Iodine in PDB 6kwf: 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: 6kwf 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)	19.84 / 1.22
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.679, 67.931, 78.81, 90, 90, 90
R / Rfree (%)	14.5 / 15.6

The binding sites of Iodine atom in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II Complexed with Xylotriose (pdb code 6kwf). 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: 6kwf:
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:I207 b:27.9 occ:1.00 HA2 A:GLY130 3.0 18.4 1.0 HB3 A:PRO126 3.1 19.6 1.0 H A:SER127 3.3 15.4 1.0 HA A:PRO126 3.3 19.0 1.0 O A:HOH349 3.3 78.6 1.0 H1 B:XYP3 3.4 17.4 1.0 H51 B:XYP2 3.5 14.9 1.0 H3 B:XYP3 3.6 28.0 1.0 O A:HOH495 3.7 33.3 1.0 O A:SER127 3.9 13.0 1.0 CA A:GLY130 3.9 15.3 1.0 CB A:PRO126 3.9 16.3 1.0 CA A:PRO126 4.0 15.8 1.0 N A:SER127 4.0 12.9 1.0 H51 B:XYP3 4.1 20.5 1.0 O2 B:XYP3 4.2 19.6 1.0 C A:GLY130 4.2 16.6 1.0 H A:GLY130 4.2 18.5 1.0 H A:THR131 4.3 20.8 1.0 C1 B:XYP3 4.3 14.5 1.0 C5 B:XYP2 4.3 12.4 1.0 H52 B:XYP2 4.3 14.9 1.0 N A:THR131 4.4 17.3 1.0 C3 B:XYP3 4.4 23.3 1.0 C2 B:XYP3 4.5 17.9 1.0 C A:PRO126 4.5 14.6 1.0 HB2 A:PRO126 4.5 19.6 1.0 HG3 A:PRO126 4.5 22.5 1.0 HA3 A:GLY130 4.6 18.4 1.0 N A:GLY130 4.6 15.4 1.0 O A:GLY130 4.7 16.5 1.0 HE1 A:TRP18 4.8 16.7 1.0 C A:SER127 4.9 12.0 1.0 CG A:PRO126 4.9 18.8 1.0 HA A:THR131 4.9 17.7 1.0 HO2 B:XYP3 4.9 23.5 1.0 C5 B:XYP3 5.0 17.1 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:I208 b:17.5 occ:1.00 HH11 A:ARG142 2.8 14.8 1.0 HD2 A:ARG142 3.0 13.2 1.0 HD3 A:ARG142 3.2 13.2 1.0 HB A:VAL114 3.4 12.0 1.0 CD A:ARG142 3.5 11.0 1.0 NH1 A:ARG142 3.6 12.4 1.0 HG21 A:VAL114 3.9 14.6 1.0 HB2 A:ARG142 4.0 12.8 1.0 HB3 A:ARG142 4.0 12.8 1.0 HH12 A:ARG142 4.0 14.8 1.0 HG23 A:VAL114 4.1 14.6 1.0 CB A:VAL114 4.2 10.0 1.0 CG2 A:VAL114 4.3 12.2 1.0 CB A:ARG142 4.3 10.6 1.0 H A:VAL114 4.5 12.1 1.0 NE A:ARG142 4.5 11.1 1.0 CZ A:ARG142 4.5 12.9 1.0 CG A:ARG142 4.5 10.7 1.0 HG11 A:VAL114 4.6 14.2 1.0 CG1 A:VAL114 5.0 11.8 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:I209 b:78.4 occ:1.00 H A:VAL123 2.6 16.8 1.0 HE21 A:GLN125 3.0 42.2 1.0 HA A:ARG122 3.1 15.5 1.0 N A:VAL123 3.5 14.0 1.0 HH11 A:ARG122 3.6 33.3 1.0 NE2 A:GLN125 3.6 35.1 1.0 HD2 A:ARG122 3.6 26.2 1.0 O A:HOH322 3.7 38.7 1.0 HB A:VAL123 3.7 17.9 1.0 HG3 A:GLN125 3.7 23.7 1.0 HG2 A:GLN125 3.9 23.7 1.0 NH1 A:ARG122 3.9 27.8 1.0 CA A:ARG122 4.0 12.9 1.0 HE22 A:GLN125 4.0 42.2 1.0 O A:GLN121 4.1 16.8 1.0 HH12 A:ARG122 4.1 33.3 1.0 CG A:GLN125 4.1 19.8 1.0 O A:VAL123 4.1 15.5 1.0 HG23 A:VAL123 4.2 24.3 1.0 CD A:GLN125 4.2 21.6 1.0 C A:ARG122 4.2 13.8 1.0 O A:HOH355 4.2 46.0 1.0 CA A:VAL123 4.4 14.9 1.0 CB A:VAL123 4.4 14.9 1.0 HB3 A:ARG122 4.5 16.7 1.0 CD A:ARG122 4.5 21.8 1.0 CZ A:ARG122 4.6 40.8 1.0 C A:VAL123 4.7 14.5 1.0 CB A:ARG122 4.8 13.9 1.0 O A:HOH392 4.8 39.2 1.0 CG2 A:VAL123 4.8 20.2 1.0 NE A:ARG122 4.9 29.7 1.0 N A:ARG122 4.9 13.2 1.0 C A:GLN121 5.0 14.0 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:I210 b:91.5 occ:1.00 HG A:SER36 2.7 20.5 0.6 OE1 A:GLN34 2.7 28.6 1.0 HE22 A:GLN34 2.8 39.5 1.0 HG1 A:THR28 2.9 14.1 0.1 HG22 A:THR28 3.1 17.8 0.8 OG1 A:THR28 3.1 11.8 0.1 HG A:SER36 3.1 18.0 0.4 OG A:SER36 3.2 15.0 0.4 HA3 A:GLY30 3.2 15.8 1.0 OG A:SER36 3.3 17.1 0.6 NE2 A:GLN34 3.4 32.9 1.0 CD A:GLN34 3.4 26.4 1.0 HB3 A:SER36 3.4 19.0 0.6 HB A:THR28 3.4 16.5 0.8 HG21 A:THR28 3.5 17.8 0.8 HB2 A:SER36 3.5 19.0 0.4 CG2 A:THR28 3.7 14.8 0.8 H A:SER36 3.8 13.4 1.0 CA A:GLY30 3.8 13.2 1.0 HA A:PHE35 3.9 12.3 1.0 CB A:SER36 3.9 15.8 1.0 N A:GLY30 3.9 11.2 1.0 HA2 A:GLY30 3.9 15.8 1.0 O A:THR28 3.9 13.0 0.8 N A:SER36 4.0 11.2 1.0 O A:THR28 4.0 12.8 0.1 CB A:THR28 4.1 13.7 0.8 HB A:THR28 4.1 15.3 0.1 H A:GLY30 4.1 13.5 1.0 HE21 A:GLN34 4.2 39.5 1.0 C A:ASN29 4.2 12.1 1.0 CB A:THR28 4.2 12.8 0.1 C A:PHE35 4.3 9.8 1.0 O A:ASN29 4.4 15.6 1.0 C A:THR28 4.4 11.6 0.8 C A:THR28 4.4 11.9 0.1 CA A:PHE35 4.5 10.2 1.0 HG23 A:THR28 4.6 17.8 0.8 CA A:SER36 4.6 9.9 1.0 HB3 A:SER36 4.7 19.0 0.4 HB2 A:SER36 4.7 19.0 0.6 HD3 A:PRO31 4.8 16.7 1.0 CG A:GLN34 4.9 14.4 1.0 HB3 A:GLN34 4.9 15.3 1.0 HA A:ASN29 4.9 14.2 1.0 CA A:THR28 4.9 11.1 0.8 N A:ASN29 4.9 11.6 1.0 CA A:ASN29 5.0 11.8 1.0 CA A:THR28 5.0 11.0 0.1 O A:PHE35 5.0 10.9 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