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

The structure of Engineered High-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex, PDB code: 3ssl 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)	34.52 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.297, 62.741, 69.783, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 17.7

The binding sites of Iodine atom in the Engineered High-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex (pdb code 3ssl). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Engineered High-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex, PDB code: 3ssl:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Engineered High-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 High-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I260 b:16.0 occ:0.62 O A:HOH261 1.7 31.1 0.4 HH21 A:ARG96 2.7 20.1 1.0 HE21 A:GLN69 2.8 29.0 1.0 HD21 A:ASN185 3.0 29.4 1.0 HE A:ARG96 3.1 17.7 1.0 HB A:VAL163 3.1 29.1 1.0 HG11 A:VAL163 3.2 35.9 1.0 HB3 A:ALA183 3.3 17.1 1.0 HG21 A:VAL163 3.3 30.9 1.0 HE2 A:PHE165 3.4 19.6 1.0 NH2 A:ARG96 3.5 16.8 1.0 HB1 A:ALA183 3.5 17.1 1.0 NE2 A:GLN69 3.7 24.2 1.0 CB A:ALA183 3.7 14.2 1.0 CB A:VAL163 3.8 24.3 1.0 HB2 A:ALA183 3.8 17.1 1.0 NE A:ARG96 3.8 14.8 1.0 CG1 A:VAL163 3.9 29.9 1.0 ND2 A:ASN185 3.9 24.5 1.0 OE1 A:GLN69 3.9 22.1 1.0 CG2 A:VAL163 4.0 25.8 1.0 HE22 A:GLN94 4.1 30.6 1.0 HH22 A:ARG96 4.1 20.1 1.0 HG12 A:VAL163 4.1 35.9 1.0 CZ A:ARG96 4.2 13.8 1.0 HG11 A:VAL150 4.2 32.7 1.0 HD22 A:ASN185 4.2 29.4 1.0 CD A:GLN69 4.2 20.9 1.0 HG23 A:VAL163 4.3 30.9 1.0 CE2 A:PHE165 4.3 16.3 1.0 HE22 A:GLN69 4.3 29.0 1.0 NE2 A:GLN94 4.5 25.5 1.0 HG3 A:GLN94 4.5 19.1 1.0 HE21 A:GLN94 4.7 30.6 1.0 HG13 A:VAL163 4.7 35.9 1.0 HZ A:PHE84 4.7 21.7 1.0 HD2 A:PHE165 4.7 18.9 1.0 HG22 A:VAL163 4.8 30.9 1.0 CG A:ASN185 4.9 19.8 1.0 CG1 A:VAL150 4.9 27.2 1.0 HG13 A:VAL150 4.9 32.7 1.0 OD1 A:ASN185 5.0 25.1 1.0 CD2 A:PHE165 5.0 15.8 1.0

Iodine binding site 2 out of 5 in the Engineered High-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 High-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I262 b:17.2 occ:0.42 O A:HOH263 2.1 18.4 0.6 O A:HOH272 2.7 31.5 0.6 H A:TRP57 3.0 10.3 1.0 HA A:PRO56 3.2 12.2 1.0 O A:HOH310 3.2 19.4 1.0 HD1 A:TYR143 3.3 14.6 1.0 HD3 A:PRO58 3.3 11.9 1.0 HB3 A:PRO56 3.3 13.9 1.0 O A:HOH408 3.4 25.5 1.0 HD2 A:PRO58 3.6 11.9 1.0 HB2 A:TRP57 3.7 11.2 1.0 N A:TRP57 3.7 8.6 1.0 O A:HOH284 3.8 13.6 1.0 CD A:PRO58 3.9 9.9 1.0 CA A:PRO56 3.9 10.1 1.0 CB A:PRO56 4.1 11.6 1.0 CD1 A:TYR143 4.1 12.2 1.0 HB2 A:TYR143 4.2 15.4 1.0 HD1 A:HIS139 4.2 30.7 1.0 C A:PRO56 4.3 9.8 1.0 CD1 A:TRP57 4.3 10.9 1.0 CB A:TRP57 4.4 9.3 1.0 O A:HOH341 4.4 33.7 1.0 HB2 A:PRO56 4.5 13.9 1.0 CA A:TRP57 4.6 9.3 1.0 O A:LEU141 4.7 15.2 1.0 HA A:TYR143 4.7 13.7 1.0 HE1 A:TYR143 4.7 13.1 1.0 HG2 A:PRO58 4.7 12.6 1.0 CG A:TRP57 4.8 9.6 1.0 CG A:PRO58 4.8 10.5 1.0 CE1 A:TYR143 4.9 10.9 1.0 CB A:TYR143 4.9 12.8 1.0 HZ1 A:LYS209 4.9 18.1 1.0 CG A:TYR143 5.0 10.8 1.0

Iodine binding site 3 out of 5 in the Engineered High-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 High-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I266 b:36.2 occ:0.35 O A:HOH267 2.7 25.4 0.7 HG1 A:THR97 3.3 17.1 1.0 HB A:THR97 3.4 13.8 1.0 HE1 A:PHE99 3.5 22.0 1.0 HZ A:PHE99 3.5 22.2 1.0 HB2 A:TYR182 3.8 18.2 1.0 OG1 A:THR97 3.9 14.2 1.0 HG21 A:THR97 4.0 17.0 1.0 CB A:THR97 4.1 11.4 1.0 CE1 A:PHE99 4.2 18.4 1.0 CZ A:PHE99 4.2 18.5 1.0 HB3 A:TYR182 4.3 18.2 1.0 CB A:TYR182 4.5 15.2 1.0 CG2 A:THR97 4.6 14.2 1.0 O A:HOH506 4.8 48.4 1.0 CG A:TYR182 4.8 17.4 1.0 HD2 A:TYR182 5.0 22.7 1.0

Iodine binding site 4 out of 5 in the Engineered High-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 4 of Engineered High-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I264 b:26.9 occ:0.31 H A:LEU207 2.5 14.0 1.0 O A:HOH265 2.8 28.2 0.7 HA A:ALA206 2.9 13.4 1.0 HA A:ASN144 2.9 14.5 1.0 O A:HOH404 3.0 39.4 1.0 O A:HOH418 3.1 26.7 1.0 H A:TYR145 3.2 14.2 1.0 N A:LEU207 3.4 11.7 1.0 HB2 A:ASN144 3.4 16.4 1.0 HG A:LEU207 3.6 15.6 1.0 CA A:ASN144 3.7 12.1 1.0 N A:TYR145 3.7 11.8 1.0 CA A:ALA206 3.8 11.1 1.0 HB2 A:LEU207 3.9 13.8 1.0 O A:HOH412 3.9 40.5 1.0 CB A:ASN144 3.9 13.7 1.0 HB3 A:ASN144 4.0 16.4 1.0 O A:HOH371 4.1 30.7 1.0 C A:ALA206 4.1 10.1 1.0 O A:SER205 4.1 17.1 1.0 C A:ASN144 4.1 12.0 1.0 O A:LEU207 4.1 14.7 1.0 HB1 A:ALA206 4.2 18.6 1.0 HB2 A:TYR145 4.3 13.1 1.0 CA A:LEU207 4.3 10.5 1.0 CB A:LEU207 4.3 11.5 1.0 CG A:LEU207 4.4 13.0 1.0 O A:TYR145 4.4 18.9 1.0 CB A:ALA206 4.5 15.5 1.0 HB3 A:TYR145 4.5 13.1 1.0 HB2 A:ALA206 4.7 18.6 1.0 CA A:TYR145 4.7 10.6 1.0 CB A:TYR145 4.7 10.9 1.0 O A:TYR143 4.7 13.7 1.0 C A:LEU207 4.7 9.6 1.0 N A:ALA206 4.8 11.4 1.0 C A:SER205 4.8 13.9 1.0 N A:ASN144 4.9 10.6 1.0 HD12 A:LEU207 5.0 16.2 1.0

Iodine binding site 5 out of 5 in the Engineered High-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 5 of Engineered High-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I268 b:38.8 occ:0.32 O A:HOH269 2.2 29.9 0.7 OD2 A:ASP180 2.5 19.5 0.5 HB2 A:LYS101 2.9 13.4 1.0 HA A:LYS101 3.1 11.2 1.0 HB2 A:ASP180 3.2 14.0 0.5 HB2 A:ASP180 3.4 15.9 0.5 O A:PHE99 3.5 9.9 1.0 HD23 A:LEU178 3.6 23.5 1.0 CG A:ASP180 3.6 15.7 0.5 CB A:LYS101 3.6 11.2 1.0 HB2 A:PHE99 3.6 11.2 1.0 HB3 A:PHE99 3.6 11.2 1.0 CA A:LYS101 3.7 9.3 1.0 H A:LYS101 3.7 11.4 1.0 N A:LYS101 3.7 9.5 1.0 HB3 A:ASP180 3.8 14.0 0.5 HG3 A:LYS101 3.8 16.7 1.0 H A:ASP180 3.9 13.1 0.5 CB A:ASP180 3.9 11.6 0.5 O A:HOH291 4.0 26.7 1.0 CB A:ASP180 4.0 13.2 0.5 HG A:LEU178 4.0 19.5 1.0 H A:ASP180 4.1 11.9 0.5 HD2 A:LYS101 4.1 22.3 1.0 CB A:PHE99 4.1 9.4 1.0 CG A:LYS101 4.2 13.9 1.0 C A:PHE99 4.3 8.0 1.0 CD2 A:LEU178 4.3 19.6 1.0 HD21 A:LEU178 4.3 23.5 1.0 C A:PHE100 4.4 10.2 1.0 HB3 A:LYS101 4.4 13.4 1.0 HB3 A:LEU178 4.6 14.7 1.0 N A:ASP180 4.6 10.9 0.5 CG A:LEU178 4.6 16.2 1.0 OD1 A:ASP180 4.6 22.1 0.5 OD2 A:ASP180 4.6 17.3 0.5 HB3 A:ASP180 4.7 15.9 0.5 CD A:LYS101 4.7 18.6 1.0 N A:ASP180 4.7 9.9 0.5 CG A:ASP180 4.9 16.1 0.5 HA A:PHE100 4.9 10.7 1.0 CA A:PHE99 4.9 7.7 1.0 O A:HOH320 4.9 21.3 1.0 O A:LEU178 4.9 9.6 1.0 O A:PHE100 4.9 11.0 1.0 CA A:ASP180 5.0 9.9 0.5 N A:PHE100 5.0 8.3 1.0 CA A:ASP180 5.0 10.3 0.5

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.