Iodine in PDB 3ssy: Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex

The structure of Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex, PDB code: 3ssy was solved by W.Wang, J.S.Grimley, L.S.Beese, H.W.Hellinga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.22 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.635, 61.821, 69.603, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.4

The binding sites of Iodine atom in the Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex (pdb code 3ssy). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex, PDB code: 3ssy:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I260 b:15.6 occ:0.77 HG1 A:THR108 2.7 16.9 1.0 HG2 A:GLN94 3.0 17.1 1.0 HE22 A:GLN94 3.0 18.8 1.0 OG1 A:THR108 3.2 14.1 1.0 HG3 A:ARG96 3.2 13.3 1.0 HB2 A:ALA110 3.3 17.5 1.0 HB A:THR108 3.3 14.9 1.0 HB3 A:GLN94 3.4 15.2 1.0 HB3 A:ALA110 3.5 17.5 1.0 O A:HOH292 3.5 20.5 1.0 NE2 A:GLN94 3.8 15.7 1.0 CB A:THR108 3.8 12.5 1.0 O A:HOH272 3.8 14.1 1.0 CG A:GLN94 3.8 14.3 1.0 O A:GLN94 3.8 14.3 1.0 CB A:ALA110 3.8 14.6 1.0 H A:ALA110 3.9 16.5 1.0 HA A:GLU95 4.0 17.6 1.0 HG23 A:THR63 4.0 16.5 1.0 H A:ARG96 4.0 15.3 1.0 CB A:GLN94 4.1 12.8 1.0 C A:GLN94 4.1 16.3 1.0 N A:ALA110 4.1 13.8 1.0 HA A:ARG109 4.1 16.8 1.0 HB2 A:ARG96 4.2 16.4 1.0 CG A:ARG96 4.2 11.1 1.0 HG23 A:ILE123 4.2 16.6 1.0 C A:THR108 4.3 14.2 1.0 CD A:GLN94 4.3 11.2 1.0 N A:ARG96 4.3 12.8 1.0 O A:THR108 4.4 14.6 1.0 HE21 A:GLN94 4.4 18.8 1.0 HH11 A:ARG96 4.4 17.8 1.0 N A:ARG109 4.4 13.2 1.0 N A:GLU95 4.4 13.9 1.0 C A:ARG109 4.5 16.1 1.0 CA A:GLU95 4.5 14.7 1.0 HA A:THR63 4.5 13.5 1.0 C A:GLU95 4.5 14.9 1.0 CA A:ARG109 4.6 14.1 1.0 HB1 A:ALA110 4.6 17.5 1.0 CA A:ALA110 4.6 13.5 1.0 HG3 A:GLN94 4.6 17.1 1.0 CB A:ARG96 4.7 13.7 1.0 CA A:THR108 4.7 12.1 1.0 NH1 A:ARG96 4.7 14.9 1.0 HG2 A:ARG96 4.7 13.3 1.0 CA A:GLN94 4.7 11.4 1.0 HG12 A:ILE123 4.8 20.3 1.0 HG21 A:THR108 4.8 17.8 1.0 HD2 A:ARG96 4.8 14.4 1.0 H A:ARG109 4.8 15.8 1.0 HB2 A:GLN94 4.9 15.2 1.0 HG1 A:THR63 4.9 15.2 1.0 CG2 A:THR108 4.9 14.9 1.0 HG21 A:ILE123 4.9 16.6 1.0 HH12 A:ARG96 4.9 17.8 1.0 CG2 A:THR63 4.9 13.8 1.0 H A:GLU95 5.0 16.7 1.0 CD A:ARG96 5.0 12.1 1.0 CG2 A:ILE123 5.0 13.9 1.0

Iodine binding site 2 out of 3 in the Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I261 b:20.8 occ:0.38 O A:HOH262 2.0 15.8 0.6 H A:TRP57 2.9 17.1 1.0 O A:HOH389 3.1 30.6 1.0 HD1 A:TYR143 3.2 18.4 1.0 HA A:PRO56 3.3 13.7 1.0 O A:HOH291 3.3 21.7 1.0 HD2 A:PRO58 3.4 16.6 1.0 O A:HOH486 3.4 40.4 1.0 HD3 A:PRO58 3.4 16.6 1.0 HB3 A:PRO56 3.4 16.1 1.0 HB2 A:TRP57 3.6 18.2 1.0 O A:HOH404 3.6 30.1 1.0 N A:TRP57 3.6 14.3 1.0 CD A:PRO58 3.8 13.9 1.0 O A:HOH271 4.0 18.1 1.0 CA A:PRO56 4.0 11.4 1.0 CD1 A:TYR143 4.1 15.3 1.0 CB A:PRO56 4.2 13.5 1.0 CD1 A:TRP57 4.2 14.6 1.0 HB2 A:TYR143 4.2 17.3 1.0 C A:PRO56 4.3 12.2 1.0 CB A:TRP57 4.3 15.2 1.0 O A:HOH371 4.4 37.9 1.0 HD1 A:HIS139 4.4 38.7 1.0 CA A:TRP57 4.6 14.7 1.0 HE1 A:TYR143 4.6 20.6 1.0 HG2 A:PRO58 4.6 14.7 1.0 CG A:TRP57 4.7 13.9 1.0 HB2 A:PRO56 4.7 16.1 1.0 HA A:TYR143 4.7 14.6 1.0 CE1 A:TYR143 4.8 17.2 1.0 CG A:PRO58 4.8 12.3 1.0 O A:LEU141 4.8 18.5 1.0 HZ1 A:LYS209 4.9 24.2 1.0 CB A:TYR143 4.9 14.5 1.0 CG A:TYR143 4.9 16.7 1.0 HG3 A:PRO56 5.0 20.2 1.0

Iodine binding site 3 out of 3 in the Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I263 b:32.4 occ:0.39 HA A:HIS199 3.2 18.7 1.0 HD2 A:TYR200 3.3 29.9 1.0 HD2 A:TYR151 3.4 24.5 1.0 O A:HOH349 3.5 25.4 1.0 HB3 A:ASN198 3.7 27.1 1.0 CA A:HIS199 3.9 15.6 1.0 C A:HIS199 3.9 16.4 1.0 N A:HIS199 4.0 14.6 1.0 HB3 A:TYR200 4.1 20.6 1.0 O A:HIS199 4.1 16.6 1.0 HE2 A:TYR151 4.2 31.0 1.0 CD2 A:TYR200 4.2 25.0 1.0 CD2 A:TYR151 4.3 20.5 1.0 H A:HIS199 4.3 17.5 1.0 C A:ASN198 4.3 21.2 1.0 O A:ASN198 4.5 20.8 1.0 N A:TYR200 4.5 15.6 1.0 HA3 A:GLY228 4.5 30.1 1.0 CB A:ASN198 4.6 22.6 1.0 CE2 A:TYR151 4.6 25.9 1.0 H A:TYR200 4.7 18.6 1.0 HB2 A:ASN198 4.8 27.1 1.0 CB A:TYR200 4.9 17.2 1.0 HE2 A:TYR200 4.9 32.1 1.0

W.Wang, J.S.Grimley, G.J.Augustine, L.S.Beese, H.W.Hellinga. Determination of Engineered Chloride-Binding Site Structures in Fluorescent Proteins Reveals Principles of Halide Recognition To Be Published.