Chlorine in PDB 4cb5: Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F)

The structure of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F), PDB code: 4cb5 was solved by S.Pautus, P.Sehr, J.Lewis, A.Fortune, A.Wolkerstorfer, O.Szolar, D.Gulligay, T.Lunardi, J.L.Decout, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.48 / 1.50
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	82.170, 82.170, 54.840, 90.00, 90.00, 120.00
R / Rfree (%)	12.672 / 15.85

The binding sites of Chlorine atom in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F) (pdb code 4cb5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F), PDB code: 4cb5:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1485 b:15.1 occ:1.00 O A:HOH2032 3.2 24.1 1.0 OG1 A:THR378 3.2 10.6 1.0 N A:THR378 3.3 9.8 1.0 CB A:THR378 3.6 11.2 1.0 CB A:ALA377 3.6 9.0 1.0 CA A:THR378 4.1 11.1 1.0 C A:ALA377 4.2 11.2 1.0 CA A:ALA377 4.2 10.9 1.0 C A:GLY359 4.5 11.1 1.0 N A:GLY359 4.6 11.6 1.0 O A:GLY359 4.6 14.8 1.0 N A:TYR360 4.6 11.6 1.0 CA A:GLY359 4.6 12.7 1.0 O A:THR378 5.0 12.6 1.0

Chlorine binding site 2 out of 3 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1486 b:13.3 occ:1.00 N A:ARG355 3.4 9.7 1.0 CG A:MET431 3.5 11.3 1.0 N A:MET431 3.5 11.1 1.0 CD A:PRO430 3.8 15.0 1.0 CA A:ILE354 3.8 12.5 1.0 CB A:MET431 3.8 11.9 1.0 N A:PRO430 3.9 13.8 1.0 CG A:ASN429 3.9 13.6 1.0 CB A:ASN429 4.0 13.1 1.0 OD1 A:ASN429 4.1 14.2 1.0 CB A:ILE354 4.1 15.6 1.0 C A:ILE354 4.1 10.7 1.0 CB A:ARG355 4.2 11.8 1.0 ND2 A:ASN429 4.2 15.0 1.0 CA A:MET431 4.3 10.3 1.0 O A:LYS353 4.3 14.3 1.0 CB A:PRO430 4.4 13.7 1.0 CG2 A:ILE354 4.4 17.3 1.0 CA A:ARG355 4.4 10.3 1.0 C A:PRO430 4.5 12.1 1.0 CA A:PRO430 4.5 13.2 1.0 C A:ASN429 4.5 12.4 1.0 CG A:PRO430 4.6 13.9 1.0 O A:HOH2020 4.7 21.1 1.0 CA A:ASN429 4.9 14.1 1.0 N A:ILE354 4.9 12.0 1.0

Chlorine binding site 3 out of 3 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 8F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1487 b:15.6 occ:1.00 NH2 A:ARG380 3.2 18.1 1.0 NH1 A:ARG380 3.4 17.8 1.0 CD1 A:ILE382 3.6 11.9 0.7 CD1 A:ILE382 3.8 12.5 0.3 CZ A:ARG380 3.8 16.1 1.0 CG1 A:ILE382 4.2 11.6 0.3 CG1 A:ILE382 4.5 12.5 0.7 CG2 A:ILE382 4.7 11.8 0.7 CG2 A:ILE382 4.8 10.9 0.3

S.Pautus, P.Sehr, J.Lewis, A.Fortune, A.Wolkerstorfer, O.Szolar, D.Gulligay, T.Lunardi, J.L.Decout, S.Cusack. New 7-Methyl-Guanosine Derivatives Targeting the Influenza Polymerase PB2 Cap-Binding Domain J.Med.Chem. V. 56 8915 2013.
ISSN: ISSN 0022-2623
PubMed: 24134208
DOI: 10.1021/JM401369Y