Bromine in PDB 6xq7: Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5

The structure of Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5, PDB code: 6xq7 was solved by L.E.Salay, N.Kozlyuk, B.A.Gilston, R.D.Gogliotti, P.P.Christov, K.Kim, M.Ovee, A.G.Waterson, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.92 / 1.80
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	102.905, 102.905, 101.769, 90, 90, 120
R / Rfree (%)	19.9 / 22.2

The structure of Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Bromine atom in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5 (pdb code 6xq7). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5, PDB code: 6xq7:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br306 b:50.8 occ:0.75 BR14 A:V6V306 0.0 50.8 0.8 C06 A:V6V306 1.9 32.9 0.8 C01 A:V6V306 2.8 31.8 0.8 C05 A:V6V306 3.0 29.3 0.8 CD2 A:LEU79 3.8 19.8 1.0 CD2 A:PHE85 4.0 21.9 1.0 CH3 A:ACT304 4.1 15.6 1.0 CE2 B:PHE85 4.1 22.6 1.0 C02 A:V6V306 4.2 31.4 0.8 OXT A:ACT304 4.3 45.3 1.0 CD A:ARG77 4.3 31.7 1.0 C04 A:V6V306 4.4 37.6 0.8 CB A:ARG77 4.5 22.5 1.0 CE2 A:PHE85 4.5 21.4 1.0 C A:ACT304 4.7 21.9 1.0 CB B:PRO87 4.8 17.0 1.0 CZ B:PHE85 4.8 18.7 1.0 C03 A:V6V306 4.8 37.0 0.8 CG A:PHE85 5.0 17.5 1.0

Bromine binding site 2 out of 7 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br307 b:127.7 occ:0.78 BR14 A:V6V307 0.0 127.7 0.8 C06 A:V6V307 1.9 55.5 0.8 C05 A:V6V307 2.9 60.5 0.8 C01 A:V6V307 3.0 27.2 0.8 C A:GLN100 3.8 23.8 1.0 CB A:GLN100 3.8 25.5 1.0 N A:ALA101 3.8 27.3 1.0 C A:ALA101 3.9 35.2 1.0 O A:GLN100 3.9 25.8 1.0 CA A:ALA101 4.1 26.9 1.0 O A:ALA101 4.1 33.8 1.0 N A:MET102 4.2 41.9 1.0 CA A:GLN100 4.3 18.0 1.0 C02 A:V6V307 4.4 46.3 0.8 C04 A:V6V307 4.4 61.6 0.8 CB A:GLU108 4.6 45.6 1.0 CB A:MET102 4.8 30.0 1.0 O A:ARG48 4.8 25.9 1.0 CA A:MET102 4.9 54.9 1.0 C03 A:V6V307 5.0 56.9 0.8

Bromine binding site 3 out of 7 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br307 b:32.9 occ:0.64 BR14 B:V6V307 0.0 32.9 0.6 C06 B:V6V307 1.9 23.3 0.6 C05 B:V6V307 2.8 21.7 0.6 C01 B:V6V307 2.9 17.7 0.6 O B:GLY56 3.1 31.3 1.0 C B:ARG57 3.3 21.8 1.0 N B:THR58 3.6 17.9 1.0 O B:ARG57 3.6 25.5 1.0 CA B:ARG57 3.8 17.4 1.0 O B:THR58 3.8 18.9 1.0 C B:GLY56 4.0 24.8 1.0 C B:THR58 4.0 18.5 1.0 CA B:THR58 4.2 18.2 1.0 N B:ARG57 4.3 17.4 1.0 C04 B:V6V307 4.3 25.9 0.6 C02 B:V6V307 4.3 21.3 0.6 N B:GLU59 4.7 21.0 1.0 C03 B:V6V307 4.8 19.0 0.6 OE1 B:GLN92 4.9 31.9 0.5

Bromine binding site 4 out of 7 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br308 b:50.7 occ:0.77 BR14 B:V6V308 0.0 50.7 0.8 C06 B:V6V308 1.9 35.0 0.8 C01 B:V6V308 2.9 30.0 0.8 C05 B:V6V308 3.0 28.7 0.8 CD2 B:LEU79 3.8 20.4 1.0 CD2 B:PHE85 4.1 22.0 1.0 CE2 A:PHE85 4.1 21.4 1.0 C02 B:V6V308 4.3 34.8 0.8 CD B:ARG77 4.4 32.5 1.0 C04 B:V6V308 4.4 37.0 0.8 OXT A:ACT304 4.4 45.3 1.0 CB B:ARG77 4.5 22.8 1.0 CE2 B:PHE85 4.6 22.6 1.0 CB A:PRO87 4.7 17.4 1.0 CZ A:PHE85 4.8 17.9 1.0 C03 B:V6V308 4.9 36.2 0.8

Bromine binding site 5 out of 7 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br309 b:34.3 occ:0.65 BR14 B:V6V309 0.0 34.3 0.7 C06 B:V6V309 1.9 27.0 0.7 C05 B:V6V309 2.8 22.9 0.7 C01 B:V6V309 2.9 17.3 0.7 CD B:ARG179 3.4 28.1 1.0 NE B:ARG179 3.6 30.9 1.0 CZ B:ARG179 3.8 30.7 1.0 NH1 B:ARG179 3.8 32.0 1.0 CB B:ARG179 4.1 23.1 1.0 C04 B:V6V309 4.3 27.1 0.7 C02 B:V6V309 4.3 18.8 0.7 CG B:ARG179 4.3 26.1 1.0 NH2 B:ARG179 4.6 18.8 1.0 C03 B:V6V309 4.8 20.1 0.7

Bromine binding site 6 out of 7 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br310 b:88.8 occ:0.60 BR14 B:V6V310 0.0 88.8 0.6 C06 B:V6V310 1.9 43.1 0.6 C01 B:V6V310 2.9 30.9 0.6 O B:HOH447 2.9 46.0 1.0 C05 B:V6V310 3.0 45.1 0.6 O B:HOH481 3.1 31.3 1.0 NZ B:LYS110 3.9 60.7 1.0 OE1 B:GLN100 3.9 51.4 1.0 CB B:GLN100 4.1 27.1 1.0 C02 B:V6V310 4.3 27.6 0.6 CD B:LYS52 4.4 34.2 1.0 CB B:ARG98 4.4 20.2 1.0 CD B:ARG98 4.4 25.9 1.0 CD B:GLN100 4.5 54.7 1.0 C04 B:V6V310 4.5 44.2 0.6 CE B:LYS52 4.8 53.1 1.0 O B:CYS99 4.9 21.8 1.0 CG B:GLN100 4.9 47.1 1.0 CG B:LYS110 4.9 36.3 1.0 C03 B:V6V310 4.9 34.0 0.6 CG B:LYS52 4.9 31.2 1.0 CE B:LYS110 5.0 52.9 1.0

Bromine binding site 7 out of 7 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with Fragment 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br311 b:144.2 occ:0.76 BR14 B:V6V311 0.0 144.2 0.8 C06 B:V6V311 1.9 54.8 0.8 C05 B:V6V311 2.7 59.1 0.8 CG B:GLN100 3.0 47.1 1.0 C01 B:V6V311 3.1 30.2 0.8 CD B:GLN100 3.5 54.7 1.0 CE B:MET102 3.5 66.8 1.0 NE2 B:GLN100 3.6 55.4 1.0 CG B:MET102 3.7 60.6 1.0 C B:ALA101 3.9 37.3 1.0 O B:ALA101 4.0 31.8 1.0 N B:MET102 4.0 42.3 1.0 N B:ALA101 4.1 28.7 1.0 C B:GLN100 4.1 24.6 1.0 C04 B:V6V311 4.2 59.8 0.8 O B:GLN100 4.3 25.2 1.0 OE1 B:GLN100 4.3 51.4 1.0 CB B:GLN100 4.3 27.1 1.0 CA B:ALA101 4.3 27.4 1.0 C02 B:V6V311 4.4 42.4 0.8 SD B:MET102 4.4 106.0 1.0 CB B:GLU108 4.5 46.5 1.0 CB B:MET102 4.6 52.1 1.0 CA B:MET102 4.7 51.5 1.0 CA B:GLN100 4.8 20.0 1.0 O B:ARG48 4.9 26.5 1.0 C03 B:V6V311 4.9 53.2 0.8

N.Kozlyuk, B.A.Gilston, L.E.Salay, R.D.Gogliotti, P.P.Christov, K.Kim, M.Ovee, A.G.Waterson, W.J.Chazin. A Fragment-Based Approach to Discovery of Rage Inhibitors To Be Published.