Iodine in PDB 6yrb: Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5

The structure of Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5, PDB code: 6yrb was solved by A.Serris, F.A.Rey, P.Guardado-Calvo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.70 / 2.35
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	67.854, 67.854, 121.891, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 26.6

The binding sites of Iodine atom in the Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5 (pdb code 6yrb). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5, PDB code: 6yrb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:I605 b:80.6 occ:1.00 O A:HOH716 3.5 48.8 1.0 CA A:GLY440 3.6 42.3 1.0 C A:GLY440 3.9 45.8 1.0 N A:GLN441 4.0 49.1 1.0 CB A:TYR437 4.1 40.5 1.0 N A:GLY440 4.1 45.2 1.0 CD1 A:TYR437 4.3 37.2 1.0 CG A:TYR437 4.5 37.4 1.0 O A:GLY440 4.6 42.3 1.0 O A:HOH724 4.9 47.5 1.0 CA A:TYR437 5.0 41.5 1.0

Iodine binding site 2 out of 6 in the Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:I606 b:0.1 occ:1.00 CB A:ASP468 3.6 55.6 1.0 N A:ASP468 3.7 41.2 1.0 CA A:MET466 3.7 43.7 1.0 C A:MET466 3.8 41.0 1.0 CB A:MET466 3.8 48.5 1.0 N A:PRO467 4.0 37.1 1.0 CD A:PRO467 4.1 32.9 1.0 CA A:ASP468 4.2 46.7 1.0 O A:MET466 4.2 38.7 1.0 N A:VAL469 4.4 58.6 1.0 OD2 A:ASP468 4.5 67.5 1.0 CG A:ASP468 4.6 62.3 1.0 CG2 A:VAL469 4.7 44.9 1.0 C A:ASP468 4.7 43.9 1.0 C A:PRO467 4.8 42.2 1.0 CG1 A:VAL469 4.8 57.5 1.0 CG A:MET466 4.8 58.3 1.0 CE A:MET466 4.9 66.8 1.0 CG A:PRO467 4.9 33.7 1.0 CA A:PRO467 5.0 38.7 1.0

Iodine binding site 3 out of 6 in the Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:I607 b:0.3 occ:1.00 NZ A:LYS442 3.6 37.7 1.0 CE A:LYS442 4.4 33.4 1.0 CD A:LYS442 4.4 34.2 1.0

Iodine binding site 4 out of 6 in the Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:I601 b:0.6 occ:1.00 N B:ASP468 3.6 42.3 1.0 CB B:ASP468 3.6 43.8 1.0 CA B:MET466 3.7 42.1 1.0 C B:MET466 3.7 45.7 1.0 CB B:MET466 3.9 42.0 1.0 N B:PRO467 3.9 43.9 1.0 CD B:PRO467 4.0 44.5 1.0 CA B:ASP468 4.1 42.4 1.0 O B:MET466 4.2 41.8 1.0 N B:VAL469 4.4 42.0 1.0 CG2 B:VAL469 4.6 42.0 1.0 C B:PRO467 4.7 43.9 1.0 OD2 B:ASP468 4.7 65.9 1.0 CG B:ASP468 4.7 57.2 1.0 C B:ASP468 4.7 50.9 1.0 CG B:PRO467 4.7 42.6 1.0 CG B:MET466 4.8 50.0 1.0 CG1 B:VAL469 4.8 56.2 1.0 CA B:PRO467 4.9 43.9 1.0

Iodine binding site 5 out of 6 in the Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:I602 b:0.5 occ:1.00 O B:PRO406 3.5 50.2 1.0 CA B:PRO406 3.8 51.2 1.0 C B:PRO406 4.1 50.6 1.0 O B:SER405 4.5 43.4 1.0 CB B:PRO406 4.5 50.5 1.0 N B:PRO406 5.0 48.8 1.0

Iodine binding site 6 out of 6 in the Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the Tetramerization Domain of the Glycoprotein Gn (Andes Virus) at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:I603 b:0.7 occ:1.00 OE2 B:GLU476 3.3 80.1 1.0 OG B:SER472 3.6 55.0 1.0 N B:LEU473 4.0 41.0 1.0 CB B:SER472 4.1 50.5 1.0 CA B:LEU473 4.2 41.2 1.0 C B:SER472 4.3 41.0 1.0 CD1 B:LEU473 4.4 41.4 1.0 CB B:LEU473 4.4 41.1 1.0 CD B:GLU476 4.5 75.8 1.0 O B:SER472 4.5 48.5 1.0 CB B:VAL469 4.8 50.9 1.0 O B:VAL469 4.8 57.6 1.0 CA B:SER472 4.9 41.0 1.0

A.Serris, R.Stass, E.A.Bignon, N.A.Muena, J.C.Manuguerra, R.K.Jangra, S.Li, K.Chandran, N.D.Tischler, J.T.Huiskonen, F.A.Rey, P.Guardado-Calvo. The Hantavirus Surface Glycoprotein Lattice and Its Fusion Control Mechanism. Cell V. 183 442 2020.
ISSN: ISSN 1097-4172
PubMed: 32937107
DOI: 10.1016/J.CELL.2020.08.023