Iodine in PDB 6kw9: Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose

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

The structure of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose, PDB code: 6kw9 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)	19.93 / 1.22
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.793, 67.799, 79.504, 90, 90, 90
R / Rfree (%)	14.5 / 15.9

The binding sites of Iodine atom in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose (pdb code 6kw9). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose, PDB code: 6kw9:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure Analysis 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 Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:96.3 occ:1.00 H A:GLY112 2.7 9.1 1.0 HG22 A:THR109 3.2 13.4 1.0 N A:GLY112 3.5 7.5 1.0 HA2 A:GLY112 3.6 9.7 1.0 H A:ASP111 3.8 8.6 0.1 H A:ASP111 3.8 8.6 0.9 CG2 A:THR109 3.9 11.2 1.0 HG21 A:THR109 3.9 13.4 1.0 CA A:GLY112 4.0 8.1 1.0 N A:ASP111 4.1 7.1 1.0 O A:HOH423 4.1 14.1 1.0 HA A:SER110 4.2 8.7 0.1 HG23 A:THR109 4.2 13.4 1.0 HA A:SER110 4.3 8.7 0.9 C A:SER110 4.4 7.0 0.9 C A:SER110 4.5 7.0 0.1 C A:ASP111 4.5 7.4 1.0 HA A:ASP111 4.6 8.7 1.0 H A:SER113 4.6 7.9 1.0 CA A:ASP111 4.6 7.3 1.0 CA A:SER110 4.7 7.2 0.1 CA A:SER110 4.7 7.2 0.9 N A:SER110 4.7 7.2 0.1 N A:SER110 4.8 7.1 0.9 C A:GLY112 4.8 7.6 1.0 HA3 A:GLY112 4.8 9.7 1.0 H A:SER110 4.9 8.7 0.1 H A:SER110 4.9 8.5 0.9 N A:SER113 4.9 6.5 1.0

Iodine binding site 2 out of 4 in the Crystal Structure Analysis 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 Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:13.9 occ:1.00 HH11 A:ARG142 2.8 12.2 1.0 HD2 A:ARG142 3.0 9.1 1.0 HD3 A:ARG142 3.1 9.1 1.0 HB A:VAL114 3.3 8.0 1.0 CD A:ARG142 3.5 7.6 1.0 NH1 A:ARG142 3.6 10.2 1.0 HB2 A:ARG142 3.9 8.0 1.0 HB3 A:ARG142 3.9 8.0 1.0 HG21 A:VAL114 4.0 8.9 1.0 HH12 A:ARG142 4.1 12.2 1.0 O A:HOH552 4.1 15.6 1.0 HG23 A:VAL114 4.1 8.9 1.0 CB A:VAL114 4.2 6.7 1.0 CB A:ARG142 4.3 6.7 1.0 CG2 A:VAL114 4.3 7.4 1.0 H A:VAL114 4.4 8.1 1.0 NE A:ARG142 4.5 7.8 1.0 CG A:ARG142 4.5 7.0 1.0 CZ A:ARG142 4.5 8.6 1.0 HG11 A:VAL114 4.6 8.9 1.0 CG1 A:VAL114 4.9 7.4 1.0

Iodine binding site 3 out of 4 in the Crystal Structure Analysis 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 Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:51.6 occ:1.00 HE21 A:GLN125 2.7 38.3 1.0 H A:VAL123 2.8 22.1 1.0 HA A:ARG122 3.2 15.8 1.0 NE2 A:GLN125 3.3 31.9 1.0 O A:HOH343 3.6 29.5 1.0 HD2 A:ARG122 3.6 20.1 1.0 N A:VAL123 3.6 18.4 1.0 HH11 A:ARG122 3.6 31.8 1.0 HE22 A:GLN125 3.7 38.3 1.0 HB A:VAL123 3.7 26.6 1.0 HG3 A:GLN125 3.8 27.9 1.0 NH1 A:ARG122 4.0 26.5 1.0 HG2 A:GLN125 4.1 27.9 1.0 CA A:ARG122 4.1 13.2 1.0 O A:HOH321 4.1 35.7 1.0 O A:GLN121 4.1 14.7 1.0 CD A:GLN125 4.2 22.8 1.0 CG A:GLN125 4.2 23.3 1.0 HH12 A:ARG122 4.2 31.8 1.0 O A:VAL123 4.3 21.1 1.0 C A:ARG122 4.4 15.9 1.0 HG23 A:VAL123 4.4 28.3 1.0 CB A:VAL123 4.5 22.1 1.0 CA A:VAL123 4.5 21.5 1.0 O A:HOH345 4.5 32.0 1.0 CD A:ARG122 4.5 16.8 1.0 HB3 A:ARG122 4.6 17.8 1.0 CZ A:ARG122 4.7 26.9 1.0 CB A:ARG122 4.9 14.8 1.0 C A:VAL123 4.9 23.8 1.0 NE A:ARG122 4.9 25.2 1.0 CG2 A:VAL123 5.0 23.6 1.0

Iodine binding site 4 out of 4 in the Crystal Structure Analysis 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 4 of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:55.2 occ:1.00 OE1 A:GLN34 2.6 11.9 0.5 HE22 A:GLN34 2.7 13.9 0.5 HG A:SER36 2.7 18.1 0.8 OG A:SER36 3.1 6.1 0.2 HG A:SER36 3.1 7.3 0.2 HA3 A:GLY30 3.1 11.4 1.0 CD A:GLN34 3.3 9.9 0.5 NE2 A:GLN34 3.3 11.6 0.5 HG2 A:GLN34 3.3 12.1 0.6 OG A:SER36 3.4 15.0 0.8 OG1 A:THR28 3.4 13.2 0.1 HG22 A:THR28 3.4 12.8 0.8 HB3 A:SER36 3.5 12.9 0.8 HB A:THR28 3.6 11.4 0.8 HB2 A:SER36 3.7 12.9 0.2 HA A:PHE35 3.8 8.6 1.0 CA A:GLY30 3.8 9.5 1.0 HG21 A:THR28 3.8 12.8 0.8 H A:SER36 3.8 8.6 1.0 HA2 A:GLY30 3.9 11.4 1.0 N A:GLY30 3.9 7.8 1.0 CB A:SER36 3.9 10.7 1.0 CG2 A:THR28 4.0 10.7 0.8 O A:THR28 4.0 9.0 0.8 N A:SER36 4.0 7.2 1.0 HG1 A:THR28 4.0 15.9 0.1 HB A:THR28 4.0 11.4 0.1 H A:GLY30 4.1 9.4 1.0 HE21 A:GLN34 4.1 13.9 0.5 CG A:GLN34 4.2 10.1 0.6 C A:PHE35 4.2 6.0 1.0 C A:ASN29 4.3 7.7 1.0 CB A:THR28 4.3 9.5 0.8 CB A:THR28 4.3 9.5 0.1 O A:THR28 4.4 7.7 0.1 CA A:PHE35 4.4 7.2 1.0 CD A:GLN34 4.5 16.9 0.6 O A:ASN29 4.5 11.0 1.0 C A:THR28 4.5 8.9 0.8 CA A:SER36 4.6 7.1 1.0 HB3 A:GLN34 4.6 9.1 0.6 C A:THR28 4.7 8.6 0.1 HD3 A:PRO31 4.7 14.2 1.0 CG A:GLN34 4.7 8.3 0.5 HB3 A:GLN34 4.7 12.3 0.5 HB3 A:SER36 4.8 12.9 0.2 HB2 A:SER36 4.8 12.9 0.8 OE1 A:GLN34 4.8 22.6 0.6 HG3 A:GLN34 4.8 12.1 0.6 N A:PHE35 4.8 6.4 1.0 HD2 A:PRO31 4.8 14.2 1.0 O A:PHE35 4.8 7.2 1.0 HG23 A:THR28 4.9 12.8 0.8 O A:GLN34 4.9 7.5 0.5 C A:GLN34 4.9 6.5 0.5 C A:GLN34 5.0 6.6 0.6 O A:GLN34 5.0 7.0 0.6 HA A:ASN29 5.0 9.6 1.0

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