Chlorine in PDB 4avg: Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2, PDB code: 4avg was solved by E.Kowalinski, C.Zubieta, A.Wolkerstorfer, O.H.Szolar, R.W.Ruigrok, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.96 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.590, 120.810, 128.200, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.2

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2 also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Chlorine atom in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2 (pdb code 4avg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2, PDB code: 4avg:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl801 b:74.8 occ:1.00 CL2 A:SL6801 0.0 74.8 1.0 C19 A:SL6801 1.8 70.6 1.0 C20 A:SL6801 2.8 60.3 1.0 C18 A:SL6801 2.8 68.5 1.0 CB A:LYS137 3.2 54.6 1.0 CD A:LYS137 3.3 63.1 1.0 NZ A:LYS134 3.5 55.3 1.0 CD A:LYS134 3.5 51.8 1.0 CG A:LYS137 3.8 56.3 1.0 C21 A:SL6801 4.0 63.4 1.0 C17 A:SL6801 4.1 62.9 1.0 CE A:LYS134 4.2 56.8 1.0 O A:LYS134 4.2 34.9 1.0 CG A:PHE105 4.4 44.2 1.0 CA A:LYS137 4.5 53.1 1.0 CA A:LYS134 4.5 36.7 1.0 CE A:LYS137 4.6 69.1 1.0 C16 A:SL6801 4.6 56.8 1.0 NZ A:LYS137 4.6 70.5 1.0 O A:HOH2036 4.6 31.2 1.0 CG1 A:ILE138 4.6 55.7 1.0 CB A:PHE105 4.6 41.0 1.0 CD1 A:PHE105 4.6 45.6 1.0 N A:ILE138 4.7 55.8 1.0 CD2 A:PHE105 4.7 48.4 1.0 C A:LYS137 4.7 52.0 1.0 CG A:LYS134 4.8 42.7 1.0 CB A:LYS134 4.8 37.3 1.0 C A:LYS134 4.8 39.4 1.0

Chlorine binding site 2 out of 4 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:74.5 occ:1.00 CL2 B:SL6801 0.0 74.5 1.0 C19 B:SL6801 1.8 62.9 1.0 C20 B:SL6801 2.8 56.5 1.0 C18 B:SL6801 2.8 61.0 1.0 CB B:LYS137 3.7 47.0 1.0 CG B:LYS137 3.9 52.3 1.0 O B:LYS134 4.0 37.6 1.0 C21 B:SL6801 4.1 55.6 1.0 C17 B:SL6801 4.1 60.6 1.0 CD B:LYS137 4.2 59.1 1.0 CG1 B:ILE138 4.2 45.6 1.0 CA B:LYS134 4.4 42.4 1.0 CD B:LYS134 4.5 49.9 1.0 CD1 B:ILE138 4.5 42.1 1.0 CB B:LYS134 4.5 43.0 1.0 CD2 B:PHE105 4.6 49.4 1.0 C16 B:SL6801 4.6 53.2 1.0 CG B:LYS134 4.6 47.0 1.0 CE B:LYS134 4.6 49.0 1.0 C B:LYS134 4.7 40.3 1.0 CE2 B:PHE105 4.7 54.0 1.0 NZ B:LYS134 4.8 55.1 1.0 CA B:LYS137 4.9 50.2 1.0

Chlorine binding site 3 out of 4 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl801 b:59.9 occ:1.00 CL2 C:SL6801 0.0 59.9 1.0 C19 C:SL6801 1.8 50.8 1.0 C20 C:SL6801 2.8 53.1 1.0 C18 C:SL6801 2.8 51.5 1.0 CB C:LYS137 3.6 65.6 1.0 CD C:LYS134 3.7 51.6 1.0 O C:LYS134 3.9 42.7 1.0 C21 C:SL6801 4.1 50.0 1.0 C17 C:SL6801 4.1 49.9 1.0 CG C:LYS137 4.1 63.6 1.0 CG1 C:ILE138 4.2 71.7 1.0 CA C:LYS134 4.3 47.3 1.0 CB C:LYS134 4.3 49.5 1.0 CD C:LYS137 4.5 64.5 1.0 CD1 C:ILE138 4.5 65.3 1.0 CG C:LYS134 4.5 48.8 1.0 C C:LYS134 4.6 46.2 1.0 C16 C:SL6801 4.6 51.5 1.0 CE C:LYS134 4.8 53.1 1.0 CA C:LYS137 4.9 62.7 1.0 N C:ILE138 5.0 74.7 1.0 CD2 C:PHE105 5.0 46.1 1.0

Chlorine binding site 4 out of 4 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl801 b:70.3 occ:1.00 CL2 D:SL6801 0.0 70.3 1.0 C19 D:SL6801 1.8 68.7 1.0 C20 D:SL6801 2.8 63.1 1.0 C18 D:SL6801 2.8 67.6 1.0 O D:LYS134 3.6 57.9 1.0 CB D:LYS137 3.6 70.2 1.0 CD D:LYS134 3.8 75.6 1.0 CG D:LYS134 3.9 69.7 1.0 NZ D:LYS134 4.0 74.3 1.0 CG1 D:ILE138 4.1 69.5 1.0 C21 D:SL6801 4.1 60.1 1.0 CA D:LYS134 4.1 64.8 1.0 C17 D:SL6801 4.1 64.2 1.0 CG D:LYS137 4.2 70.7 1.0 C D:LYS134 4.3 61.6 1.0 CB D:LYS134 4.4 66.7 1.0 CD D:LYS137 4.4 73.7 1.0 CD1 D:ILE138 4.5 73.5 1.0 CE D:LYS134 4.5 70.7 1.0 C16 D:SL6801 4.6 59.6 1.0 N D:ILE138 4.8 63.9 1.0 CA D:LYS137 4.9 68.9 1.0 O D:HOH2026 5.0 39.9 1.0

E.Kowalinski, C.Zubieta, A.Wolkerstorfer, O.H.Szolar, R.W.Ruigrok, S.Cusack. Structural Analysis of Specific Metal Chelating Inhibitor Binding to the Endonuclease Domain of Influenza PH1N1 (2009) Polymerase. Plos Pathog. V. 8 2831 2012.
ISSN: ISSN 1553-7366
PubMed: 22876177
DOI: 10.1371/JOURNAL.PPAT.1002831