Bromine in PDB 4mk1: 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease

The structure of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 4mk1 was solved by J.D.Bauman, D.Patel, K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.32 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.932, 101.655, 66.212, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 19.8

The structure of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Bromine atom in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease (pdb code 4mk1). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 4mk1:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Br307 b:0.4 occ:0.96 BR A:27Y307 0.0 0.4 1.0 C04 A:27Y307 1.9 53.2 1.0 O A:HOH514 2.8 33.3 1.0 C06 A:27Y307 2.9 44.5 1.0 HG12 A:ILE38 2.9 40.9 1.0 C03 A:27Y307 2.9 44.8 1.0 O A:HOH518 3.2 61.0 1.0 HE2 A:LYS34 3.3 79.1 1.0 HE3 A:LYS34 3.3 79.1 1.0 HG13 A:ILE38 3.4 40.9 1.0 CG1 A:ILE38 3.6 34.1 1.0 HA A:ILE38 3.7 34.5 1.0 CE A:LYS34 3.8 65.9 1.0 O A:HOH510 3.9 36.8 1.0 N07 A:27Y307 4.1 32.5 1.0 C02 A:27Y307 4.2 31.2 1.0 HD11 A:ILE38 4.2 52.8 1.0 HD2 A:LYS34 4.4 66.0 1.0 HO1 A:EDO306 4.4 75.3 1.0 CA A:ILE38 4.4 28.7 1.0 CD1 A:ILE38 4.5 44.0 1.0 HB3 A:HIS41 4.6 31.7 1.0 CB A:ILE38 4.6 29.9 1.0 N A:ILE38 4.7 28.3 1.0 C08 A:27Y307 4.7 25.6 1.0 CD A:LYS34 4.7 55.0 1.0 HB1 A:ALA37 4.7 34.7 1.0 HZ3 A:LYS34 4.8 80.3 1.0 HB3 A:ALA37 4.8 34.7 1.0 HG23 A:ILE38 4.8 36.0 1.0 NZ A:LYS34 4.9 66.9 1.0 C04 A:27Y308 4.9 35.0 0.7 H A:ILE38 4.9 34.0 1.0 HD13 A:ILE38 5.0 52.8 1.0 C A:ALA37 5.0 28.0 1.0 HB2 A:HIS41 5.0 31.7 1.0 O A:ALA37 5.0 25.7 1.0

Bromine binding site 2 out of 3 in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Br308 b:47.5 occ:0.68 BR A:27Y308 0.0 47.5 0.7 C04 A:27Y308 1.9 35.0 0.7 HD11 A:ILE38 2.8 52.8 1.0 OE1 A:GLU26 2.8 73.8 1.0 C03 A:27Y308 2.9 31.5 0.7 C06 A:27Y308 2.9 40.4 0.7 HZ3 A:LYS34 3.2 80.3 1.0 HD13 A:ILE38 3.4 52.8 1.0 HD2 A:TYR24 3.4 66.1 1.0 HZ2 A:LYS34 3.5 80.3 1.0 HE2 A:LYS34 3.5 79.1 1.0 CD1 A:ILE38 3.5 44.0 1.0 NZ A:LYS34 3.7 66.9 1.0 HB2 A:TYR24 3.7 60.1 1.0 HG2 A:MET21 3.7 48.7 1.0 HA A:MET21 3.7 39.5 1.0 CD A:GLU26 4.0 74.3 1.0 CD2 A:TYR24 4.0 55.1 1.0 CE A:LYS34 4.1 65.9 1.0 HD12 A:ILE38 4.2 52.8 1.0 N07 A:27Y308 4.2 40.7 0.7 C02 A:27Y308 4.2 27.6 0.7 HG12 A:ILE38 4.2 40.9 1.0 HB3 A:TYR24 4.3 60.1 1.0 CB A:TYR24 4.3 50.1 1.0 CG A:TYR24 4.4 53.8 1.0 OE2 A:GLU26 4.4 82.0 1.0 HZ1 A:LYS34 4.5 80.3 1.0 CG1 A:ILE38 4.5 34.1 1.0 HE3 A:LYS34 4.6 79.1 1.0 CG A:MET21 4.6 40.6 1.0 CA A:MET21 4.6 32.9 1.0 C08 A:27Y308 4.7 31.5 0.7 HG3 A:LYS34 4.7 61.2 1.0 HG3 A:MET21 4.7 48.7 1.0 O A:ALA20 4.8 35.3 1.0 HB2 A:GLU26 4.8 56.6 1.0 CE2 A:TYR24 4.8 54.0 1.0 HG2 A:LYS34 4.8 61.2 1.0 HG13 A:ILE38 4.9 40.9 1.0 HB1 A:ALA20 4.9 38.0 1.0 HE2 A:TYR24 4.9 64.8 1.0 N A:MET21 4.9 31.8 1.0 HE2 A:MET21 4.9 39.1 1.0

Bromine binding site 3 out of 3 in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Br309 b:74.8 occ:0.65 BR A:27Y309 0.0 74.8 0.7 C04 A:27Y309 1.9 33.8 0.7 C06 A:27Y309 2.9 41.8 0.7 C03 A:27Y309 2.9 39.6 0.7 HA A:ASP83 2.9 55.9 1.0 HB2 A:GLU23 3.0 55.7 1.0 OE1 A:GLU23 3.1 69.7 1.0 HB2 A:ASP83 3.1 61.0 1.0 HB3 A:ASP83 3.1 61.0 1.0 CD A:GLU23 3.2 85.5 1.0 OE2 A:GLU23 3.4 97.6 1.0 CB A:ASP83 3.4 50.8 1.0 CA A:ASP83 3.6 46.6 1.0 O A:HOH422 3.7 55.1 1.0 CB A:GLU23 3.7 46.4 1.0 HA A:ALA20 3.8 42.8 1.0 O A:HOH529 3.8 78.0 1.0 CG A:GLU23 3.9 66.6 1.0 HB3 A:LYS19 3.9 56.0 1.0 O A:LYS19 3.9 38.8 1.0 HB3 A:GLU23 4.0 55.7 1.0 HG3 A:GLU23 4.0 79.9 1.0 H A:ARG84 4.1 44.8 1.0 N07 A:27Y309 4.1 41.3 0.7 C02 A:27Y309 4.2 31.9 0.7 C A:LYS19 4.3 37.8 1.0 N A:ASP83 4.5 34.2 1.0 CA A:ALA20 4.6 35.7 1.0 N A:ALA20 4.7 32.2 1.0 C08 A:27Y309 4.7 32.4 0.7 N A:ARG84 4.7 37.3 1.0 C A:ASP83 4.7 38.1 1.0 HG2 A:GLU23 4.7 79.9 1.0 CB A:LYS19 4.8 46.6 1.0 H A:ASP83 4.8 41.0 1.0 H A:GLU23 4.8 51.0 1.0 CG A:ASP83 4.9 58.5 1.0 O A:ARG82 4.9 31.2 1.0

J.D.Bauman, D.Patel, S.F.Baker, R.S.Vijayan, A.Xiang, A.K.Parhi, L.Martinez-Sobrido, E.J.Lavoie, K.Das, E.Arnold. Crystallographic Fragment Screening and Structure-Based Optimization Yields A New Class of Influenza Endonuclease Inhibitors. Acs Chem.Biol. V. 8 2501 2013.
ISSN: ISSN 1554-8929
PubMed: 23978130
DOI: 10.1021/CB400400J