Iodine in PDB 4xqd: X-Ray Structure Analysis of Xylanase-Wt at PH4.0

All present enzymatic activity of X-Ray Structure Analysis of Xylanase-Wt at PH4.0:
3.2.1.8;

The structure of X-Ray Structure Analysis of Xylanase-Wt at PH4.0, PDB code: 4xqd was solved by Q.Wan, J.M.Park, D.M.Riccardi, L.B.Hanson, Z.Fisher, J.C.Smith, A.Ostermann, T.Schrader, D.E.Graham, L.Coates, P.Langan, A.Y.Kovalevsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.863, 69.630, 78.185, 90.00, 117.51, 90.00
R / Rfree (%)	19 / 22.3

The binding sites of Iodine atom in the X-Ray Structure Analysis of Xylanase-Wt at PH4.0 (pdb code 4xqd). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the X-Ray Structure Analysis of Xylanase-Wt at PH4.0, PDB code: 4xqd:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the X-Ray Structure Analysis of Xylanase-Wt at PH4.0


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Structure Analysis of Xylanase-Wt at PH4.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:15.8 occ:1.00 N A:ASN82 3.7 14.5 1.0 CB A:ARG81 4.0 16.1 1.0 CA A:ARG81 4.1 15.8 1.0 CB A:LEU84 4.2 16.3 1.0 CG A:ARG81 4.3 19.5 1.0 CG2 A:ILE129 4.4 16.6 1.0 C A:ARG81 4.4 17.6 1.0 CG1 A:ILE129 4.4 13.3 1.0 CA A:ASN82 4.5 16.4 1.0 N A:LEU84 4.5 16.7 1.0 CD1 A:LEU84 4.6 14.6 1.0 CA A:LEU84 4.6 17.3 1.0 CB A:ASN82 4.9 17.9 1.0 CG A:LEU84 5.0 17.6 1.0 CB A:ILE129 5.0 13.8 1.0

Iodine binding site 2 out of 6 in the X-Ray Structure Analysis of Xylanase-Wt at PH4.0


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of X-Ray Structure Analysis of Xylanase-Wt at PH4.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:21.3 occ:0.33 OG A:SER184 3.4 20.5 1.0 ND2 A:ASN67 3.8 18.1 1.0 N A:ALA185 3.8 13.6 1.0 CB A:SER65 3.8 19.5 1.0 CA A:ALA185 3.8 14.8 1.0 CB A:SER184 3.9 17.4 1.0 C A:SER184 3.9 16.5 1.0 C A:ALA185 4.0 15.9 1.0 N A:SER186 4.0 12.8 1.0 O A:SER184 4.0 16.3 1.0 O A:HOH484 4.2 34.4 1.0 O A:SER65 4.2 18.7 1.0 O A:HOH488 4.5 39.5 1.0 C A:SER65 4.5 17.2 1.0 CB A:SER186 4.5 17.7 1.0 CA A:SER184 4.5 16.6 1.0 O A:ALA185 4.6 14.5 1.0 CA A:SER65 4.8 17.4 1.0 OG A:SER65 4.8 22.1 1.0 CG A:ASN67 4.8 15.7 1.0 CB A:ASN67 4.9 16.7 1.0 CA A:SER186 4.9 15.8 1.0

Iodine binding site 3 out of 6 in the X-Ray Structure Analysis of Xylanase-Wt at PH4.0


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of X-Ray Structure Analysis of Xylanase-Wt at PH4.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:33.4 occ:0.39 N A:VAL123 3.4 18.5 1.0 NH1 A:ARG122 3.8 37.7 1.0 NE2 A:GLN125 3.9 29.9 1.0 CA A:ARG122 4.0 19.5 1.0 O A:GLN121 4.0 25.2 1.0 CG A:GLN125 4.1 20.9 1.0 CZ A:ARG122 4.1 34.9 1.0 C A:ARG122 4.2 19.4 1.0 CD A:GLN125 4.2 25.3 1.0 O A:VAL123 4.3 19.8 1.0 CB A:VAL123 4.3 18.9 1.0 CA A:VAL123 4.3 18.6 1.0 NE A:ARG122 4.5 32.0 1.0 CD A:ARG122 4.6 27.7 1.0 NH2 A:ARG122 4.7 35.9 1.0 CG2 A:VAL123 4.7 22.8 1.0 CB A:ARG122 4.8 22.2 1.0 C A:VAL123 4.8 19.7 1.0 C A:GLN121 4.9 21.3 1.0 N A:ARG122 4.9 18.6 1.0

Iodine binding site 4 out of 6 in the X-Ray Structure Analysis of Xylanase-Wt at PH4.0


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of X-Ray Structure Analysis of Xylanase-Wt at PH4.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:15.4 occ:1.00 O B:HOH306 3.6 13.6 1.0 N B:SER146 3.6 14.5 1.0 OG B:SER146 3.9 16.5 1.0 CA B:ARG145 4.1 15.9 1.0 CB B:ARG145 4.1 13.9 1.0 N B:SER147 4.2 14.9 1.0 O B:HOH330 4.3 20.2 1.0 C B:ARG145 4.4 17.3 1.0 CA B:SER146 4.5 14.9 1.0 C B:SER146 4.7 15.3 1.0 CB B:SER146 4.9 16.1 1.0 CB B:SER147 5.0 17.2 1.0

Iodine binding site 5 out of 6 in the X-Ray Structure Analysis of Xylanase-Wt at PH4.0


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of X-Ray Structure Analysis of Xylanase-Wt at PH4.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:I202 b:23.5 occ:0.37 OG B:SER184 3.4 21.5 1.0 ND2 B:ASN67 3.7 19.5 1.0 CB B:SER65 3.8 15.6 1.0 N B:ALA185 3.9 13.9 1.0 CA B:ALA185 3.9 14.0 1.0 C B:SER184 3.9 15.9 1.0 CB B:SER184 3.9 16.1 1.0 O B:SER184 4.0 16.0 1.0 N B:SER186 4.1 13.0 1.0 C B:ALA185 4.1 15.7 1.0 O B:SER65 4.3 16.0 1.0 C B:SER65 4.5 15.5 1.0 CB B:SER186 4.6 17.1 1.0 CA B:SER184 4.6 16.3 1.0 CG B:ASN67 4.7 16.7 1.0 OG B:SER65 4.8 23.5 1.0 O B:ALA185 4.8 14.9 1.0 CB B:ASN67 4.8 15.3 1.0 CA B:SER65 4.8 14.9 1.0 N B:TYR66 5.0 14.6 1.0 CA B:SER186 5.0 16.7 1.0

Iodine binding site 6 out of 6 in the X-Ray Structure Analysis of Xylanase-Wt at PH4.0


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of X-Ray Structure Analysis of Xylanase-Wt at PH4.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:I203 b:28.8 occ:0.29 O B:HOH515 3.1 32.0 1.0 O B:ASN38 3.6 19.0 1.0 O B:GLY24 3.6 23.6 1.0 C B:GLY24 3.7 21.9 1.0 OG1 B:THR26 3.7 27.8 1.0 N B:VAL25 3.9 21.1 1.0 N B:THR26 4.0 19.4 1.0 CA B:TRP39 4.1 16.3 1.0 CA B:VAL25 4.1 19.6 1.0 C B:VAL25 4.1 21.1 1.0 CA B:GLY24 4.2 22.1 1.0 N B:SER40 4.2 17.1 1.0 C B:ASN38 4.3 16.1 1.0 CB B:THR26 4.4 23.2 1.0 C B:TRP39 4.5 14.1 1.0 N B:TRP39 4.5 14.1 1.0 CB B:SER40 4.6 19.7 1.0 O B:VAL25 4.8 23.0 1.0 CA B:THR26 4.8 22.4 1.0

Q.Wan, J.M.Parks, B.L.Hanson, S.Z.Fisher, A.Ostermann, T.E.Schrader, D.E.Graham, L.Coates, P.Langan, A.Kovalevsky. Direct Determination of Protonation States and Visualization of Hydrogen Bonding in A Glycoside Hydrolase with Neutron Crystallography. Proc.Natl.Acad.Sci.Usa V. 112 12384 2015.
ISSN: ESSN 1091-6490
PubMed: 26392527
DOI: 10.1073/PNAS.1504986112