Iodine in PDB 9ful: Crystal Structure of SNAR1.3 in Complex with Iodide

The structure of Crystal Structure of SNAR1.3 in Complex with Iodide, PDB code: 9ful was solved by G.R.Roberts, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.36 / 1.88
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.506, 70.506, 119.356, 90, 90, 120
R / Rfree (%)	20.8 / 23

The binding sites of Iodine atom in the Crystal Structure of SNAR1.3 in Complex with Iodide (pdb code 9ful). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of SNAR1.3 in Complex with Iodide, PDB code: 9ful:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Crystal Structure of SNAR1.3 in Complex with Iodide


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 SNAR1.3 in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:54.6 occ:0.60 I A:IOD301 0.0 54.6 0.6 I A:IOD301 2.1 40.6 0.2 HH12 A:ARG23 2.4 82.1 1.0 NH1 A:ARG23 3.2 68.2 1.0 HA A:ALA19 3.3 54.5 1.0 HH22 A:ARG23 3.3 93.3 1.0 HE2 A:PHE132 3.4 64.8 1.0 HH22 A:ARG124 3.6 88.4 1.0 HG21 A:ILE14 3.6 60.4 1.0 HH11 A:ARG23 3.6 82.1 1.0 H42 A:PG4304 3.8 78.9 1.0 HB A:VAL22 3.8 47.6 1.0 HG11 A:VAL22 3.9 47.8 1.0 NH2 A:ARG23 3.9 77.6 1.0 HB1 A:ALA19 3.9 55.4 1.0 CZ A:ARG23 4.0 68.7 1.0 O3 A:PG4304 4.0 79.2 1.0 HB2 A:ALA19 4.1 55.4 1.0 HZ A:PHE132 4.1 53.1 1.0 CE2 A:PHE132 4.1 53.8 1.0 CA A:ALA19 4.1 45.2 1.0 NH2 A:ARG124 4.2 73.5 1.0 CB A:ALA19 4.3 46.0 1.0 HG23 A:VAL22 4.4 47.5 1.0 C4 A:PG4304 4.4 65.6 1.0 HH12 A:ARG124 4.4 94.1 1.0 HG21 A:VAL22 4.5 47.5 1.0 HG13 A:ILE14 4.5 58.6 1.0 CB A:VAL22 4.5 39.5 1.0 CG1 A:VAL22 4.5 39.7 1.0 CZ A:PHE132 4.5 44.1 1.0 HG12 A:VAL22 4.5 47.8 1.0 HH21 A:ARG124 4.5 88.4 1.0 CG2 A:ILE14 4.6 50.1 1.0 NH1 A:ARG124 4.6 78.2 1.0 HG3 A:ARG23 4.6 57.9 1.0 O A:ALA19 4.6 42.7 1.0 HH21 A:ARG23 4.7 93.3 1.0 CG2 A:VAL22 4.7 39.4 1.0 HB2 A:ALA95 4.7 49.2 1.0 HB1 A:ALA95 4.8 49.2 1.0 HG22 A:ILE14 4.8 60.4 1.0 HD12 A:ILE14 4.8 59.3 1.0 HH11 A:ARG124 4.9 94.1 1.0 CZ A:ARG124 4.9 70.6 1.0 C A:ALA19 4.9 44.1 1.0 H41 A:PG4304 5.0 78.9 1.0

Iodine binding site 2 out of 5 in the Crystal Structure of SNAR1.3 in Complex with Iodide


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 SNAR1.3 in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:40.6 occ:0.25 I A:IOD301 0.0 40.6 0.2 I A:IOD301 2.1 54.6 0.6 HZ A:PHE132 2.7 53.1 1.0 HG23 A:VAL22 2.8 47.5 1.0 HG21 A:VAL22 2.9 47.5 1.0 HA A:ALA19 3.1 54.5 1.0 HG21 A:ILE14 3.1 60.4 1.0 CG2 A:VAL22 3.2 39.4 1.0 HG11 A:VAL22 3.3 47.8 1.0 HB A:VAL22 3.3 47.6 1.0 HA2 A:GLY99 3.3 47.3 1.0 HE2 A:PHE132 3.3 64.8 1.0 CZ A:PHE132 3.4 44.1 1.0 CB A:VAL22 3.6 39.5 1.0 CE2 A:PHE132 3.7 53.8 1.0 HA3 A:GLY99 3.7 47.3 1.0 HA A:ALA95 3.8 46.8 1.0 HB1 A:ALA95 3.9 49.2 1.0 CG1 A:VAL22 3.9 39.7 1.0 CA A:GLY99 4.0 39.3 1.0 HD12 A:ILE14 4.0 59.3 1.0 CG2 A:ILE14 4.0 50.1 1.0 HH12 A:ARG23 4.1 82.1 1.0 CA A:ALA19 4.1 45.2 1.0 HG22 A:VAL22 4.1 47.5 1.0 HG23 A:ILE14 4.2 60.4 1.0 HB2 A:ALA95 4.3 49.2 1.0 O A:GLY18 4.3 41.5 1.0 HG22 A:ILE14 4.4 60.4 1.0 HG12 A:VAL22 4.4 47.8 1.0 CB A:ALA95 4.4 40.8 1.0 HB2 A:ALA19 4.5 55.4 1.0 CE1 A:PHE132 4.5 44.6 1.0 CA A:ALA95 4.5 38.9 1.0 N A:ALA19 4.5 44.5 1.0 HG13 A:ILE14 4.6 58.6 1.0 H42 A:PG4304 4.6 78.9 1.0 H A:GLU100 4.6 50.9 1.0 C A:GLY18 4.7 44.5 1.0 N A:GLY99 4.7 39.8 1.0 HG13 A:VAL22 4.7 47.8 1.0 HE1 A:PHE132 4.7 53.8 1.0 NH1 A:ARG23 4.7 68.2 1.0 CB A:ALA19 4.7 46.0 1.0 H A:GLY99 4.8 47.9 1.0 HB1 A:ALA19 4.8 55.4 1.0 HH22 A:ARG124 4.9 88.4 1.0 O A:ALA19 4.9 42.7 1.0 CD1 A:ILE14 4.9 49.2 1.0 HH11 A:ARG23 4.9 82.1 1.0 O A:ALA95 4.9 39.8 1.0 H A:VAL22 5.0 48.1 1.0 CD2 A:PHE132 5.0 50.0 1.0 C A:ALA19 5.0 44.1 1.0

Iodine binding site 3 out of 5 in the Crystal Structure of SNAR1.3 in Complex with Iodide


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 SNAR1.3 in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:38.9 occ:0.85 H A:ASP125 2.9 46.6 1.0 HG3 A:ARG65 3.2 48.1 1.0 HB3 A:MET64 3.2 48.1 1.0 H21 A:PG4304 3.5 72.7 1.0 O A:HOH514 3.6 52.0 1.0 HB3 A:ARG124 3.6 57.4 1.0 HB2 A:ASP125 3.6 43.5 1.0 O1 A:PG4304 3.6 55.8 1.0 HG2 A:PRO128 3.7 43.9 1.0 N A:ASP125 3.7 38.7 1.0 HD2 A:ARG124 3.7 69.9 1.0 HG3 A:PRO128 3.8 43.9 1.0 HA A:ARG124 3.8 53.5 1.0 CG A:ARG65 4.0 39.9 1.0 CG A:PRO128 4.1 36.4 1.0 HO1 A:PG4304 4.1 67.1 1.0 HG2 A:ARG65 4.2 48.1 1.0 CB A:MET64 4.2 39.9 1.0 CB A:ASP125 4.3 36.1 1.0 HG2 A:MET64 4.3 65.2 1.0 HD12 A:LEU68 4.3 67.6 1.0 CG A:ASP125 4.3 36.5 1.0 HD3 A:ARG65 4.3 47.5 1.0 CA A:ARG124 4.3 44.4 1.0 HB2 A:PRO128 4.3 43.3 1.0 CB A:ARG124 4.4 47.7 1.0 H A:ARG65 4.4 43.5 1.0 OD2 A:ASP125 4.4 34.4 1.0 C2 A:PG4304 4.4 60.4 1.0 C A:ARG124 4.5 41.6 1.0 H32 A:PG4304 4.5 79.4 1.0 HB2 A:MET64 4.6 48.1 1.0 N A:ARG65 4.6 36.1 1.0 O A:HOH488 4.6 69.2 1.0 CD A:ARG124 4.6 58.1 1.0 CA A:ASP125 4.6 36.6 1.0 C1 A:PG4304 4.6 55.7 1.0 H31 A:PG4304 4.6 79.4 1.0 HD11 A:LEU68 4.6 67.6 1.0 HE3 A:MET64 4.6 56.4 1.0 CG A:MET64 4.7 54.1 1.0 CD A:ARG65 4.7 39.4 1.0 HA A:ARG65 4.7 45.7 1.0 NE A:ARG124 4.8 65.0 1.0 CB A:PRO128 4.8 35.9 1.0 HE A:ARG124 4.8 78.2 1.0 OD1 A:ASP125 4.8 36.7 1.0 HE A:ARG65 4.8 44.6 1.0 C A:MET64 4.9 38.3 1.0 H22 A:PG4304 4.9 72.7 1.0 CD1 A:LEU68 4.9 56.1 1.0 C3 A:PG4304 5.0 66.0 1.0 SD A:MET64 5.0 63.3 1.0

Iodine binding site 4 out of 5 in the Crystal Structure of SNAR1.3 in Complex with Iodide


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 SNAR1.3 in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:72.2 occ:0.67 O A:HOH511 3.1 68.4 1.0 HA A:PRO156 3.2 66.4 1.0 HB3 A:PRO156 3.3 68.5 1.0 HE2 A:PHE161 3.4 58.2 1.0 HG2 A:LYS155 3.6 71.9 1.0 HB3 A:LYS155 3.6 70.9 1.0 HZ A:PHE161 3.8 58.8 1.0 CB A:PRO156 3.9 56.9 1.0 CA A:PRO156 3.9 55.2 1.0 HB2 A:PRO156 4.0 68.5 1.0 HD3 A:LYS155 4.0 82.8 1.0 HA3 A:GLY188 4.0 94.1 1.0 H A:SER189 4.1 103.8 1.0 CE2 A:PHE161 4.1 48.3 1.0 HE2 A:LYS155 4.2 77.5 1.0 CZ A:PHE161 4.3 48.8 1.0 CG A:LYS155 4.3 59.7 1.0 O A:PRO182 4.3 86.2 1.0 HB2 A:SER189 4.3 99.1 1.0 CB A:LYS155 4.4 58.9 1.0 CD A:LYS155 4.5 68.8 1.0 HB3 A:SER189 4.6 99.1 1.0 N A:SER189 4.7 86.4 1.0 C A:PRO156 4.8 54.3 1.0 O A:PRO156 4.8 56.9 1.0 CE A:LYS155 4.9 64.4 1.0 CB A:SER189 4.9 82.4 1.0 N A:PRO156 4.9 58.7 1.0 C A:PRO182 4.9 86.0 1.0 CA A:GLY188 5.0 78.2 1.0

Iodine binding site 5 out of 5 in the Crystal Structure of SNAR1.3 in Complex with Iodide


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 SNAR1.3 in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:60.0 occ:0.40 HE3 A:LYS166 3.4 56.5 1.0 HZ2 A:LYS166 3.5 58.6 1.0 HZ1 A:LYS166 3.7 58.6 1.0 NZ A:LYS166 3.9 48.6 1.0 CE A:LYS166 4.1 46.9 1.0 HD2 A:LYS166 4.7 47.2 1.0 HE2 A:LYS166 4.7 56.5 1.0 HZ3 A:LYS166 4.8 58.6 1.0

T.M.Lister, G.W.Roberts, E.J.Hossack, F.Zhao, A.J.Burke, L.O.Johannissen, F.J.Hardy, A.A.V.Millman, D.Leys, I.Larrosa, A.P.Green. Engineered Enzymes For Enantioselective Nucleophilic Aromatic Substitutions. Nature 2025.
ISSN: ESSN 1476-4687
PubMed: 39814071
DOI: 10.1038/S41586-025-08611-0