Bromine in PDB 4f8l: X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf

The structure of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf, PDB code: 4f8l was solved by R.Bao, L.Esser, D.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.08 / 1.50
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	26.108, 54.164, 101.626, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 18.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Bromine atom in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf (pdb code 4f8l). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 36 binding sites of Bromine where determined in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf, PDB code: 4f8l:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br202 b:74.1 occ:0.62 HA A:THR12 2.9 11.8 1.0 H2 A:HOH312 3.4 23.8 1.0 O A:HOH312 3.4 20.0 1.0 CA A:THR12 3.8 10.0 1.0 H1 A:HOH312 3.9 23.8 1.0 CG2 A:THR12 3.9 20.0 1.0 CB A:THR12 4.0 20.0 1.0 O A:THR12 4.1 17.8 1.0 C A:THR12 4.3 14.7 1.0 O A:ASN11 4.7 11.7 1.0 H1 A:HOH395 4.8 31.5 1.0 O A:HOH336 4.9 30.3 1.0 N A:THR12 4.9 9.0 1.0 H1 A:HOH361 5.0 36.1 1.0

Bromine binding site 2 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br203 b:23.3 occ:0.57 H A:TYR60 2.5 17.0 1.0 HA A:ASP59 3.2 19.3 1.0 H2 A:HOH420 3.3 47.6 1.0 N A:TYR60 3.4 14.3 1.0 HD1 A:TYR60 3.4 19.1 1.0 HB2 A:TYR60 3.4 19.3 1.0 O A:HOH420 3.8 39.8 1.0 O A:TYR60 4.0 17.3 1.0 CA A:ASP59 4.0 16.2 1.0 HB3 A:ASP59 4.0 26.1 1.0 C A:ASP59 4.2 13.7 1.0 CB A:TYR60 4.2 16.2 1.0 CA A:TYR60 4.2 16.2 1.0 CD1 A:TYR60 4.3 16.1 1.0 OD1 A:ASP59 4.4 27.3 1.0 CB A:ASP59 4.4 21.9 1.0 C A:TYR60 4.6 17.2 1.0 O A:GLY58 4.6 20.1 1.0 H1 A:HOH420 4.7 47.6 1.0 CG A:TYR60 4.7 16.7 1.0 CG A:ASP59 4.9 27.8 1.0 HB3 A:TYR60 5.0 19.3 1.0

Bromine binding site 3 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br204 b:28.5 occ:0.46 O A:HOH333 2.4 34.5 1.0 H A:GLY72 2.5 15.8 1.0 HG12 A:ILE73 2.8 31.4 1.0 H A:ILE73 2.9 17.5 1.0 H2 A:HOH333 3.0 41.2 1.0 H1 A:HOH333 3.0 41.2 1.0 H2 A:HOH340 3.1 39.6 1.0 N A:GLY72 3.2 13.3 1.0 HA A:VAL71 3.4 11.2 1.0 O A:HOH340 3.4 33.1 1.0 N A:ILE73 3.6 14.7 1.0 HA3 A:GLY72 3.7 17.6 1.0 CG1 A:ILE73 3.7 26.3 1.0 HD11 A:ILE73 3.8 26.6 1.0 HD13 A:ILE73 3.8 26.6 1.0 HG13 A:VAL71 3.8 11.2 1.0 CA A:GLY72 3.9 14.8 1.0 CD1 A:ILE73 4.0 22.3 1.0 C A:VAL71 4.0 11.1 1.0 CA A:VAL71 4.1 9.4 1.0 HG13 A:ILE73 4.2 31.4 1.0 HG12 A:VAL71 4.2 11.2 1.0 C A:GLY72 4.3 16.9 1.0 H1 A:HOH340 4.4 39.6 1.0 CG1 A:VAL71 4.4 9.5 1.0 CB A:ILE73 4.6 16.8 1.0 HB A:ILE73 4.6 19.9 1.0 CA A:ILE73 4.7 17.4 1.0 HA2 A:GLY72 4.8 17.6 1.0 HD12 A:ILE73 4.9 26.6 1.0 CB A:VAL71 4.9 12.1 1.0 O A:TRP70 5.0 10.8 1.0 H2 A:HOH376 5.0 31.1 1.0

Bromine binding site 4 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br205 b:23.3 occ:0.42 HG1 A:THR28 2.4 14.8 1.0 HG1 A:THR30 2.7 24.9 1.0 O A:ASP7 2.9 16.7 1.0 OG1 A:THR28 3.0 12.5 1.0 OD1 A:ASP7 3.1 31.1 1.0 H A:THR30 3.3 15.4 1.0 HB3 A:ASP7 3.3 22.2 1.0 OG1 A:THR30 3.4 20.9 1.0 HB A:THR28 3.5 12.1 1.0 O A:THR28 3.5 10.2 1.0 CG A:ASP7 3.6 25.9 1.0 C A:ASP7 3.6 15.4 1.0 C A:THR28 3.7 8.8 1.0 HB A:THR30 3.7 24.0 1.0 HB3 A:ALA9 3.7 13.6 1.0 CB A:THR28 3.8 10.2 1.0 HA A:LEU29 3.8 10.9 1.0 N A:THR30 3.8 13.0 1.0 H A:ALA9 3.8 10.3 1.0 CB A:ASP7 3.9 18.6 1.0 HA A:PHE8 3.9 15.6 1.0 H1 A:HOH382 4.0 27.5 1.0 N A:LEU29 4.0 8.3 1.0 CB A:THR30 4.0 20.1 1.0 CA A:LEU29 4.2 9.2 1.0 N A:ALA9 4.2 8.7 1.0 HB2 A:ALA9 4.2 13.6 1.0 C A:LEU29 4.2 11.1 1.0 N A:PHE8 4.3 11.9 1.0 H2 A:HOH344 4.3 12.4 1.0 CA A:THR28 4.4 9.9 1.0 CB A:ALA9 4.4 11.5 1.0 OD2 A:ASP7 4.4 28.1 1.0 CA A:ASP7 4.4 16.3 1.0 CA A:PHE8 4.4 13.1 1.0 H A:LEU29 4.5 9.8 1.0 H2 A:HOH382 4.6 27.5 1.0 CA A:THR30 4.6 17.0 1.0 C A:PHE8 4.6 12.6 1.0 O A:HOH382 4.7 23.1 1.0 H2 A:HOH405 4.7 52.0 1.0 HB2 A:ASP7 4.7 22.2 1.0 O A:HOH342 4.8 21.5 1.0 H A:THR28 4.9 11.1 1.0 CA A:ALA9 4.9 10.3 1.0 H A:PHE8 5.0 14.1 1.0

Bromine binding site 5 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br206 b:43.0 occ:0.51 H A:ASP86 2.4 23.5 1.0 HD2 A:LYS85 2.6 42.4 1.0 HA A:LYS85 3.2 27.6 1.0 HB2 A:ASP86 3.2 25.4 1.0 N A:ASP86 3.2 19.7 1.0 HE3 A:LYS85 3.4 45.5 1.0 CD A:LYS85 3.5 35.5 1.0 HB3 A:LYS85 3.7 29.9 1.0 CB A:ASP86 3.8 21.4 1.0 CG A:ASP86 3.9 27.2 1.0 CA A:LYS85 3.9 23.2 1.0 CE A:LYS85 3.9 38.1 1.0 C A:LYS85 4.0 22.5 1.0 CB A:LYS85 4.1 25.1 1.0 CA A:ASP86 4.1 19.4 1.0 HD3 A:LYS85 4.1 42.4 1.0 OD1 A:ASP86 4.2 23.0 1.0 HE2 A:LYS85 4.2 45.5 1.0 OD2 A:ASP86 4.2 27.4 1.0 H2 A:HOH318 4.2 34.7 1.0 H1 A:HOH318 4.3 34.7 1.0 CG A:LYS85 4.3 30.7 1.0 HG3 A:LYS85 4.5 36.6 1.0 HB3 A:ASP86 4.7 25.4 1.0 O A:HOH318 4.7 29.1 1.0 HA A:ASP86 4.8 23.1 1.0 O A:PRO84 5.0 25.0 1.0

Bromine binding site 6 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br207 b:33.5 occ:0.51 H A:LYS88 2.4 19.6 1.0 O A:HOH331 3.0 30.7 1.0 HA A:ILE87 3.1 17.5 1.0 N A:LYS88 3.2 16.4 1.0 H1 A:HOH411 3.4 60.9 1.0 HB2 A:LYS88 3.5 23.6 1.0 H1 A:HOH331 3.5 36.6 1.0 HG23 A:ILE87 3.6 18.3 1.0 H2 A:HOH331 3.7 36.6 1.0 O A:LYS88 3.8 17.4 1.0 HG3 A:MET67 3.8 15.1 1.0 CA A:ILE87 3.9 14.7 1.0 C A:ILE87 4.1 13.3 1.0 CA A:LYS88 4.1 15.5 1.0 O A:HOH411 4.2 50.9 1.0 CB A:LYS88 4.2 19.8 1.0 SD A:MET67 4.2 16.4 0.9 O A:ASP86 4.3 20.0 1.0 C A:LYS88 4.3 16.1 1.0 CG2 A:ILE87 4.4 15.4 1.0 H2 A:HOH411 4.4 60.9 1.0 HG22 A:ILE87 4.5 18.3 1.0 CG A:MET67 4.5 12.7 1.0 HG3 A:LYS88 4.6 28.6 1.0 HG12 A:ILE87 4.6 25.4 1.0 CB A:ILE87 4.7 15.9 1.0 HB3 A:LYS88 4.9 23.6 1.0 CG A:LYS88 5.0 24.0 1.0 N A:ILE87 5.0 15.1 1.0

Bromine binding site 7 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br208 b:27.1 occ:0.49 HE21 A:GLN136 2.6 29.0 1.0 HG3 A:GLN136 2.9 26.2 1.0 HD3 A:PRO101 3.2 15.0 1.0 HG3 A:PRO101 3.3 14.9 1.0 HB3 A:ALA17 3.4 18.2 1.0 NE2 A:GLN136 3.5 24.3 1.0 H1 A:HOH363 3.5 44.0 1.0 HB1 A:ALA17 3.6 18.2 1.0 CG A:GLN136 3.8 22.0 1.0 CB A:ALA17 3.9 15.3 1.0 CD A:PRO101 3.9 12.6 1.0 O A:HOH363 4.0 36.8 1.0 CG A:PRO101 4.0 12.5 1.0 HE22 A:GLN136 4.0 29.0 1.0 CD A:GLN136 4.2 24.8 1.0 HA A:GLN136 4.2 20.4 1.0 HB2 A:ALA17 4.3 18.2 1.0 HD2 A:PRO101 4.3 15.0 1.0 HB3 A:PRO101 4.3 15.1 1.0 HB2 A:GLN136 4.4 18.9 1.0 HG2 A:GLN136 4.5 26.2 1.0 H2 A:HOH363 4.5 44.0 1.0 CB A:GLN136 4.6 15.9 1.0 HG2 A:PRO101 4.8 14.9 1.0 CB A:PRO101 4.8 12.7 1.0 CA A:GLN136 4.9 17.1 1.0 OE1 A:GLU139 4.9 34.5 0.5 H1 A:HOH422 5.0 38.9 1.0

Bromine binding site 8 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br209 b:32.1 occ:0.53 H A:VAL122 2.5 15.5 1.0 HA A:THR121 2.9 16.1 1.0 HG23 A:VAL122 3.1 14.9 1.0 H1 A:HOH390 3.2 33.8 1.0 H1 A:HOH319 3.2 29.3 1.0 H2 A:HOH436 3.2 44.8 1.0 N A:VAL122 3.4 13.1 1.0 H1 A:HOH424 3.4 47.7 1.0 HG23 A:THR121 3.5 20.2 1.0 HB A:VAL122 3.5 15.5 1.0 CA A:THR121 3.8 13.6 1.0 CG2 A:VAL122 3.8 12.6 1.0 O A:HOH424 3.9 39.9 1.0 O A:HOH319 3.9 24.6 1.0 H2 A:HOH319 3.9 29.3 1.0 H1 A:HOH444 3.9 73.1 1.0 O A:HOH390 4.0 28.3 1.0 H2 A:HOH444 4.0 73.1 1.0 CB A:VAL122 4.0 13.0 1.0 HG21 A:VAL122 4.1 14.9 1.0 C A:THR121 4.1 12.6 1.0 O A:HOH444 4.1 61.1 1.0 O A:HOH436 4.2 37.4 1.0 H2 A:HOH389 4.2 54.8 1.0 CG2 A:THR121 4.2 17.0 1.0 H2 A:HOH390 4.2 33.8 1.0 O A:SER120 4.3 19.0 1.0 HG22 A:THR121 4.3 20.2 1.0 O A:HOH437 4.3 44.6 1.0 CA A:VAL122 4.3 12.8 1.0 H1 A:HOH436 4.4 44.8 1.0 CB A:THR121 4.6 15.1 1.0 HG22 A:VAL122 4.6 14.9 1.0 H2 A:HOH437 4.7 53.3 1.0 H2 A:HOH424 4.7 47.7 1.0 H1 A:HOH389 4.8 54.8 1.0 N A:THR121 4.8 14.5 1.0 C A:SER120 4.9 17.9 1.0 H1 A:HOH437 4.9 53.3 1.0 O A:HOH389 5.0 45.8 1.0 OG1 A:THR121 5.0 17.1 1.0 O A:VAL122 5.0 15.0 1.0

Bromine binding site 9 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br210 b:35.4 occ:0.54 HA A:ASN124 3.1 16.9 1.0 HG12 A:VAL122 3.3 16.9 1.0 HG A:SER125 3.5 25.6 1.0 H A:SER125 3.6 17.1 1.0 OG A:SER125 3.7 21.5 1.0 CA A:ASN124 3.7 14.2 1.0 N A:SER125 3.8 14.4 1.0 HG11 A:VAL122 3.8 16.9 1.0 C A:ASN124 3.8 14.1 1.0 N A:ASN124 3.9 12.7 1.0 H1 A:HOH364 4.0 27.1 1.0 CG1 A:VAL122 4.0 14.2 1.0 HB3 A:SER125 4.0 22.5 1.0 C A:ILE123 4.1 15.5 1.0 O A:ILE123 4.2 14.4 1.0 H A:ASN124 4.2 15.1 1.0 O A:HOH364 4.3 22.7 1.0 CB A:SER125 4.3 18.9 1.0 O A:ASN124 4.4 12.6 1.0 HG13 A:VAL122 4.5 16.9 1.0 CA A:SER125 4.7 14.9 1.0 HA A:ILE123 4.8 16.9 1.0 H1 A:HOH436 4.9 44.8 1.0 HD21 A:ASN124 4.9 18.6 1.0 HB A:VAL122 4.9 15.5 1.0 CA A:ILE123 4.9 14.2 1.0 O A:HOH356 4.9 33.1 1.0 O A:VAL122 4.9 15.0 1.0

Bromine binding site 10 out of 36 in the X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of X-Ray Structure of Psaa From Yersinia Pestis, in Complex with Galactose and Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ A:Br211 b:23.8 occ:0.67 HZ2 A:LYS126 2.4 22.1 1.0 H A:VAL6 2.7 16.6 1.0 HA A:HIS5 2.9 20.5 1.0 HD2 A:LYS126 3.1 18.5 1.0 NZ A:LYS126 3.3 18.6 1.0 N A:VAL6 3.5 14.0 1.0 H2 A:HOH358 3.6 49.7 1.0 O A:VAL6 3.7 14.5 1.0 HZ3 A:LYS126 3.7 22.1 1.0 CA A:HIS5 3.8 17.2 1.0 HZ1 A:LYS126 3.8 22.1 1.0 H2 A:HOH408 3.8 52.5 1.0 HE3 A:LYS126 3.9 17.9 1.0 CD A:LYS126 3.9 15.6 1.0 CE A:LYS126 3.9 15.1 1.0 HB A:VAL6 4.0 15.4 1.0 HB2 A:HIS5 4.0 22.8 1.0 C A:HIS5 4.1 15.3 1.0 CB A:HIS5 4.3 19.1 1.0 HD3 A:LYS126 4.3 18.5 1.0 HB3 A:HIS5 4.3 22.8 1.0 O A:PHE4 4.4 18.9 1.0 HE1 A:PHE4 4.4 21.9 1.0 CA A:VAL6 4.4 12.5 1.0 C A:VAL6 4.5 14.6 1.0 O A:HOH358 4.6 41.5 1.0 CB A:VAL6 4.7 12.9 1.0 HD1 A:PHE4 4.7 24.1 1.0 O A:HOH408 4.7 43.9 1.0 CE1 A:PHE4 4.8 18.4 1.0 N A:HIS5 4.8 17.5 1.0 HE2 A:LYS126 4.9 17.9 1.0 HG23 A:VAL6 4.9 17.7 1.0 H2 A:HOH399 5.0 44.5 1.0 CD1 A:PHE4 5.0 20.3 1.0 H1 A:HOH408 5.0 52.5 1.0 C A:PHE4 5.0 19.6 1.0

R.Bao, M.K.Nair, W.K.Tang, L.Esser, A.Sadhukhan, R.L.Holland, D.Xia, D.M.Schifferli. Structural Basis For the Specific Recognition of Dual Receptors By the Homopolymeric pH 6 Antigen (Psa) Fimbriae of Yersinia Pestis. Proc.Natl.Acad.Sci.Usa V. 110 1065 2013.
ISSN: ISSN 0027-8424
PubMed: 23277582
DOI: 10.1073/PNAS.1212431110