Iodine in PDB 3sv5: Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex

The structure of Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex, PDB code: 3sv5 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)	45.60 / 1.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.488, 63.025, 66.070, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 18.3

The binding sites of Iodine atom in the Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex (pdb code 3sv5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex, PDB code: 3sv5:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Engineered Medium-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 Medium-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I261 b:16.8 occ:0.21 C2 A:EDO260 0.9 20.9 0.8 C1 A:EDO260 1.1 20.6 0.8 H21 A:EDO260 1.4 25.0 0.8 O1 A:EDO260 1.5 20.5 0.8 O2 A:EDO260 1.5 20.1 0.8 H12 A:EDO260 2.0 24.7 0.8 H11 A:EDO260 2.0 24.7 0.8 H22 A:EDO260 2.0 25.0 0.8 HH A:TYR203 2.3 25.5 1.0 HO2 A:EDO260 2.3 24.1 0.8 HO1 A:EDO260 2.4 24.5 0.8 HG1 A:THR69 2.8 20.4 1.0 HE21 A:GLN183 2.9 16.4 1.0 OH A:TYR203 3.0 21.3 1.0 HH21 A:ARG96 3.3 12.6 1.0 HG21 A:THR69 3.4 17.1 1.0 OG1 A:THR69 3.5 17.0 1.0 HB2 A:CR266 3.6 16.5 1.0 HD12 A:LEU201 3.6 18.2 1.0 NE2 A:GLN183 3.7 13.7 1.0 HD11 A:ILE152 3.7 20.8 1.0 HH22 A:ARG96 3.7 12.6 1.0 OE1 A:GLN183 3.8 12.5 1.0 NH2 A:ARG96 3.8 10.5 1.0 HG11 A:VAL150 3.9 19.5 1.0 HO2 A:FMT263 3.9 22.5 0.7 O2 A:CR266 3.9 11.6 1.0 HE2 A:TYR203 4.0 18.6 1.0 HG23 A:THR69 4.0 17.1 1.0 CZ A:TYR203 4.1 18.0 1.0 CG2 A:THR69 4.1 14.2 1.0 HD13 A:LEU201 4.1 18.2 1.0 CD A:GLN183 4.2 12.1 1.0 HD2 A:CR266 4.2 14.7 1.0 CB2 A:CR266 4.2 13.8 1.0 CD1 A:LEU201 4.3 15.2 1.0 CB A:THR69 4.3 14.8 1.0 O2 A:FMT263 4.4 18.8 0.7 HZ A:PHE84 4.4 18.2 1.0 HE22 A:GLN183 4.4 16.4 1.0 CE2 A:TYR203 4.4 15.5 1.0 HD11 A:LEU201 4.5 18.2 1.0 HG21 A:VAL150 4.5 17.4 1.0 CD1 A:ILE152 4.6 17.4 1.0 HD12 A:ILE152 4.7 20.8 1.0 HB A:THR69 4.7 17.7 1.0 C2 A:CR266 4.7 10.2 1.0 HE2 A:PHE165 4.7 15.5 1.0 CG1 A:VAL150 4.8 16.3 1.0 CA2 A:CR266 4.8 10.2 1.0 HD13 A:ILE152 4.9 20.8 1.0 HE21 A:GLN94 4.9 15.1 1.0 CZ A:PHE84 4.9 15.2 1.0 HB A:VAL150 4.9 17.3 1.0 HG22 A:THR69 4.9 17.1 1.0 HE2 A:PHE84 5.0 18.6 1.0 CD2 A:CR266 5.0 12.3 1.0 HZ A:PHE165 5.0 16.6 1.0

Iodine binding site 2 out of 4 in the Engineered Medium-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 Medium-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I262 b:17.1 occ:0.51 O A:HOH268 2.4 7.8 0.5 HG1 A:THR108 2.6 15.5 1.0 HG2 A:GLN94 2.8 15.1 1.0 OG1 A:THR108 3.0 12.9 1.0 HE22 A:GLN94 3.2 15.1 1.0 HG3 A:ARG96 3.2 12.8 1.0 O A:GLN94 3.2 14.1 1.0 HB A:THR108 3.4 12.7 1.0 HB3 A:ALA110 3.5 15.2 1.0 HB3 A:GLN94 3.5 13.4 1.0 HB2 A:ALA110 3.5 15.2 1.0 O A:HOH275 3.6 11.2 1.0 CG A:GLN94 3.7 12.6 1.0 HA A:GLU95 3.8 12.5 1.0 CB A:THR108 3.8 10.6 1.0 C A:GLN94 3.8 11.6 1.0 NE2 A:GLN94 3.9 12.7 1.0 HG23 A:THR63 3.9 12.7 1.0 H A:ALA110 3.9 12.6 1.0 CB A:ALA110 3.9 12.8 1.0 HH11 A:ARG96 4.0 14.4 1.0 CB A:GLN94 4.0 11.2 1.0 H A:ARG96 4.0 11.6 1.0 CG A:ARG96 4.2 10.7 1.0 N A:ALA110 4.2 10.6 1.0 HB2 A:ARG96 4.2 13.2 1.0 HA A:THR63 4.3 9.4 1.0 HA A:ARG109 4.3 13.9 1.0 N A:ARG96 4.3 9.7 1.0 O A:HOH271 4.3 16.3 1.0 CD A:GLN94 4.3 13.7 1.0 C A:THR108 4.3 12.4 1.0 CA A:GLU95 4.3 10.5 1.0 N A:GLU95 4.3 10.5 1.0 HG3 A:GLN94 4.3 15.1 1.0 NH1 A:ARG96 4.4 12.0 1.0 O A:THR108 4.4 12.3 1.0 C A:GLU95 4.4 9.6 1.0 HG23 A:ILE123 4.5 18.2 1.0 HH12 A:ARG96 4.5 14.4 1.0 CA A:GLN94 4.6 10.8 1.0 HE21 A:GLN94 4.6 15.1 1.0 N A:ARG109 4.6 11.6 1.0 C A:ARG109 4.6 12.1 1.0 HG2 A:ARG96 4.7 12.8 1.0 CB A:ARG96 4.7 11.0 1.0 HB1 A:ALA110 4.7 15.2 1.0 HG21 A:THR108 4.7 15.4 1.0 CA A:THR108 4.7 9.3 1.0 CA A:ARG109 4.7 11.6 1.0 CA A:ALA110 4.7 9.7 1.0 HD2 A:ARG96 4.8 13.3 1.0 CG2 A:THR63 4.9 10.6 1.0 HB2 A:GLN94 4.9 13.4 1.0 CG2 A:THR108 4.9 12.9 1.0 HG12 A:ILE123 5.0 14.0 1.0 H A:GLU95 5.0 12.5 1.0

Iodine binding site 3 out of 4 in the Engineered Medium-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 Medium-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I264 b:17.8 occ:0.87 H A:TRP57 2.9 9.6 1.0 HA A:PRO56 3.2 13.1 1.0 HD1 A:TYR143 3.4 12.1 1.0 HD3 A:PRO58 3.5 9.4 1.0 O A:HOH331 3.5 23.4 1.0 HB3 A:PRO56 3.5 16.4 1.0 HB2 A:TRP57 3.6 12.6 1.0 N A:TRP57 3.6 8.0 1.0 O A:HOH452 3.6 22.4 1.0 HD2 A:HIS139 3.7 29.5 1.0 HD2 A:PRO58 3.7 9.4 1.0 O A:HOH437 3.8 37.5 1.0 CA A:PRO56 3.9 11.0 1.0 O A:HOH308 4.0 16.7 1.0 CD A:PRO58 4.0 7.9 1.0 CD1 A:TRP57 4.1 10.5 1.0 CB A:PRO56 4.2 13.7 1.0 CD1 A:TYR143 4.2 10.1 1.0 O A:HOH295 4.2 36.5 1.0 C A:PRO56 4.3 9.9 1.0 CB A:TRP57 4.4 10.6 1.0 HB2 A:TYR143 4.4 13.2 1.0 HE1 A:TYR143 4.6 15.2 1.0 CA A:TRP57 4.6 8.5 1.0 CD2 A:HIS139 4.6 24.6 1.0 CG A:TRP57 4.6 9.7 1.0 HB2 A:PRO56 4.7 16.4 1.0 CE1 A:TYR143 4.8 12.7 1.0 HZ1 A:LYS209 4.9 17.1 1.0 HG2 A:PRO58 4.9 14.4 1.0

Iodine binding site 4 out of 4 in the Engineered Medium-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 Medium-Affinity Halide-Binding Protein Derived From Yfp: Iodide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I265 b:69.4 occ:1.00 H A:VAL176 2.8 21.4 1.0 HG22 A:VAL176 3.1 31.9 1.0 HB2 A:SER175 3.2 22.8 1.0 HA A:SER175 3.4 23.4 1.0 N A:VAL176 3.6 17.9 1.0 CB A:SER175 4.0 19.1 1.0 CA A:SER175 4.0 19.6 1.0 CG2 A:VAL176 4.1 26.6 1.0 O A:VAL176 4.2 19.1 1.0 HG23 A:VAL176 4.3 31.9 1.0 O A:HOH453 4.3 40.4 1.0 C A:SER175 4.3 21.8 1.0 HB3 A:SER175 4.3 22.8 1.0 HG13 A:VAL176 4.6 30.7 1.0 CA A:VAL176 4.6 20.2 1.0 HG21 A:VAL176 4.6 31.9 1.0 CB A:VAL176 4.8 24.0 1.0 C A:VAL176 4.8 19.6 1.0

J.S.Grimley, L.Li, W.Wang, L.Wen, L.S.Beese, H.W.Hellinga, G.J.Augustine. Visualization of Synaptic Inhibition with An Optogenetic Sensor Developed By Cell-Free Protein Engineering Automation. J.Neurosci. V. 33 16297 2013.
ISSN: ISSN 0270-6474
PubMed: 24107961
DOI: 10.1523/JNEUROSCI.4616-11.2013