Iodine in PDB 2d97: Structure of Vil-Xylanase

All present enzymatic activity of Structure of Vil-Xylanase:
3.2.1.8;

The structure of Structure of Vil-Xylanase, PDB code: 2d97 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)	18.98 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.347, 38.585, 57.162, 90.00, 110.31, 90.00
R / Rfree (%)	19.8 / 22.8

The binding sites of Iodine atom in the Structure of Vil-Xylanase (pdb code 2d97). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Structure of Vil-Xylanase, PDB code: 2d97:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Structure of Vil-Xylanase


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-Xylanase within 5.0Å range: probe atom residue distance (Å) B Occ A:I9 b:34.1 occ:0.24 IE A:IYR9 0.0 34.1 0.2 CE A:IYR9 2.1 22.6 1.0 CD A:IYR9 3.0 20.1 1.0 CF A:IYR9 3.1 22.0 1.0 OF A:IYR9 3.3 20.2 1.0 CC A:IYR9 4.3 19.2 1.0 CG A:IYR9 4.4 19.8 1.0 CH A:IYR9 4.8 18.6 1.0

Iodine binding site 2 out of 5 in the Structure of Vil-Xylanase


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-Xylanase within 5.0Å range: probe atom residue distance (Å) B Occ A:I73 b:38.8 occ:0.29 IE A:IYR73 0.0 38.8 0.3 CE A:IYR73 2.1 29.7 1.0 CF A:IYR73 3.0 30.1 1.0 CD A:IYR73 3.1 27.2 1.0 OF A:IYR73 3.2 32.6 1.0 CE2 A:TYR88 3.5 23.1 1.0 CD2 A:TYR88 3.5 22.5 1.0 OG A:SER75 3.6 23.6 1.0 CB A:GLU177 3.8 16.0 1.0 CG1 A:VAL46 4.2 18.5 1.0 CG A:TYR77 4.2 16.5 1.0 CB A:TYR77 4.2 12.1 1.0 CD1 A:TYR77 4.3 18.1 1.0 CG A:IYR73 4.4 27.0 1.0 CC A:IYR73 4.4 23.2 1.0 CG A:GLU177 4.6 16.7 1.0 CG2 A:VAL46 4.7 18.2 1.0 O A:ALA175 4.7 12.6 1.0 CB A:ALA175 4.7 14.7 1.0 CD2 A:TYR77 4.8 14.5 1.0 CZ A:TYR88 4.8 23.6 1.0 N A:GLU177 4.8 12.7 1.0 CH A:IYR73 4.9 23.6 1.0 CA A:GLU177 4.9 15.9 1.0 CG A:TYR88 4.9 20.3 1.0 CE1 A:TYR77 4.9 20.6 1.0 CB A:SER75 4.9 19.5 1.0 O A:IYR73 5.0 14.9 1.0

Iodine binding site 3 out of 5 in the Structure of Vil-Xylanase


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-Xylanase within 5.0Å range: probe atom residue distance (Å) B Occ A:I135 b:42.3 occ:0.75 I1 A:TYI135 0.0 42.3 0.8 CE1 A:TYI135 2.1 38.2 1.0 CZ A:TYI135 3.0 39.6 1.0 CD1 A:TYI135 3.0 34.4 1.0 OH A:TYI135 3.2 40.4 1.0 O A:HOH277 3.3 45.9 1.0 NE A:ARG119 3.6 39.7 1.0 CD A:ARG119 3.8 35.1 1.0 CG A:ARG119 3.9 31.9 1.0 N A:GLN121 4.2 23.2 1.0 CB A:GLN121 4.2 24.9 1.0 CE2 A:TYI135 4.3 39.8 1.0 CZ A:ARG119 4.3 41.9 1.0 C A:THR120 4.3 22.6 1.0 CG A:TYI135 4.3 31.9 1.0 CA A:THR120 4.5 22.4 1.0 CA A:GLN121 4.7 22.6 1.0 N A:THR120 4.8 21.7 1.0 NH1 A:ARG119 4.8 43.6 1.0 O A:THR120 4.8 21.3 1.0 CD2 A:TYI135 4.8 36.5 1.0 C A:ARG119 5.0 23.1 1.0

Iodine binding site 4 out of 5 in the Structure of Vil-Xylanase


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-Xylanase within 5.0Å range: probe atom residue distance (Å) B Occ A:I135 b:48.3 occ:0.35 I2 A:TYI135 0.0 48.3 0.3 CE2 A:TYI135 2.1 39.8 1.0 CD2 A:TYI135 3.0 36.5 1.0 CZ A:TYI135 3.0 39.6 1.0 OH A:TYI135 3.2 40.4 1.0 CG A:TYI135 4.3 31.9 1.0 CE1 A:TYI135 4.3 38.2 1.0 NE2 A:GLN121 4.8 30.2 1.0 CD1 A:TYI135 4.9 34.4 1.0

Iodine binding site 5 out of 5 in the Structure of Vil-Xylanase


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-Xylanase within 5.0Å range: probe atom residue distance (Å) B Occ A:I179 b:40.2 occ:0.52 IE A:IYR179 0.0 40.2 0.5 CE A:IYR179 2.1 32.2 1.0 CF A:IYR179 3.0 32.3 1.0 CD A:IYR179 3.0 28.9 1.0 OF A:IYR179 3.1 34.7 1.0 O A:HOH233 3.6 30.9 1.0 OD1 A:ASN44 4.0 19.3 1.0 CB A:ASN44 4.0 15.2 1.0 CG A:ASN44 4.2 18.6 1.0 CG A:IYR179 4.3 30.1 1.0 CE1 A:PHE180 4.3 16.8 1.0 CC A:IYR179 4.4 27.0 1.0 CH A:IYR179 4.8 26.8 1.0 CD1 A:PHE180 4.9 14.8 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