Iodine in PDB 9daj: Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir

The structure of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir, PDB code: 9daj was solved by S.H.Pham, N.Neetu, B.Sankaran, B.V.V.Prasad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.86 / 2.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.722, 97.722, 44.62, 90, 90, 120
R / Rfree (%)	22.4 / 27.1

The structure of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Iodine atom in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir (pdb code 9daj). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir, PDB code: 9daj:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:63.3 occ:1.00 H A:THR113 3.0 61.9 1.0 HG2 A:ARG112 3.1 66.7 1.0 HA A:ARG112 3.2 38.1 1.0 HG3 A:ARG112 3.2 66.7 1.0 CG A:ARG112 3.6 55.4 1.0 HB A:THR113 3.8 52.7 1.0 N A:THR113 3.8 51.4 1.0 CA A:ARG112 4.0 31.6 1.0 CB A:ARG112 4.4 36.5 1.0 C A:ARG112 4.4 43.5 1.0 CB A:THR113 4.5 43.8 1.0 O A:GLY111 4.6 45.0 1.0 OG1 A:THR113 4.6 68.9 1.0 HD3 A:ARG112 4.7 69.5 1.0 CA A:THR113 4.7 52.9 1.0 CD A:ARG112 4.8 57.8 1.0 HG1 A:THR113 4.8 82.8 1.0 HB3 A:ARG112 4.9 44.0 1.0

Iodine binding site 2 out of 8 in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:91.2 occ:1.00 HA A:PHE40 3.3 43.1 1.0 HD1 A:PHE40 4.0 41.5 1.0 CA A:PHE40 4.1 35.8 1.0 HB3 A:PHE40 4.1 43.1 1.0 C A:PHE40 4.2 37.6 1.0 O A:PHE40 4.3 43.7 1.0 CB A:PHE40 4.6 35.8 1.0 N A:GLY41 4.7 51.3 1.0 CD1 A:PHE40 4.8 34.5 1.0 H A:GLY41 4.9 61.7 1.0

Iodine binding site 3 out of 8 in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:55.0 occ:0.50 HZ3 A:LYS88 3.2 42.4 1.0 HZ2 A:LYS88 3.3 42.4 1.0 NZ A:LYS88 3.7 35.2 1.0 HA A:SER7 3.7 38.6 1.0 HB3 A:TRP6 3.7 51.5 1.0 HE2 A:LYS88 3.8 47.3 1.0 HB2 A:TRP6 4.1 51.5 1.0 O A:HOH316 4.1 40.5 0.5 HD21 A:LEU94 4.2 51.3 1.0 CE A:LYS88 4.3 39.3 1.0 O A:TRP6 4.3 41.4 1.0 CB A:TRP6 4.3 42.8 1.0 C A:TRP6 4.4 45.4 1.0 N A:SER7 4.4 41.6 1.0 HZ1 A:LYS88 4.4 42.4 1.0 CA A:SER7 4.4 32.0 1.0 HD11 A:LEU94 4.4 55.9 1.0 HB3 A:SER7 4.6 58.9 1.0 H A:SER7 4.7 50.0 1.0 HE3 A:LYS88 4.9 47.3 1.0 CB A:SER7 5.0 48.9 1.0

Iodine binding site 4 out of 8 in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:82.4 occ:1.00 H A:ASN11 2.7 40.4 1.0 HA A:VAL10 3.1 51.6 1.0 HB A:VAL10 3.3 28.8 1.0 HB2 A:ASN11 3.4 36.8 1.0 N A:ASN11 3.5 33.5 1.0 O A:HOH316 3.7 40.5 0.5 CA A:VAL10 3.9 42.9 1.0 HZ3 A:TRP16 4.0 39.4 1.0 CB A:VAL10 4.0 23.8 1.0 CB A:ASN11 4.2 30.6 1.0 HG12 A:VAL10 4.2 56.3 1.0 C A:VAL10 4.2 35.2 1.0 HB3 A:ASN11 4.4 36.8 1.0 CA A:ASN11 4.5 41.3 1.0 CG1 A:VAL10 4.6 46.8 1.0 O A:ILE9 4.7 24.7 1.0 CZ3 A:TRP16 4.8 32.7 1.0 O A:HOH310 4.9 48.0 1.0 HG11 A:VAL10 4.9 56.3 1.0

Iodine binding site 5 out of 8 in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:130.7 occ:1.00 H A:LYS37 2.8 47.0 1.0 HB2 A:LYS37 3.5 71.0 1.0 HA A:ALA36 3.6 57.6 1.0 N A:LYS37 3.6 39.0 1.0 HB3 A:GLU38 3.8 54.7 1.0 H A:GLU38 3.9 45.0 1.0 N A:GLU38 4.3 37.3 1.0 HB2 A:ALA36 4.3 49.5 1.0 CB A:LYS37 4.4 59.0 1.0 CA A:LYS37 4.4 53.2 1.0 CA A:ALA36 4.4 47.9 1.0 C A:ALA36 4.5 55.6 1.0 C A:LYS37 4.6 52.6 1.0 CB A:GLU38 4.7 45.5 1.0 HG3 A:LYS37 4.8 62.0 1.0 CB A:ALA36 4.8 41.1 1.0 O A:GLU38 4.9 44.1 1.0 HB2 A:GLU38 4.9 54.7 1.0

Iodine binding site 6 out of 8 in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:107.1 occ:1.00 HD3 A:ARG57 3.2 41.2 1.0 HD2 A:PHE55 3.4 30.5 1.0 HB3 A:SER52 3.5 53.5 1.0 HG3 A:GLN172 3.6 55.5 1.0 HB2 A:SER52 3.7 53.5 1.0 C A:GLN172 3.8 60.2 1.0 HG2 A:GLN172 4.0 55.5 1.0 HB2 A:ARG57 4.0 36.7 1.0 HE2 A:PHE55 4.0 43.2 1.0 CD A:ARG57 4.0 34.2 1.0 CB A:SER52 4.1 44.4 1.0 HD2 A:ARG57 4.1 41.2 1.0 O A:GLN172 4.1 80.1 1.0 CD2 A:PHE55 4.1 25.3 1.0 HB3 A:HIS50 4.2 49.7 1.0 HB2 A:HIS50 4.2 49.7 1.0 CG A:GLN172 4.2 46.1 1.0 HB3 A:ARG57 4.4 36.7 1.0 CE2 A:PHE55 4.4 35.9 1.0 CB A:ARG57 4.6 30.4 1.0 CB A:HIS50 4.7 41.3 1.0 HG A:SER52 4.7 71.2 1.0 HB3 A:PHE55 4.8 44.6 1.0 H A:SER52 4.8 54.2 1.0 NE A:ARG57 4.9 53.0 1.0 CG A:ARG57 4.9 38.0 1.0 N A:SER52 4.9 45.0 1.0 OG A:SER52 4.9 59.2 1.0 HB3 A:GLN172 5.0 53.9 1.0 CA A:GLN172 5.0 64.3 1.0 CB A:GLN172 5.0 44.8 1.0

Iodine binding site 7 out of 8 in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:I207 b:99.6 occ:1.00 HB3 A:LYS45 3.2 60.6 1.0 HB2 A:PRO43 3.5 49.3 1.0 HG2 A:GLN46 3.5 68.7 1.0 HG2 A:LYS45 3.8 93.3 1.0 HG2 A:PRO43 4.0 61.9 1.0 HB3 A:PRO43 4.0 49.3 1.0 HG3 A:GLN46 4.1 68.7 1.0 CB A:LYS45 4.1 50.3 1.0 CB A:PRO43 4.1 41.7 1.0 CG A:GLN46 4.2 57.1 1.0 HE21 A:GLN46 4.4 92.5 1.0 HB2 A:LYS45 4.4 60.6 1.0 CG A:LYS45 4.4 77.6 1.0 CG A:PRO43 4.6 51.4 1.0 NE2 A:GLN46 4.7 77.0 1.0 CD A:GLN46 4.7 82.7 1.0 H A:GLN46 4.8 70.4 1.0 HG3 A:LYS45 4.9 93.3 1.0

Iodine binding site 8 out of 8 in the Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Human Norovirus Gii.4 Sydney Protease in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:I208 b:116.9 occ:1.00 O A:HOH323 3.1 50.9 1.0 HB2 A:PRO22 3.3 52.3 1.0 HB2 A:SER23 3.3 37.2 1.0 HB3 A:PRO63 3.3 51.4 1.0 HG A:SER23 3.4 69.5 1.0 HD2 A:PRO22 3.5 58.4 1.0 OG A:SER23 3.5 57.8 1.0 HG2 A:PRO22 3.8 39.9 1.0 CB A:SER23 3.9 30.8 1.0 H A:SER23 3.9 59.7 1.0 CB A:PRO22 4.1 43.5 1.0 HG A:SER21 4.2 54.3 1.0 CD A:PRO22 4.2 48.5 1.0 CG A:PRO22 4.2 33.1 1.0 N A:SER23 4.3 49.6 1.0 CB A:PRO63 4.3 42.7 1.0 HA A:PRO63 4.4 55.8 1.0 OG A:SER21 4.6 45.1 1.0 HB3 A:SER23 4.7 37.2 1.0 HG3 A:PRO63 4.7 61.2 1.0 HD3 A:PRO63 4.7 46.5 1.0 CA A:SER23 4.7 33.3 1.0 C A:PRO22 4.8 34.8 1.0 N A:PRO22 4.8 37.2 1.0 HB2 A:PRO63 4.8 51.4 1.0 HB2 A:SER21 4.8 38.6 1.0 HB3 A:PRO22 4.8 52.3 1.0 CA A:PRO22 4.8 40.6 1.0 CA A:PRO63 4.9 46.4 1.0 HD3 A:PRO22 5.0 58.4 1.0 HH11 A:ARG59 5.0 84.5 1.0 HH12 A:ARG59 5.0 84.5 1.0 CG A:PRO63 5.0 50.8 1.0

S.Pham, B.Zhao, N.Neetu, B.Sankaran, K.Patil, S.Ramani, Y.Song, M.K.Estes, T.Palzkill, B.V.V.Prasad. Conformational Flexibility Is A Critical Factor in Designing Broad-Spectrum Human Norovirus Protease Inhibitors. J.Virol. 75724 2025.
ISSN: ESSN 1098-5514
PubMed: 39873493
DOI: 10.1128/JVI.01757-24