Iodine in PDB 2d8o: Structure of Vil-Thaumatin

The structure of Structure of Vil-Thaumatin, PDB code: 2d8o was solved by H.Miyatake, T.Hasegawa, A.Yamano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.41 / 2.38
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.144, 57.144, 151.905, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 26.2

The binding sites of Iodine atom in the Structure of Vil-Thaumatin (pdb code 2d8o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Structure of Vil-Thaumatin, PDB code: 2d8o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Structure of Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I57 b:23.9 occ:0.88 IE A:IYR57 0.0 23.9 0.9 CE A:IYR57 2.1 20.4 1.0 CD A:IYR57 3.0 17.9 1.0 CF A:IYR57 3.0 21.9 1.0 OF A:IYR57 3.2 23.6 1.0 CG A:IYR57 4.3 21.6 1.0 CC A:IYR57 4.3 19.6 1.0 CH A:IYR57 4.9 20.0 1.0 O A:CYS56 5.0 21.4 1.0

Iodine binding site 2 out of 7 in the Structure of Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I95 b:31.5 occ:0.59 I1 A:TYI95 0.0 31.5 0.6 CE1 A:TYI95 2.1 29.1 1.0 CZ A:TYI95 3.0 28.3 1.0 CD1 A:TYI95 3.0 28.2 1.0 OH A:TYI95 3.2 28.7 1.0 OE1 A:GLN94 3.9 31.4 1.0 CE2 A:TYI95 4.3 26.4 1.0 CG A:TYI95 4.4 27.5 1.0 CB A:GLN94 4.6 28.1 1.0 CD2 A:TYI95 4.9 25.4 1.0 CD A:GLN94 4.9 30.0 1.0

Iodine binding site 3 out of 7 in the Structure of Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I95 b:25.7 occ:0.81 I2 A:TYI95 0.0 25.7 0.8 CE2 A:TYI95 2.1 26.4 1.0 CZ A:TYI95 3.0 28.3 1.0 CD2 A:TYI95 3.0 25.4 1.0 OH A:TYI95 3.1 28.7 1.0 CE1 A:TYI95 4.3 29.1 1.0 CG A:TYI95 4.4 27.5 1.0 CD1 A:TYI95 4.8 28.2 1.0

Iodine binding site 4 out of 7 in the Structure of Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I169 b:17.6 occ:0.22 IE A:IYR169 0.0 17.6 0.2 CE A:IYR169 2.1 16.7 1.0 CF A:IYR169 3.0 18.4 1.0 CD A:IYR169 3.1 17.6 1.0 OF A:IYR169 3.1 20.2 1.0 CB A:PRO135 3.4 26.1 1.0 CB A:LYS137 3.9 28.6 1.0 CG A:PRO135 4.3 26.4 1.0 CG A:IYR169 4.3 17.7 1.0 CC A:IYR169 4.4 18.6 1.0 CG A:LEU138 4.4 18.9 1.0 N A:LYS137 4.4 28.3 1.0 CG A:LYS137 4.4 28.8 1.0 CA A:LYS137 4.6 28.3 1.0 CA A:PRO135 4.6 26.1 1.0 CD A:LYS137 4.7 31.1 1.0 CH A:IYR169 4.9 17.8 1.0 C A:PRO135 4.9 27.1 1.0 N A:LEU138 4.9 25.4 1.0 CD2 A:LEU138 4.9 17.1 1.0 CD1 A:LEU138 5.0 17.6 1.0

Iodine binding site 5 out of 7 in the Structure of Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:32.1 occ:0.73 O A:GLY96 3.7 31.4 1.0 CA A:GLY195 3.8 24.6 1.0 OD1 A:ASN93 3.9 27.2 1.0 CA A:GLY96 3.9 29.7 1.0 C A:GLY96 4.0 31.5 1.0 C A:GLY195 4.4 24.3 1.0 N A:GLY195 4.6 24.8 1.0 O A:GLY195 4.8 24.5 1.0 CG A:ASN93 4.8 26.2 1.0 N A:SER196 4.9 23.6 1.0 N A:GLY96 4.9 27.0 1.0 CB A:ASN93 5.0 24.5 1.0 N A:LYS97 5.0 31.5 1.0

Iodine binding site 6 out of 7 in the Structure of Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:49.2 occ:0.55 NH2 A:ARG125 3.6 37.9 1.0 NH1 A:ARG8 3.6 28.7 1.0 CG A:ASN113 4.0 19.8 1.0 CB A:PRO205 4.0 24.4 1.0 ND2 A:ASN113 4.2 18.6 1.0 CB A:ASN113 4.2 19.0 1.0 OD1 A:ASN113 4.3 18.8 1.0 CZ A:ARG125 4.3 37.0 1.0 OG1 A:THR202 4.5 17.6 1.0 CZ A:ARG8 4.5 30.7 1.0 NH2 A:ARG8 4.6 30.7 1.0 O A:HOH312 4.6 24.9 1.0 CA A:PRO205 4.6 25.4 1.0 O A:PRO205 4.7 28.3 1.0 NH1 A:ARG125 4.7 40.1 1.0 CB A:THR202 4.7 19.2 1.0 CG2 A:THR202 4.9 18.1 1.0 C A:PRO205 5.0 27.5 1.0

Iodine binding site 7 out of 7 in the Structure of Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:30.3 occ:0.33 N A:GLN30 3.4 24.5 1.0 CD2 A:LEU75 3.8 25.2 1.0 CB A:GLN30 3.9 21.2 1.0 CG A:ARG29 4.0 27.6 1.0 CA A:ARG29 4.2 25.4 1.0 CA A:GLN30 4.2 23.1 1.0 C A:ARG29 4.2 24.9 1.0 CD1 A:LEU75 4.5 25.5 1.0 CB A:ARG29 4.7 25.5 1.0 CG A:LEU75 4.7 25.5 1.0

H.Miyatake, T.Hasegawa, A.Yamano. New Methods to Prepare Iodinated Derivatives By Vaporizing Iodine Labelling (Vil) and Hydrogen Peroxide Vil (Hyper-Vil) Acta Crystallogr.,Sect.D V. 62 280 2006.
ISSN: ISSN 0907-4449
PubMed: 16510975
DOI: 10.1107/S0907444905041909