Iodine in PDB 6k9w: Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose

All present enzymatic activity of Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose:
3.2.1.8;

The structure of Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose, PDB code: 6k9w was solved by C.Li, Q.Wan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.13 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.192, 59.526, 69.856, 90, 90, 90
R / Rfree (%)	13.6 / 14.4

The binding sites of Iodine atom in the Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose (pdb code 6k9w). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose, PDB code: 6k9w:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:7.7 occ:1.00 H A:SER146 2.8 8.5 1.0 HB2 A:ARG145 3.4 8.4 1.0 HG A:SER146 3.4 10.3 0.8 HA A:ARG145 3.5 8.3 1.0 O A:HOH411 3.5 10.2 1.0 O A:HOH351 3.6 8.0 1.0 N A:SER146 3.6 7.0 1.0 H A:SER147 3.7 9.0 1.0 OG A:SER146 3.8 8.6 0.8 O A:HOH317 3.9 13.9 1.0 HB2 A:SER146 4.0 10.7 0.2 CB A:ARG145 4.1 7.0 1.0 CA A:ARG145 4.1 6.9 1.0 HB2 A:SER147 4.2 9.7 1.0 HB3 A:ARG145 4.3 8.4 1.0 N A:SER147 4.3 7.5 1.0 C A:ARG145 4.4 6.6 1.0 O A:HOH601 4.5 13.0 1.0 CA A:SER146 4.5 7.6 1.0 HG A:SER147 4.6 9.4 1.0 CB A:SER146 4.7 8.9 1.0 HG A:SER146 4.7 10.5 0.2 C A:SER146 4.8 7.5 1.0 CB A:SER147 5.0 8.1 1.0

Iodine binding site 2 out of 3 in the Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:22.1 occ:1.00 HE A:ARG119 3.0 22.8 1.0 HB2 A:GLN121 3.4 11.6 1.0 HE1 A:TYR135 3.4 13.4 1.0 HA A:THR120 3.4 8.3 1.0 HG2 A:ARG119 3.5 12.1 1.0 O A:HOH394 3.6 35.5 1.0 O A:HOH597 3.7 48.1 1.0 HD1 A:TYR135 3.8 11.3 1.0 NE A:ARG119 3.8 19.0 1.0 C A:THR120 3.9 6.9 1.0 O A:ARG119 3.9 8.0 1.0 CA A:THR120 4.0 6.9 1.0 N A:GLN121 4.1 8.1 1.0 CE1 A:TYR135 4.1 11.2 1.0 HB3 A:GLN121 4.1 11.6 1.0 CB A:GLN121 4.1 9.7 1.0 O A:HOH345 4.1 11.2 1.0 H A:GLN121 4.2 9.7 1.0 HD2 A:ARG119 4.2 17.6 1.0 HH21 A:ARG119 4.3 27.7 1.0 C A:ARG119 4.3 6.7 1.0 CD1 A:TYR135 4.3 9.4 1.0 CG A:ARG119 4.3 10.1 1.0 O A:THR120 4.3 7.6 1.0 CD A:ARG119 4.4 14.7 1.0 N A:THR120 4.4 7.5 1.0 HB3 A:ARG119 4.5 10.5 1.0 O A:HOH482 4.6 16.6 1.0 CA A:GLN121 4.7 8.4 1.0 CZ A:ARG119 4.8 22.0 1.0 CB A:ARG119 4.9 8.8 1.0 NH2 A:ARG119 4.9 23.1 1.0 HG1 A:THR103 4.9 19.2 1.0

Iodine binding site 3 out of 3 in the Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structures of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:16.5 occ:0.44 O A:HOH469 3.2 29.6 1.0 O A:HOH608 3.2 41.3 1.0 HG21 A:THR2 3.8 30.9 0.8 O A:HOH307 3.9 57.1 1.0 HB A:THR2 4.0 29.1 0.8 O A:HOH574 4.0 42.5 1.0 O A:HOH566 4.1 27.8 1.0 CG2 A:THR2 4.5 25.8 0.8 O A:THR2 4.6 20.1 0.8 CB A:THR2 4.9 24.3 0.8 HG1 A:THR2 5.0 30.7 0.8

Z.Li, X.Zhang, C.Li, A.Kovalevsky, Q.Wan. Studying the Role of A Single Mutation of A Family 11 Glycoside Hydrolase Using High-Resolution X-Ray Crystallography. Protein J. V. 39 671 2020.
ISSN: ISSN 1572-3887
PubMed: 33128114
DOI: 10.1007/S10930-020-09938-5