Bromine in PDB 5t6s: Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol

The structure of Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol, PDB code: 5t6s was solved by R.U.Kadam, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.50 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.419, 231.490, 127.850, 90.00, 96.88, 90.00
R / Rfree (%)	20.4 / 25

The structure of Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Bromine atom in the Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol (pdb code 5t6s). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol, PDB code: 5t6s:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in the Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol


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 the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br201 b:90.2 occ:1.00 BR5 B:75U201 0.0 90.2 1.0 C3 B:75U201 1.9 73.8 1.0 C4 B:75U201 2.8 68.2 1.0 C2 B:75U201 2.9 64.0 1.0 O B:HOH382 3.1 54.6 1.0 O35 B:75U201 3.1 63.5 1.0 O B:HOH303 3.2 51.3 1.0 NE2 E:GLN311 3.4 36.6 1.0 CD E:GLN311 3.8 36.2 1.0 CB F:SER93 4.0 25.4 1.0 C9 B:75U201 4.1 59.7 1.0 OG1 B:THR59 4.1 85.9 1.0 C1 B:75U201 4.2 59.6 1.0 O F:SER93 4.2 29.5 1.0 CG E:GLN311 4.3 34.9 1.0 OE1 F:GLU97 4.3 43.5 1.0 C F:SER93 4.3 29.4 1.0 OE1 E:GLN311 4.4 36.2 1.0 C10 B:75U201 4.7 58.3 1.0 N F:TYR94 4.7 30.1 1.0 CA F:SER93 4.8 27.3 1.0 CB F:GLU97 4.8 32.6 1.0

Bromine binding site 2 out of 6 in the Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol


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 the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br202 b:98.4 occ:1.00 BR5 B:75U202 0.0 98.4 1.0 C3 B:75U202 1.9 77.9 1.0 C4 B:75U202 2.8 68.9 1.0 C2 B:75U202 2.9 68.8 1.0 O D:HOH372 2.9 30.2 1.0 O35 B:75U202 3.2 64.9 1.0 O B:HOH339 3.3 35.4 1.0 NE2 A:GLN311 3.3 28.2 1.0 CD A:GLN311 3.8 29.9 1.0 C9 B:75U202 4.0 64.0 1.0 O A:HOH608 4.1 51.8 1.0 OG1 D:THR59 4.1 75.4 1.0 O B:SER93 4.1 28.3 1.0 CB B:SER93 4.1 30.3 1.0 OE1 B:GLU97 4.2 46.5 1.0 C1 B:75U202 4.2 65.0 1.0 OE1 A:GLN311 4.3 31.8 1.0 C B:SER93 4.3 27.4 1.0 CG A:GLN311 4.3 30.0 1.0 CG2 D:THR59 4.3 75.0 1.0 CB B:GLU97 4.6 34.3 1.0 CB D:THR59 4.6 74.2 1.0 C10 B:75U202 4.6 63.3 1.0 N B:TYR94 4.7 29.8 1.0 CA B:SER93 4.8 28.4 1.0 CD B:GLU97 4.9 44.3 1.0 CG B:GLU97 4.9 41.6 1.0

Bromine binding site 3 out of 6 in the Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol


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 the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol within 5.0Å range: probe atom residue distance (Å) B Occ F:Br201 b:99.7 occ:1.00 BR5 F:75U201 0.0 99.7 1.0 C3 F:75U201 1.9 81.0 1.0 C4 F:75U201 2.8 71.1 1.0 C2 F:75U201 2.9 71.5 1.0 O C:HOH641 3.0 37.7 1.0 O35 F:75U201 3.1 75.3 1.0 NE2 C:GLN311 3.7 29.2 1.0 CB D:SER93 3.9 19.7 1.0 C9 F:75U201 4.0 66.0 1.0 CG2 F:THR59 4.1 59.8 1.0 CD C:GLN311 4.1 31.4 1.0 C1 F:75U201 4.2 63.6 1.0 O D:SER93 4.3 24.3 1.0 C D:SER93 4.3 27.8 1.0 OE1 C:GLN311 4.5 34.7 1.0 OE1 D:GLU97 4.5 38.4 1.0 N D:TYR94 4.6 27.2 1.0 C10 F:75U201 4.6 63.5 1.0 O C:HOH637 4.7 47.5 1.0 CA D:SER93 4.7 23.5 1.0 CG C:GLN311 4.7 28.5 1.0 CB F:THR59 4.8 63.0 1.0 OG1 F:THR59 4.8 62.5 1.0 OG D:SER93 4.9 39.8 1.0 CB D:GLU97 5.0 26.6 1.0 CA D:TYR94 5.0 23.4 1.0

Bromine binding site 4 out of 6 in the Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol


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 the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol within 5.0Å range: probe atom residue distance (Å) B Occ H:Br201 b:0.7 occ:1.00 BR5 H:75U201 0.0 0.7 1.0 C3 H:75U201 1.9 90.6 1.0 C4 H:75U201 2.8 82.4 1.0 C2 H:75U201 2.9 84.0 1.0 O G:HOH532 3.0 49.0 1.0 O35 H:75U201 3.1 83.7 1.0 NE2 G:GLN311 3.5 41.9 1.0 CB H:SER93 4.0 32.2 1.0 CD G:GLN311 4.0 46.3 1.0 C9 H:75U201 4.0 75.6 1.0 O H:SER93 4.1 33.7 1.0 C1 H:75U201 4.2 80.1 1.0 C H:SER93 4.3 34.2 1.0 CG2 J:THR59 4.3 77.6 1.0 OE1 G:GLN311 4.5 48.7 1.0 OE1 H:GLU97 4.5 46.9 1.0 CG G:GLN311 4.5 45.2 1.0 N H:TYR94 4.6 31.3 1.0 C10 H:75U201 4.6 76.6 1.0 CA H:SER93 4.7 36.2 1.0 CB H:GLU97 4.9 42.7 1.0 CB J:THR59 4.9 80.5 1.0 CA H:TYR94 4.9 28.8 1.0

Bromine binding site 5 out of 6 in the Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol


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 the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol within 5.0Å range: probe atom residue distance (Å) B Occ J:Br201 b:0.7 occ:1.00 BR5 J:75U201 0.0 0.7 1.0 C3 J:75U201 1.9 88.5 1.0 C4 J:75U201 2.8 79.5 1.0 C2 J:75U201 2.9 80.6 1.0 O I:HOH586 2.9 34.4 1.0 O35 J:75U201 3.1 80.9 1.0 O J:HOH323 3.3 36.0 1.0 NE2 I:GLN311 3.5 31.3 1.0 CB J:SER93 3.7 31.3 1.0 CD I:GLN311 4.0 29.9 1.0 C9 J:75U201 4.0 74.6 1.0 C J:SER93 4.1 33.7 1.0 O J:SER93 4.1 29.1 1.0 C1 J:75U201 4.2 73.9 1.0 N J:TYR94 4.4 36.1 1.0 OE1 J:GLU97 4.4 46.6 1.0 OE1 I:GLN311 4.4 32.8 1.0 CA J:SER93 4.5 34.3 1.0 C10 J:75U201 4.6 72.5 1.0 CG I:GLN311 4.6 26.1 1.0 CG2 L:THR59 4.6 72.1 1.0 CA J:TYR94 4.8 35.9 1.0 OG J:SER93 4.8 33.9 1.0 CB J:GLU97 4.9 35.5 1.0

Bromine binding site 6 out of 6 in the Crystal Structure of the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol


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 the A/Shanghai/2/2013 (H7N9) Influenza Virus Hemagglutinin in Complex with the Antiviral Drug Arbidol within 5.0Å range: probe atom residue distance (Å) B Occ L:Br201 b:94.0 occ:1.00 BR5 L:75U201 0.0 94.0 1.0 C3 L:75U201 1.9 75.6 1.0 C4 L:75U201 2.8 68.0 1.0 C2 L:75U201 2.9 66.5 1.0 O H:HOH332 3.1 50.5 1.0 O35 L:75U201 3.1 63.9 1.0 NE2 K:GLN311 3.7 45.3 1.0 CG2 H:THR59 4.0 79.3 1.0 OG1 H:THR59 4.0 82.2 1.0 CB L:SER93 4.0 27.8 1.0 CD K:GLN311 4.1 42.6 1.0 C9 L:75U201 4.1 62.0 1.0 C1 L:75U201 4.2 60.5 1.0 OE1 L:GLU97 4.5 42.9 1.0 CB H:THR59 4.5 79.5 1.0 OE1 K:GLN311 4.5 40.2 1.0 O L:SER93 4.5 36.0 1.0 CG K:GLN311 4.6 39.2 1.0 C L:SER93 4.6 33.9 1.0 C10 L:75U201 4.7 58.9 1.0 O H:HOH317 4.8 59.2 1.0 CA L:SER93 4.9 32.2 1.0 N L:TYR94 5.0 28.4 1.0 OG L:SER93 5.0 26.3 1.0

R.U.Kadam, I.A.Wilson. Structural Basis of Influenza Virus Fusion Inhibition By the Antiviral Drug Arbidol. Proc. Natl. Acad. Sci. V. 114 206 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28003465
DOI: 10.1073/PNAS.1617020114