Iodine in PDB 5jsi: Structure of Membrane Protein

The structure of Structure of Membrane Protein, PDB code: 5jsi was solved by I.Melnikov, V.Polovinkin, K.Kovalev, V.Shevchenko, I.Gushchin, A.Popov, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.80 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.793, 56.771, 57.286, 63.61, 78.48, 80.21
R / Rfree (%)	17.7 / 22

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Iodine atom in the Structure of Membrane Protein (pdb code 5jsi). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 22 binding sites of Iodine where determined in the Structure of Membrane Protein, PDB code: 5jsi:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I313 b:63.6 occ:0.46 CD1 A:TRP59 3.7 47.8 1.0 OE1 A:GLU3 3.9 69.8 1.0 O A:GLU2 3.9 57.6 1.0 NE1 A:TRP59 3.9 49.7 1.0 CB A:TYR6 3.9 55.8 1.0 C A:GLU2 4.3 61.2 1.0 CG A:TYR6 4.4 57.0 1.0 CA A:GLU3 4.6 64.2 1.0 O A:TRP59 4.7 57.0 1.0 N A:GLU3 4.7 60.5 1.0 CB A:GLU2 4.7 62.5 1.0 CD A:GLU3 4.9 70.6 1.0 CA A:GLU60 4.9 69.4 1.0 CD2 A:TYR6 4.9 58.6 1.0 CG A:TRP59 4.9 47.0 1.0

Iodine binding site 2 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I314 b:0.3 occ:0.52 N A:ASP185 3.2 80.6 1.0 C A:PHE184 3.2 82.3 1.0 CA A:ASP185 3.5 72.5 1.0 CG A:PRO179 3.5 60.5 1.0 O A:PHE184 3.5 93.0 1.0 CD A:PRO179 3.6 63.1 1.0 CB A:PRO179 3.6 61.0 1.0 N A:PHE184 3.7 83.7 1.0 CA A:PHE184 3.8 81.4 1.0 CA A:PRO179 3.8 62.0 1.0 CB A:PHE184 3.9 78.7 1.0 N A:PRO179 4.0 60.7 1.0 CB A:ASP185 4.0 72.9 1.0 CZ A:ARG188 4.2 54.3 1.0 NE A:ARG188 4.4 53.5 1.0 NH2 A:ARG188 4.4 60.4 1.0 NH1 A:ARG188 4.6 57.0 1.0 O A:GLY182 4.6 76.8 1.0 C A:ASP185 4.8 69.3 1.0 CD A:ARG188 4.8 48.4 1.0 C A:ALA178 4.9 57.2 1.0 C A:ASP183 5.0 83.0 1.0 CB A:ARG188 5.0 41.8 1.0

Iodine binding site 3 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I315 b:40.2 occ:0.48 ND2 A:ASN123 3.1 71.8 1.0 OH A:TYR114 3.2 39.8 1.0 OG1 A:THR127 3.5 38.9 1.0 CB A:THR127 4.0 29.9 1.0 CG2 A:THR127 4.2 29.1 1.0 CZ A:TYR114 4.2 40.4 1.0 CG A:ASN123 4.3 69.4 1.0 CA A:GLU124 4.3 39.6 1.0 CE2 A:TYR114 4.3 37.5 1.0 O A:ASN123 4.4 39.0 1.0 N A:GLU124 4.5 41.2 1.0 C A:ASN123 4.5 40.7 1.0 CG A:GLU124 4.6 59.9 1.0 OE2 A:GLU124 4.8 71.8 1.0 CB A:ASN123 4.9 56.7 1.0 CD A:GLU124 4.9 61.9 1.0 CB A:GLU124 5.0 50.4 1.0

Iodine binding site 4 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I316 b:48.4 occ:0.28 OE2 A:GLU116 2.0 55.7 1.0 CD A:GLU116 2.9 59.1 1.0 NH1 A:ARG188 3.2 57.0 1.0 OE1 A:GLU116 3.2 60.8 1.0 OH A:TYR70 3.4 30.2 1.0 OH A:TYR192 3.6 35.5 1.0 CZ A:ARG188 3.7 54.3 1.0 CE2 A:TYR192 3.8 29.7 1.0 O A:HOH412 3.9 37.4 1.0 CD2 A:TYR176 4.0 23.0 1.0 CA A:TYR176 4.1 30.0 1.0 CZ A:TYR192 4.1 30.4 1.0 NE A:ARG188 4.2 53.5 1.0 CB A:TYR176 4.3 24.2 1.0 CG A:GLU116 4.3 52.0 1.0 CD A:ARG188 4.3 48.4 1.0 NH2 A:ARG188 4.4 60.4 1.0 CE1 A:TYR70 4.4 36.0 1.0 CZ A:TYR70 4.4 30.3 1.0 N A:TYR176 4.5 26.6 1.0 CG A:TYR176 4.6 24.5 1.0 C19 A:LYR200 4.7 24.1 1.0 O A:GLY175 4.8 28.8 1.0 C A:GLY175 4.8 29.3 1.0 CE2 A:TYR176 5.0 24.7 1.0 CD2 A:TYR192 5.0 30.1 1.0

Iodine binding site 5 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I317 b:94.8 occ:0.62 CG A:ARG89 3.7 51.7 1.0 CB A:ALA93 3.9 51.1 1.0 CA A:ARG89 4.2 48.7 1.0 N A:LYS90 4.2 48.5 1.0 O A:LYS90 4.3 45.0 1.0 CB A:ARG89 4.4 51.5 1.0 O A:THR88 4.5 51.3 1.0 C A:ARG89 4.8 45.7 1.0

Iodine binding site 6 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I318 b:68.0 occ:0.79 NE1 A:TRP101 3.6 44.7 1.0 CD1 A:TRP101 4.0 45.9 1.0 ND2 A:ASN100 4.0 45.3 1.0 CA A:ALA97 4.1 48.3 1.0 CB A:ASN100 4.2 38.5 1.0 NH1 A:ARG89 4.3 48.9 1.0 OE1 A:GLU96 4.5 74.5 1.0 CG A:ASN100 4.5 47.6 1.0 O A:GLU96 4.5 46.0 1.0 CB A:ALA97 4.6 52.0 1.0 N A:ALA97 4.6 51.5 1.0 CG A:GLU96 4.7 56.1 1.0 C A:GLU96 4.8 50.4 1.0 CE2 A:TRP101 4.9 42.7 1.0

Iodine binding site 7 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I319 b:0.7 occ:0.84 CD2 A:TYR39 4.0 43.2 1.0 C15 A:LFA308 4.0 39.5 1.0 CE2 A:TYR39 4.1 42.5 1.0 CA A:ARG36 4.1 38.0 1.0 CB A:ARG36 4.1 42.0 1.0 N A:ARG36 4.4 34.8 1.0 O A:HOH428 4.4 45.0 1.0 CG A:ARG36 4.5 49.5 1.0 OD1 B:ASN95 4.7 59.7 1.0 NE A:ARG36 4.7 66.7 1.0 O B:HOH422 4.9 60.8 1.0 O A:PRO32 4.9 49.6 1.0 C A:ARG35 5.0 35.5 1.0

Iodine binding site 8 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I320 b:33.2 occ:0.23 OD1 A:ASN160 3.0 26.8 1.0 ND2 A:ASN163 3.4 30.1 1.0 CB A:ASN163 4.1 25.5 1.0 CG A:ASN160 4.1 24.8 1.0 CA A:ASN160 4.1 22.9 1.0 O A:GLU159 4.2 23.6 1.0 C11 A:LFA307 4.2 44.0 1.0 CG A:ASN163 4.2 31.0 1.0 CG A:GLU159 4.4 31.0 1.0 N A:ASN160 4.4 20.8 1.0 C A:GLU159 4.4 22.8 1.0 CB A:ASN160 4.6 21.7 1.0 C13 A:LFA307 4.8 39.6 1.0

Iodine binding site 9 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I321 b:52.1 occ:0.57 NE A:ARG212 3.8 44.6 1.0 NH1 A:ARG212 3.9 59.0 1.0 CG A:GLN209 3.9 38.4 1.0 NE2 A:GLN209 3.9 43.2 1.0 CD2 A:LEU208 4.2 33.0 1.0 CZ A:ARG212 4.3 50.6 1.0 CZ A:PHE22 4.3 34.6 1.0 CG1 A:VAL205 4.4 30.8 1.0 CD A:GLN209 4.5 43.4 1.0 CG A:LEU208 4.5 31.2 1.0 CE2 A:PHE22 4.6 36.3 1.0 CD A:ARG212 4.8 43.2 1.0 O A:VAL205 4.8 24.4 1.0

Iodine binding site 10 out of 22 in the Structure of Membrane Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Membrane Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:I311 b:53.9 occ:0.46 O B:HOH438 2.6 45.1 1.0 OH B:TYR50 3.1 41.2 1.0 O A:HOH405 3.4 41.4 1.0 CD2 A:LEU68 3.5 43.0 1.0 ND1 A:HIS51 3.9 45.5 1.0 CE1 A:HIS51 3.9 34.9 1.0 CE2 B:TYR50 4.0 36.2 1.0 CZ B:TYR50 4.1 39.0 1.0 C19 A:LFA301 4.1 48.4 1.0 CE2 A:TYR50 4.3 42.6 1.0 C20 A:LFA301 4.4 48.4 1.0 CE B:LYS54 4.4 53.7 1.0 CD A:LYS54 4.5 53.2 1.0 CG A:LYS54 4.5 47.4 1.0 OH A:TYR50 4.7 46.4 1.0 CB A:LYS54 4.9 39.4 1.0 CZ A:TYR50 4.9 43.1 1.0

I.Melnikov, V.Polovinkin, K.Kovalev, I.Gushchin, M.Shevtsov, V.Shevchenko, A.Mishin, A.Alekseev, F.Rodriguez-Valera, V.Borshchevskiy, V.Cherezov, G.A.Leonard, V.Gordeliy, A.Popov. Fast Iodide-Sad Phasing For High-Throughput Membrane Protein Structure Determination. Sci Adv V. 3 02952 2017.
ISSN: ESSN 2375-2548
PubMed: 28508075
DOI: 10.1126/SCIADV.1602952