Iodine in PDB 2dfb: Xylanase II From Tricoderma Reesei at 100K

All present enzymatic activity of Xylanase II From Tricoderma Reesei at 100K:
3.2.1.8;

The structure of Xylanase II From Tricoderma Reesei at 100K, PDB code: 2dfb was solved by K.Harata, T.Akiba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 1.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.970, 58.510, 69.800, 90.00, 90.00, 90.00
R / Rfree (%)	10.8 / 12.1

The binding sites of Iodine atom in the Xylanase II From Tricoderma Reesei at 100K (pdb code 2dfb). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Xylanase II From Tricoderma Reesei at 100K, PDB code: 2dfb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:I192 b:10.9 occ:1.00 O A:HOH206 3.5 13.6 1.0 O A:HOH202 3.5 11.7 1.0 N A:SER146 3.6 10.8 1.0 OG A:SER146 3.9 13.8 1.0 CB A:ARG145 4.1 10.3 1.0 CA A:ARG145 4.1 10.6 1.0 O A:HOH232 4.2 17.6 1.0 N A:SER147 4.3 11.0 1.0 C A:ARG145 4.4 10.5 1.0 CA A:SER146 4.5 11.4 1.0 C A:SER146 4.7 11.1 1.0 CB A:SER146 4.8 12.4 1.0

Iodine binding site 2 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:I193 b:17.4 occ:0.58 NE A:ARG119 3.5 23.6 1.0 O A:HOH475 3.5 34.2 0.5 NH2 A:ARG119 3.7 43.2 1.0 O A:ARG119 3.9 12.8 1.0 C A:THR120 3.9 11.5 1.0 CZ A:ARG119 3.9 30.6 1.0 O A:HOH427 4.0 35.4 1.0 CA A:THR120 4.0 11.9 1.0 CE1 A:TYR135 4.1 15.9 1.0 N A:GLN121 4.1 13.3 1.0 O A:HOH224 4.2 16.1 1.0 C A:ARG119 4.2 11.6 1.0 CB A:GLN121 4.3 14.4 1.0 CG A:ARG119 4.3 13.2 1.0 CD1 A:TYR135 4.3 14.2 1.0 N A:THR120 4.3 11.5 1.0 O A:THR120 4.3 12.6 1.0 O A:HOH405 4.4 41.8 1.0 CD A:ARG119 4.4 16.1 1.0 O A:HOH271 4.4 19.5 1.0 CB A:ARG119 4.6 12.7 1.0 CA A:GLN121 4.8 12.8 1.0 O A:HOH276 4.9 18.8 1.0

Iodine binding site 3 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:I194 b:14.0 occ:0.27 O A:PRO68 3.4 15.0 1.0 N A:GLY70 3.7 11.8 1.0 CA A:GLY94 3.9 11.3 1.0 CG2 A:THR95 4.0 12.3 1.0 C A:GLY94 4.0 11.0 1.0 C A:PRO68 4.1 12.2 1.0 N A:THR95 4.1 11.1 1.0 CA A:ASN69 4.1 12.4 1.0 O A:GLY70 4.2 11.1 1.0 N A:ASN69 4.4 11.9 1.0 C A:ASN69 4.5 11.4 1.0 CG A:PRO68 4.5 14.1 1.0 O A:HOH435 4.5 45.6 1.0 O A:HOH363 4.6 29.7 1.0 CA A:GLY70 4.6 11.9 1.0 O A:GLY94 4.7 12.2 1.0 CB A:PRO68 4.8 13.5 1.0 CA A:THR95 4.8 11.2 1.0 C A:GLY70 4.8 10.8 1.0 CB A:THR95 5.0 11.5 1.0

Iodine binding site 4 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:I195 b:16.1 occ:0.22 OG A:SER65 3.1 19.8 0.3 OG A:SER184 3.3 17.1 1.0 N A:ALA185 3.8 11.1 1.0 CA A:ALA185 3.9 11.1 1.0 CB A:SER65 3.9 15.7 1.0 CB A:SER184 3.9 13.7 1.0 ND2 A:ASN67 3.9 18.6 1.0 C A:SER184 3.9 11.6 1.0 C A:ALA185 4.0 10.8 1.0 O A:SER184 4.1 12.8 1.0 N A:SER186 4.2 11.0 1.0 O A:HOH313 4.3 25.8 1.0 O A:SER65 4.4 11.7 1.0 CB A:SER186 4.5 14.1 1.0 CA A:SER184 4.6 12.3 1.0 O A:ALA185 4.6 11.8 1.0 C A:SER65 4.6 11.2 1.0 OG A:SER65 4.8 16.9 0.7 CA A:SER65 4.9 11.9 1.0 CG A:ASN67 5.0 14.5 1.0 CA A:SER186 5.0 11.6 1.0

Iodine binding site 5 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:I196 b:21.4 occ:0.33 NE2 A:GLN125 3.5 26.8 1.0 N A:VAL123 3.5 14.9 1.0 O A:HOH395 3.8 35.4 0.9 NH1 A:ARG122 4.0 20.5 1.0 CA A:ARG122 4.1 12.8 1.0 O A:HOH463 4.2 37.4 1.0 O A:GLN121 4.3 17.2 1.0 CG A:GLN125 4.3 16.1 1.0 O A:VAL123 4.3 16.3 1.0 C A:ARG122 4.3 13.2 1.0 CB A:VAL123 4.3 17.1 1.0 CD A:GLN125 4.4 18.9 1.0 CA A:VAL123 4.4 15.2 1.0 O A:HOH418 4.4 38.1 0.7 CD A:ARG122 4.6 16.2 1.0 O A:HOH383 4.7 46.1 1.0 CG2 A:VAL123 4.7 20.6 1.0 CZ A:ARG122 4.8 18.2 1.0 C A:VAL123 4.8 15.2 1.0 CB A:ARG122 4.9 13.1 1.0

Iodine binding site 6 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:I197 b:23.2 occ:0.26 OE1 A:GLN34 2.0 18.6 0.7 NE2 A:GLN34 2.7 30.5 0.3 CD A:GLN34 2.8 16.0 0.7 NE2 A:GLN34 2.9 29.1 0.7 OG A:SER36 3.1 17.1 0.6 OG A:SER36 3.5 14.7 0.4 CD A:GLN34 3.6 20.6 0.3 CA A:GLY30 3.6 13.2 1.0 CG A:GLN34 3.7 14.6 0.3 N A:GLY30 3.8 12.6 1.0 O A:THR28 3.8 15.9 1.0 N A:SER36 3.9 11.6 1.0 CB A:SER36 3.9 14.6 1.0 C A:PHE35 4.1 10.7 1.0 C A:ASN29 4.2 12.8 1.0 CG A:GLN34 4.2 14.1 0.7 CA A:PHE35 4.2 11.3 1.0 CG2 A:THR28 4.4 16.0 1.0 O A:ASN29 4.4 17.0 1.0 CA A:SER36 4.5 11.6 1.0 C A:THR28 4.6 12.4 1.0 N A:PHE35 4.6 11.5 1.0 O A:PHE35 4.6 11.9 1.0 CB A:THR28 4.6 13.2 1.0 OE1 A:GLN34 4.7 33.6 0.3 C A:GLN34 4.8 10.8 1.0 O A:GLN34 4.8 11.5 1.0 CB A:GLN34 4.8 15.3 0.7 CB A:GLN34 4.9 11.9 0.3 C A:GLY30 5.0 13.5 1.0 CD A:PRO31 5.0 19.0 1.0

N.Watanabe, T.Akiba, R.Kanai, K.Harata. Structure of An Orthorhombic Form of Xylanase II From Trichoderma Reesei and Analysis of Thermal Displacement. Acta Crystallogr.,Sect.D V. 62 784 2006.
ISSN: ISSN 0907-4449
PubMed: 16790934
DOI: 10.1107/S0907444906017379