Chlorine in PDB 5wfm: Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024), PDB code: 5wfm was solved by G.Kumar, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.90 / 2.25
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.902, 90.902, 133.737, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 22.5

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024) also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024) (pdb code 5wfm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024), PDB code: 5wfm:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:86.5 occ:0.49 CL1 A:KU5205 0.0 86.5 0.5 C9 A:KU5205 1.2 77.8 0.5 C25 A:KU5205 1.7 77.3 0.5 C8 A:KU5205 2.0 75.9 0.5 O5 A:KU5205 2.3 74.3 0.5 C10 A:KU5205 2.4 78.5 0.5 S1 A:KU5205 2.5 66.7 0.5 C24 A:KU5205 2.7 72.7 0.5 C20 A:KU5205 2.7 77.1 0.5 O4 A:KU5205 3.1 79.9 0.5 C7 A:KU5205 3.1 69.3 0.5 C19 A:KU5205 3.1 83.5 0.5 C13 A:KU5205 3.3 73.1 0.5 S2 A:KU5205 3.4 82.3 0.5 C18 A:KU5205 3.4 81.7 0.5 C11 A:KU5205 3.6 76.3 0.5 CD1 A:ILE38 3.7 50.9 1.0 O6 A:KU5205 3.9 65.7 0.5 C12 A:KU5205 3.9 74.0 0.5 C23 A:KU5205 4.0 71.2 0.5 CG1 A:ILE38 4.0 56.9 1.0 C21 A:KU5205 4.0 73.8 0.5 CE A:LYS34 4.1 84.6 1.0 N3 A:KU5205 4.1 69.8 0.5 C6 A:KU5205 4.2 71.9 0.5 N3 A:KU5205 4.5 71.1 0.5 C22 A:KU5205 4.5 72.3 0.5 N2 A:KU5205 4.6 66.0 0.5 N4 A:KU5205 4.6 78.4 0.5 N2 A:KU5205 4.7 66.2 0.5 NZ A:LYS34 4.7 83.6 1.0 C6 A:KU5205 4.8 72.5 0.5 O4 A:KU5205 5.0 82.4 0.5 C5 A:KU5205 5.0 67.8 0.5 C5 A:KU5205 5.0 68.1 0.5

Chlorine binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:91.5 occ:0.51 CL1 A:KU5205 0.0 91.5 0.5 S1 A:KU5205 0.9 86.3 0.5 O6 A:KU5205 1.1 89.6 0.5 C8 A:KU5205 1.5 90.8 0.5 C25 A:KU5205 1.7 91.3 0.5 C13 A:KU5205 2.0 93.6 0.5 O5 A:KU5205 2.2 84.1 0.5 C7 A:KU5205 2.3 75.6 0.5 C24 A:KU5205 2.7 90.2 0.5 C20 A:KU5205 2.7 93.5 0.5 C9 A:KU5205 2.8 90.0 0.5 C6 A:KU5205 2.8 72.5 0.5 N3 A:KU5205 3.1 71.1 0.5 S2 A:KU5205 3.2 98.2 0.5 C12 A:KU5205 3.4 93.4 0.5 N3 A:KU5205 3.6 69.8 0.5 C6 A:KU5205 3.7 71.9 0.5 C10 A:KU5205 3.9 90.0 0.5 C23 A:KU5205 4.0 89.8 0.5 C5 A:KU5205 4.0 68.1 0.5 C21 A:KU5205 4.0 92.3 0.5 CD1 A:PHE105 4.1 90.4 1.0 C11 A:KU5205 4.1 91.4 0.5 C5 A:KU5205 4.2 67.8 0.5 C22 A:KU5205 4.5 90.2 0.5 O3 A:KU5205 4.5 67.3 0.5 O3 A:KU5205 4.5 67.8 0.5 OH A:TYR24 4.6 88.3 1.0 C7 A:KU5205 4.7 69.3 0.5 CE1 A:PHE105 4.8 90.8 1.0 C19 A:KU5205 4.8 86.3 0.5 O4 A:KU5205 4.9 82.4 0.5 C2 A:KU5205 4.9 65.0 0.5 CB A:PHE105 4.9 82.6 1.0 CG A:PHE105 5.0 86.1 1.0 C2 A:KU5205 5.0 64.7 0.5

D.Beylkin, G.Kumar, W.Zhou, J.Park, T.Jeevan, C.Lagisetti, R.Harfoot, R.J.Webby, S.W.White, T.R.Webb. Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease. Sci Rep V. 7 17139 2017.
ISSN: ESSN 2045-2322
PubMed: 29215062
DOI: 10.1038/S41598-017-17419-6