:LEU207 3.7 22.3 1.0 CB D:THR205 3.7 18.5 1.0 N D:PHE206 3.7 14.5 1.0 CD1 D:LEU207 3.7 26.1 1.0 CB D:LEU207 4.1 25.5 1.0 CB D:PHE206 4.2 24.0 1.0 CE2 D:TYR153 4.3 28.5 1.0 CD2 D:LEU102 4.3 25.9 1.0 CA D:PHE206 4.3 29.6 1.0 OG1 D:THR205 4.4 18.2 1.0 CA D:THR205 4.4 21.4 1.0 C D:THR205 4.4 19.6 1.0 CG2 D:THR205 4.4 30.3 1.0 C D:PHE206 4.5 36.2 1.0 CD2 D:TYR153 4.5 28.0 1.0 CA D:LEU207 4.5 25.3 1.0 O D:THR229 4.8 40.6 1.0 OG1 D:THR104 4.8 58.3 1.0 CD2 D:LEU207 4.9 20.4 1.0

Bromine binding site 9 out of 9 in the Crystal Structure of VV2_1132, A Lysr Family Transcriptional Regulator


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 VV2_1132, A Lysr Family Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ D:Br402 b:62.7 occ:1.00 N D:LYS92 3.5 36.3 1.0 CG D:LYS92 3.7 68.4 1.0 CB D:LYS92 3.9 50.9 1.0 CD D:ARG98 4.0 20.4 1.0 CG2 D:THR96 4.0 32.9 1.0 CG D:ARG98 4.0 24.1 1.0 O D:SER90 4.1 39.7 1.0 CA D:LYS92 4.3 45.3 1.0 CA D:LEU91 4.3 35.1 1.0 C D:LEU91 4.4 39.0 1.0 CB D:THR96 4.7 35.0 1.0 C D:SER90 4.7 37.4 1.0 CD1 D:LEU91 4.8 37.3 1.0 CE D:LYS92 4.8 65.5 1.0 OE2 C:GLU227 4.8 54.4 1.0 OG D:SER127 4.9 31.7 1.0 CD D:LYS92 4.9 70.7 1.0 N D:LEU91 4.9 38.1 1.0 CB D:SER127 5.0 19.3 1.0

Y.Jang, G.Choi, S.Hong, I.Jo, J.Ahn, S.H.Choi, N.C.Ha. A Novel Tetrameric Assembly Configuration in VV2_1132, A Lysr-Type Transcriptional Regulator Invibrio Vulnificus Mol. Cells V. 41 301 2018.
ISSN: ISSN 0219-1032
PubMed: 29487273
DOI: 10.14348/MOLCELLS.2018.2190