Iodine in PDB 2d8p: Structure of Hyper-Vil-Thaumatin

The structure of Structure of Hyper-Vil-Thaumatin, PDB code: 2d8p 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)	31.70 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.727, 57.727, 150.955, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Structure of Hyper-Vil-Thaumatin (pdb code 2d8p). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Structure of Hyper-Vil-Thaumatin, PDB code: 2d8p:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in the Structure of Hyper-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 Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I11 b:32.4 occ:0.82 I1 A:TYI11 0.0 32.4 0.8 CE1 A:TYI11 2.1 34.1 1.0 CZ A:TYI11 3.0 33.8 1.0 CD1 A:TYI11 3.0 31.9 1.0 OH A:TYI11 3.2 34.4 1.0 CG2 A:VAL110 3.8 19.1 1.0 CG1 A:VAL13 4.0 15.2 1.0 CG2 A:THR54 4.1 18.6 1.0 SG A:CYS9 4.1 23.4 1.0 CE2 A:TYI11 4.3 35.8 1.0 CG1 A:VAL110 4.3 19.2 1.0 CB A:CYS9 4.3 19.6 1.0 CG A:TYI11 4.3 31.3 1.0 CB A:VAL110 4.7 19.2 1.0 SG A:CYS204 4.7 22.0 1.0 CD2 A:TYI11 4.8 32.8 1.0

Iodine binding site 2 out of 14 in the Structure of Hyper-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 Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I11 b:38.2 occ:0.79 I2 A:TYI11 0.0 38.2 0.8 CE2 A:TYI11 2.1 35.8 1.0 CZ A:TYI11 3.0 33.8 1.0 CD2 A:TYI11 3.0 32.8 1.0 OH A:TYI11 3.2 34.4 1.0 OG A:SER10 3.5 24.2 1.0 CE1 A:TYI11 4.3 34.1 1.0 CG A:TYI11 4.3 31.3 1.0 CD1 A:TYI11 4.8 31.9 1.0 CB A:SER10 4.9 23.3 1.0

Iodine binding site 3 out of 14 in the Structure of Hyper-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 Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I57 b:32.2 occ:1.00 I1 A:TYI57 0.0 32.2 1.0 CE1 A:TYI57 2.1 29.9 1.0 CZ A:TYI57 2.9 28.5 1.0 OH A:TYI57 3.0 27.8 1.0 CD1 A:TYI57 3.1 27.9 1.0 CE2 A:TYI57 4.2 29.9 1.0 CG A:TYI57 4.4 27.5 1.0 CD2 A:TYI57 4.8 27.8 1.0

Iodine binding site 4 out of 14 in the Structure of Hyper-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 Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I57 b:32.5 occ:0.81 I2 A:TYI57 0.0 32.5 0.8 CE2 A:TYI57 2.1 29.9 1.0 CZ A:TYI57 2.9 28.5 1.0 CD2 A:TYI57 3.1 27.8 1.0 OH A:TYI57 3.1 27.8 1.0 CB A:ASP55 3.4 25.6 1.0 O A:ASP55 3.7 22.4 1.0 C A:ASP55 3.9 23.0 1.0 CA A:ASP55 3.9 23.1 1.0 CG A:ASP55 3.9 26.6 1.0 CE1 A:TYI57 4.2 29.9 1.0 OD2 A:ASP55 4.3 29.6 1.0 CE A:LYS67 4.3 22.3 1.0 CG A:TYI57 4.4 27.5 1.0 OD1 A:ASP55 4.5 29.1 1.0 N A:CYS56 4.7 22.1 1.0 CD A:LYS67 4.8 23.2 1.0 CD1 A:TYI57 4.8 27.9 1.0 NZ A:LYS67 4.9 23.3 1.0 CG A:LYS67 4.9 22.4 1.0 O A:CYS56 5.0 20.9 1.0

Iodine binding site 5 out of 14 in the Structure of Hyper-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 Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I95 b:41.3 occ:0.72 I1 A:TYI95 0.0 41.3 0.7 CE1 A:TYI95 2.1 40.1 1.0 CD1 A:TYI95 3.0 38.7 1.0 CZ A:TYI95 3.1 39.8 1.0 OH A:TYI95 3.2 40.4 1.0 I2 A:TYI99 4.2 44.7 0.7 OE1 A:GLN94 4.3 35.4 1.0 CG A:TYI95 4.4 37.9 1.0 CE2 A:TYI95 4.4 39.9 1.0 CB A:GLN94 4.5 30.9 1.0 CD2 A:TYI95 4.9 38.8 1.0

Iodine binding site 6 out of 14 in the Structure of Hyper-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 Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I95 b:41.1 occ:0.99 I2 A:TYI95 0.0 41.1 1.0 CE2 A:TYI95 2.1 39.9 1.0 CD2 A:TYI95 3.0 38.8 1.0 CZ A:TYI95 3.0 39.8 1.0 OH A:TYI95 3.2 40.4 1.0 CE1 A:TYI95 4.3 40.1 1.0 CG A:TYI95 4.3 37.9 1.0 CD1 A:TYI95 4.8 38.7 1.0

Iodine binding site 7 out of 14 in the Structure of Hyper-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 Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I99 b:41.5 occ:0.71 I1 A:TYI99 0.0 41.5 0.7 CE1 A:TYI99 2.1 44.7 1.0 CD1 A:TYI99 3.1 42.7 1.0 CZ A:TYI99 3.1 44.6 1.0 OH A:TYI99 3.3 46.5 1.0 OD1 A:ASP101 3.6 24.1 1.0 OG A:SER91 3.8 27.8 1.0 CA A:PHE90 3.9 23.9 1.0 N A:PHE90 3.9 23.5 1.0 C A:PHE90 3.9 24.4 1.0 N A:SER91 4.1 25.6 1.0 C A:GLU89 4.3 23.2 1.0 O A:PHE90 4.3 24.9 1.0 O A:HOH310 4.3 25.6 1.0 CG A:TYI99 4.4 41.3 1.0 CE2 A:TYI99 4.4 45.1 1.0 CB A:GLU89 4.4 21.1 1.0 CB A:SER91 4.4 26.0 1.0 O A:TYI99 4.5 33.4 1.0 O A:GLU89 4.6 25.2 1.0 CG A:ASP101 4.8 23.6 1.0 CD2 A:TYI99 4.9 43.4 1.0 CA A:SER91 4.9 25.8 1.0

Iodine binding site 8 out of 14 in the Structure of Hyper-Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I99 b:44.7 occ:0.67 I2 A:TYI99 0.0 44.7 0.7 CE2 A:TYI99 2.1 45.1 1.0 CD2 A:TYI99 3.0 43.4 1.0 CZ A:TYI99 3.1 44.6 1.0 OH A:TYI99 3.2 46.5 1.0 CG A:GLN94 3.7 31.3 1.0 CB A:GLN94 3.9 30.9 1.0 I1 A:TYI95 4.2 41.3 0.7 CB A:SER91 4.2 26.0 1.0 CG A:TYI99 4.3 41.3 1.0 CE1 A:TYI99 4.4 44.7 1.0 OE1 A:GLN94 4.5 35.4 1.0 OG A:SER91 4.5 27.8 1.0 CD A:GLN94 4.6 32.6 1.0 ND2 A:ASN46 4.7 40.8 1.0 CD1 A:TYI99 4.9 42.7 1.0

Iodine binding site 9 out of 14 in the Structure of Hyper-Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I169 b:27.3 occ:0.97 IE A:IYR169 0.0 27.3 1.0 CE A:IYR169 2.1 17.9 1.0 CF A:IYR169 3.0 18.3 1.0 CD A:IYR169 3.0 17.3 1.0 OF A:IYR169 3.2 15.9 1.0 CB A:PRO135 3.7 18.0 1.0 I A:IOD306 3.9 44.5 0.6 CB A:LYS137 4.0 23.4 1.0 CG A:IYR169 4.4 16.4 1.0 CC A:IYR169 4.4 17.6 1.0 CD A:LYS137 4.4 29.6 1.0 CG A:PRO135 4.4 19.7 1.0 CG A:LEU138 4.5 16.8 1.0 CG A:LYS137 4.7 26.5 1.0 N A:LYS137 4.7 19.6 1.0 CA A:LYS137 4.9 20.1 1.0 CH A:IYR169 4.9 15.7 1.0 CD1 A:LEU138 5.0 15.3 1.0

Iodine binding site 10 out of 14 in the Structure of Hyper-Vil-Thaumatin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Hyper-Vil-Thaumatin within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:48.9 occ:0.30 OD1 A:ASN93 3.5 28.7 1.0 O A:HOH326 3.8 24.1 1.0 CA A:GLY195 4.0 27.6 1.0 O A:GLY96 4.0 36.7 1.0 CA A:GLY96 4.1 34.8 1.0 C A:GLY96 4.2 36.3 1.0 CB A:ASN93 4.2 28.3 1.0 CG A:ASN93 4.2 27.6 1.0 CA A:ASN93 4.3 28.6 1.0 C A:GLY195 4.4 27.7 1.0 OG A:SER196 4.4 28.5 1.0 N A:GLY96 4.7 34.0 1.0 N A:SER196 4.7 28.0 1.0 O A:GLY195 4.9 28.4 1.0 N A:LYS97 5.0 36.9 1.0 N A:GLY195 5.0 28.8 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