Iodine in PDB 4cb6: Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)

The structure of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11), PDB code: 4cb6 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)	45.41 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.170, 31.130, 98.790, 90.00, 118.27, 90.00
R / Rfree (%)	21.141 / 27.45

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iodine atom in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) (pdb code 4cb6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 18 binding sites of Iodine where determined in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11), PDB code: 4cb6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1484 b:18.5 occ:1.00 NH1 A:ARG355 3.4 35.5 1.0 CG A:MET431 3.6 17.2 1.0 N A:ARG355 3.7 16.5 1.0 O A:HOH2031 3.7 24.9 1.0 N A:MET431 3.9 16.6 1.0 CD A:PRO430 4.0 17.5 1.0 CA A:ILE354 4.2 17.5 1.0 O A:HOH2032 4.2 24.3 1.0 CB A:PRO430 4.2 15.7 1.0 N A:PRO430 4.2 15.0 1.0 CG2 A:ILE354 4.3 20.1 1.0 CG A:ASN429 4.3 21.3 1.0 CB A:MET431 4.3 17.3 1.0 CB A:ARG355 4.3 17.1 1.0 CG A:ARG355 4.3 20.0 1.0 CG A:PRO430 4.3 17.1 1.0 ND2 A:ASN429 4.3 21.4 1.0 CD A:ARG355 4.4 21.5 1.0 C A:ILE354 4.4 17.7 1.0 OD1 A:ASN429 4.5 22.7 1.0 CB A:ASN429 4.5 19.5 1.0 O A:LYS353 4.6 19.5 1.0 CZ A:ARG355 4.6 31.6 1.0 CA A:ARG355 4.6 16.5 1.0 CA A:PRO430 4.6 16.4 1.0 CB A:ILE354 4.7 19.3 1.0 CA A:MET431 4.7 15.5 1.0 C A:PRO430 4.8 15.0 1.0 O A:ARG355 4.9 14.3 1.0 CG1 A:ILE354 4.9 21.6 1.0 NE A:ARG355 5.0 28.3 1.0 C A:ASN429 5.0 16.6 1.0

Iodine binding site 2 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1485 b:21.4 occ:1.00 N A:ASN456 3.6 27.1 1.0 CA A:ASN456 3.6 27.4 1.0 N A:MET460 3.7 24.5 1.0 N A:MET458 3.9 26.3 1.0 C A:ASN456 4.0 25.8 1.0 CD A:ARG479 4.0 14.9 1.0 NE A:ARG479 4.0 14.0 1.0 CB A:MET460 4.1 23.4 1.0 CB A:MET458 4.1 25.7 1.0 N A:GLY459 4.2 26.1 1.0 O A:HOH2078 4.2 22.3 1.0 N A:VAL457 4.2 25.1 1.0 OD1 A:ASP455 4.3 28.5 1.0 CA A:MET460 4.3 22.2 1.0 O A:MET460 4.3 22.1 1.0 C A:MET460 4.4 22.8 1.0 CA A:MET458 4.4 25.2 1.0 CB A:ILE454 4.4 17.8 1.0 CG A:ARG479 4.5 15.3 1.0 C A:MET458 4.5 27.6 1.0 O A:ASN456 4.5 27.2 1.0 CD1 A:ILE454 4.6 19.1 1.0 O A:HOH2077 4.7 28.9 1.0 N A:ASP455 4.7 21.6 1.0 C A:ASP455 4.8 25.4 1.0 CG A:MET460 4.8 24.9 1.0 C A:GLY459 4.8 28.0 1.0 CE A:MET458 4.8 30.2 1.0 CG1 A:ILE454 4.9 18.4 1.0 CA A:GLY459 4.9 26.4 1.0 CG A:MET458 4.9 25.8 1.0 C A:VAL457 5.0 29.1 1.0

Iodine binding site 3 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1486 b:31.3 occ:0.50 I A:IOD1486 0.0 31.3 0.5 I A:IOD1486 1.8 28.4 0.5 C8 A:29R1483 3.5 20.8 1.0 CD1 A:PHE325 3.6 19.4 1.0 CE1 A:PHE325 3.6 20.0 1.0 C12 A:29R1483 4.0 23.5 1.0 CB A:MET431 4.0 17.3 1.0 C11 A:29R1483 4.0 22.6 1.0 N9 A:29R1483 4.1 19.7 1.0 CG A:MET431 4.3 17.2 1.0 CG A:PHE325 4.3 17.3 1.0 CZ A:PHE325 4.4 17.8 1.0 CE1 A:HIS432 4.4 18.6 1.0 O A:HOH2032 4.5 24.3 1.0 C13 A:29R1483 4.6 28.9 1.0 CE A:MET431 4.6 18.1 1.0 CE1 A:PHE404 4.6 13.9 1.0 N7 A:29R1483 4.7 19.7 1.0 CD1 A:PHE404 4.7 14.2 1.0 CE2 A:PHE325 5.0 15.6 1.0 CD2 A:PHE325 5.0 16.9 1.0 ND1 A:HIS432 5.0 18.0 1.0 CB A:PHE325 5.0 17.9 1.0

Iodine binding site 4 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1486 b:28.4 occ:0.50 I A:IOD1486 0.0 28.4 0.5 I A:IOD1486 1.8 31.3 0.5 CB A:MET431 3.9 17.3 1.0 CE1 A:HIS432 3.9 18.6 1.0 ND2 A:ASN429 4.1 21.4 1.0 CG A:MET431 4.1 17.2 1.0 O A:HOH2032 4.2 24.3 1.0 ND1 A:HIS432 4.3 18.0 1.0 C11 A:29R1483 4.4 22.6 1.0 C8 A:29R1483 4.4 20.8 1.0 C12 A:29R1483 4.6 23.5 1.0 OD1 A:ASN429 4.6 22.7 1.0 C13 A:29R1483 4.7 28.9 1.0 CE1 A:PHE325 4.7 20.0 1.0 CD1 A:PHE325 4.8 19.4 1.0 N9 A:29R1483 4.8 19.7 1.0 CG A:ASN429 4.8 21.3 1.0 O A:HOH2034 4.9 25.3 1.0

Iodine binding site 5 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1487 b:58.5 occ:1.00 N A:ASN429 3.4 18.6 1.0 ND1 A:HIS432 3.7 18.0 1.0 CG A:HIS432 3.8 17.7 1.0 CG A:ASN429 3.8 21.3 1.0 CA A:LEU428 3.9 20.9 1.0 OD1 A:ASN429 4.0 22.7 1.0 CB A:HIS432 4.0 17.4 1.0 ND2 A:ASN429 4.1 21.4 1.0 C A:LEU428 4.2 18.4 1.0 CB A:ASN429 4.2 19.5 1.0 CB A:LEU428 4.3 21.5 1.0 CE1 A:HIS432 4.3 18.6 1.0 CA A:ASN429 4.4 17.8 1.0 CG A:LEU428 4.5 24.2 1.0 CD2 A:HIS432 4.5 18.8 1.0 NE2 A:HIS432 4.8 17.6 1.0 O A:HOH2084 4.8 31.5 1.0

Iodine binding site 6 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1488 b:57.3 occ:1.00 CE1 A:HIS357 3.7 18.9 1.0 NZ A:LYS339 3.8 33.9 1.0 CE A:LYS339 3.9 31.0 1.0 C14 A:29R1483 4.2 33.1 1.0 C31 A:29R1483 4.2 22.4 1.0 CD A:LYS339 4.5 31.9 1.0 C11 A:29R1483 4.5 22.6 1.0 NE2 A:HIS357 4.5 19.3 1.0 N3 A:29R1483 4.5 16.4 1.0 O A:HOH2034 4.6 25.3 1.0 C33 A:29R1483 4.6 31.4 1.0 O17 A:29R1483 4.7 43.9 1.0 ND1 A:HIS357 4.7 20.5 1.0 C15 A:29R1483 4.8 37.9 1.0 C32 A:29R1483 4.9 24.9 1.0

Iodine binding site 7 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1489 b:43.0 occ:1.00 NE2 A:GLN447 3.9 36.4 1.0 CD A:PRO465 3.9 18.2 1.0 CB A:PRO465 4.0 20.7 1.0 N A:ASP466 4.0 23.6 1.0 CG A:PRO465 4.1 18.2 1.0 CG A:ASP466 4.2 23.4 1.0 CB A:ASP466 4.2 25.5 1.0 N A:PRO465 4.3 18.5 1.0 OD2 A:ASP466 4.4 25.6 1.0 OE1 A:GLN447 4.4 43.4 1.0 OD1 A:ASP466 4.5 20.7 1.0 CA A:PRO465 4.6 18.0 1.0 CD A:GLN447 4.6 35.0 1.0 C A:PRO465 4.6 21.4 1.0 CB A:LEU464 4.7 19.8 1.0 CA A:ASP466 4.7 23.6 1.0

Iodine binding site 8 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1490 b:55.6 occ:0.50 CB A:GLN447 3.9 27.0 1.0 CG A:GLN447 4.1 31.3 1.0 CA A:VAL444 4.2 19.1 1.0 CG2 A:VAL444 4.4 21.6 1.0 ND2 A:ASN448 4.4 29.0 1.0 O A:LYS443 4.5 21.0 1.0 CB A:VAL444 4.7 20.4 1.0 N A:VAL444 4.7 19.2 1.0 C A:LYS443 4.8 18.9 1.0 CG1 A:VAL444 4.9 21.7 1.0

Iodine binding site 9 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ B:I1484 b:45.2 occ:0.50 I B:IOD1484 0.0 45.2 0.5 I B:IOD1484 1.9 41.5 0.5 CD1 B:PHE325 3.6 30.0 1.0 CE1 B:PHE325 3.6 29.6 1.0 C8 B:29R1483 3.7 26.6 1.0 CB B:MET431 4.1 25.4 1.0 C14 B:29R1483 4.1 44.2 1.0 C11 B:29R1483 4.1 31.9 1.0 C12 B:29R1483 4.1 36.2 1.0 N9 B:29R1483 4.3 27.4 1.0 CG B:MET431 4.3 25.4 1.0 CE1 B:HIS432 4.4 34.5 1.0 CG B:PHE325 4.4 29.4 1.0 CZ B:PHE325 4.5 28.4 1.0 CE B:MET431 4.7 29.3 1.0 N7 B:29R1483 4.7 23.9 1.0 CE1 B:PHE404 4.8 20.7 1.0 C13 B:29R1483 4.8 39.4 1.0 CD1 B:PHE404 4.9 21.0 1.0 ND1 B:HIS432 4.9 32.5 1.0

Iodine binding site 10 out of 18 in the Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Influenza A H5N1 PB2 Cap-Binding Domain with Bound Cap Analogue (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ B:I1484 b:41.5 occ:0.50 I B:IOD1484 0.0 41.5 0.5 I B:IOD1484 1.9 45.2 0.5 C14 B:29R1483 3.9 44.2 1.0 CB B:MET431 4.1 25.4 1.0 ND2 B:ASN429 4.1 25.4 1.0 C11 B:29R1483 4.1 31.9 1.0 CG B:MET431 4.2 25.4 1.0 CE1 B:HIS432 4.2 34.5 1.0 C8 B:29R1483 4.2 26.6 1.0 C12 B:29R1483 4.5 36.2 1.0 ND1 B:HIS432 4.6 32.5 1.0 N9 B:29R1483 4.6 27.4 1.0 O17 B:29R1483 4.7 54.6 1.0 OD1 B:ASN429 4.8 26.7 1.0 C13 B:29R1483 4.8 39.4 1.0 C15 B:29R1483 4.8 51.1 1.0 CG B:ASN429 4.9 25.6 1.0 I B:IOD1488 4.9 18.1 0.5 CE1 B:PHE325 5.0 29.6 1.0

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