Iodine in PDB 6kwc: Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II

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

The structure of Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II, PDB code: 6kwc 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)	19.92 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.495, 59.185, 69.841, 90, 90, 90
R / Rfree (%)	15.7 / 17.2

The binding sites of Iodine atom in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II (pdb code 6kwc). 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, PDB code: 6kwc:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:19.0 occ:1.00 H A:SER146 2.8 21.3 1.0 HB2 A:ARG145 3.4 22.0 1.0 HG A:SER146 3.4 24.1 0.7 HA A:ARG145 3.5 20.9 1.0 O A:HOH375 3.6 22.1 1.0 O A:HOH318 3.6 17.6 1.0 N A:SER146 3.6 17.8 1.0 H A:SER147 3.7 21.0 1.0 OG A:SER146 3.9 20.1 0.7 CB A:ARG145 4.1 18.3 1.0 CA A:ARG145 4.1 17.4 1.0 O A:HOH305 4.2 24.1 1.0 N A:SER147 4.3 17.5 1.0 HB2 A:SER146 4.3 24.0 0.3 HB3 A:ARG145 4.3 22.0 1.0 HB2 A:SER147 4.3 21.7 1.0 C A:ARG145 4.4 17.5 1.0 O A:HOH551 4.5 26.0 1.0 HG A:SER146 4.5 24.4 0.3 CA A:SER146 4.5 18.6 1.0 HG A:SER147 4.6 21.8 1.0 C A:SER146 4.7 18.9 1.0 CB A:SER146 4.8 20.0 1.0

Iodine binding site 2 out of 4 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:32.8 occ:1.00 HE A:ARG119 3.1 37.4 1.0 HE1 A:TYR135 3.4 27.5 1.0 HB2 A:GLN121 3.4 24.5 1.0 HA A:THR120 3.4 22.8 1.0 HG2 A:ARG119 3.5 26.8 1.0 HD1 A:TYR135 3.8 25.6 1.0 NE A:ARG119 3.9 31.1 1.0 O A:ARG119 4.0 19.8 1.0 C A:THR120 4.0 18.6 1.0 CA A:THR120 4.0 19.0 1.0 CE1 A:TYR135 4.1 22.9 1.0 O A:HOH342 4.1 24.0 1.0 N A:GLN121 4.2 20.1 1.0 HH21 A:ARG119 4.2 42.4 1.0 CB A:GLN121 4.2 20.4 1.0 CG A:ARG119 4.3 22.3 1.0 H A:GLN121 4.3 24.1 1.0 C A:ARG119 4.3 18.9 1.0 O A:THR120 4.3 18.8 1.0 HB3 A:GLN121 4.3 24.5 1.0 CD1 A:TYR135 4.3 21.4 1.0 HB3 A:ARG119 4.4 22.9 1.0 HD2 A:ARG119 4.4 31.9 1.0 N A:THR120 4.4 18.1 1.0 CD A:ARG119 4.5 26.6 1.0 O A:HOH459 4.6 27.4 1.0 O A:HOH301 4.8 65.3 1.0 CA A:GLN121 4.8 20.0 1.0 CB A:ARG119 4.8 19.1 1.0 NH2 A:ARG119 4.8 35.4 1.0 CZ A:ARG119 4.8 34.5 1.0

Iodine binding site 3 out of 4 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:189.4 occ:1.00 H A:MET169 2.9 24.6 0.5 H A:MET169 2.9 24.6 0.5 H A:MET169 2.9 24.6 0.0 HG2 A:MET169 3.1 25.6 0.8 HA A:THR168 3.3 24.4 0.5 HE3 A:LYS56 3.3 27.6 1.0 HA A:THR168 3.3 25.4 0.0 HA A:THR168 3.4 24.9 0.5 O A:HOH405 3.5 27.5 1.0 HG23 A:THR168 3.7 25.9 0.0 HG23 A:THR168 3.7 28.3 0.5 N A:MET169 3.8 20.5 1.0 HG3 A:LYS56 3.9 26.4 1.0 HB2 A:MET169 4.0 24.1 1.0 CG A:MET169 4.0 21.3 1.0 HD2 A:LYS56 4.1 26.8 1.0 CE A:LYS56 4.2 23.0 1.0 CA A:THR168 4.2 20.4 0.5 HZ2 A:LYS56 4.2 29.2 1.0 CA A:THR168 4.2 21.2 0.0 CA A:THR168 4.2 20.8 0.5 HG3 A:MET169 4.3 25.6 1.0 O A:HOH316 4.3 28.2 1.0 HB A:THR168 4.3 27.6 0.5 CB A:MET169 4.4 20.1 1.0 HG22 A:THR168 4.4 29.6 0.5 O A:HOH479 4.4 52.6 1.0 CG2 A:THR168 4.5 21.6 0.0 CG2 A:THR168 4.5 23.6 0.5 C A:THR168 4.5 19.9 0.5 CD A:LYS56 4.5 22.3 1.0 C A:THR168 4.5 20.3 0.5 C A:THR168 4.5 21.0 0.0 NZ A:LYS56 4.6 24.3 1.0 O A:GLY167 4.7 22.3 1.0 HG22 A:THR168 4.7 28.3 0.5 CG A:LYS56 4.7 22.0 1.0 HG22 A:THR168 4.7 25.9 0.0 CA A:MET169 4.7 18.9 1.0 HZ1 A:LYS56 4.7 29.2 1.0 CB A:THR168 4.7 23.0 0.5 HA A:THR55 4.7 24.4 1.0 CB A:THR168 4.9 21.5 0.0 CB A:THR168 4.9 23.1 0.5 HE2 A:LYS56 4.9 27.6 1.0

Iodine binding site 4 out of 4 in the Crystal Structure Analysis of Endo-Beta-1,4-Xylanase II


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:34.9 occ:1.00 HB3 A:SER1 3.2 36.5 1.0 HG A:SER1 3.8 65.3 1.0 O A:HOH399 3.8 29.4 1.0 O A:HOH484 3.8 46.2 1.0 CB A:SER1 4.0 30.4 1.0 OG A:SER1 4.1 54.4 1.0 H A:THR2 4.3 30.5 0.8 HB2 A:SER1 4.5 36.5 1.0 O A:THR2 4.6 25.1 0.8 HA A:SER1 5.0 39.8 1.0 N A:THR2 5.0 25.4 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