Iodine in PDB 4xqw: X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0

All present enzymatic activity of X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0:
3.2.1.8;

The structure of X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0, PDB code: 4xqw 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)	32.93 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.990, 59.627, 69.552, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 17.9

The binding sites of Iodine atom in the X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0 (pdb code 4xqw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0, PDB code: 4xqw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0


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-N44E with Mes at PH6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:15.6 occ:1.00 O A:HOH336 3.4 17.6 1.0 N A:SER146 3.6 14.5 1.0 O A:HOH318 3.6 15.6 1.0 OG A:SER146 3.9 17.4 1.0 CA A:ARG145 4.1 14.4 1.0 CB A:ARG145 4.1 14.7 1.0 O A:HOH346 4.1 20.0 1.0 N A:SER147 4.2 14.9 1.0 C A:ARG145 4.3 16.4 1.0 CA A:SER146 4.5 15.2 1.0 O A:HOH376 4.5 22.7 1.0 C A:SER146 4.7 15.7 1.0 CB A:SER146 4.8 17.9 1.0 CB A:SER147 5.0 14.5 1.0

Iodine binding site 2 out of 5 in the X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0


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-N44E with Mes at PH6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:23.8 occ:0.55 O A:HOH516 3.7 32.9 1.0 O A:HOH359 3.9 36.0 1.0 C A:THR120 3.9 14.2 1.0 NE A:ARG119 4.0 26.2 1.0 O A:ARG119 4.0 15.7 1.0 CA A:THR120 4.0 14.8 1.0 N A:GLN121 4.1 15.5 1.0 CE1 A:TYR135 4.1 19.1 1.0 O A:HOH392 4.2 21.3 1.0 CB A:GLN121 4.2 17.4 1.0 C A:ARG119 4.3 15.0 1.0 O A:THR120 4.3 14.4 1.0 CD1 A:TYR135 4.3 18.2 1.0 CG A:ARG119 4.3 17.1 1.0 N A:THR120 4.4 13.9 1.0 CD A:ARG119 4.4 21.3 1.0 O A:HOH496 4.5 33.8 1.0 O A:HOH401 4.6 21.3 1.0 CA A:GLN121 4.7 15.6 1.0 CB A:ARG119 4.9 16.6 1.0 CZ A:ARG119 4.9 29.8 1.0

Iodine binding site 3 out of 5 in the X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0


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-N44E with Mes at PH6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:29.0 occ:0.44 N A:MET169 3.5 16.0 1.0 CA A:THR168 3.9 16.8 1.0 O A:HOH306 3.9 27.6 1.0 CG A:MET169 4.0 18.4 1.0 O A:HOH333 4.0 25.7 1.0 CE A:LYS56 4.1 21.4 1.0 CG2 A:THR168 4.1 23.2 1.0 C A:THR168 4.2 15.9 1.0 O A:HOH428 4.3 33.8 1.0 O A:GLY167 4.3 21.3 1.0 NZ A:LYS56 4.4 24.0 1.0 CB A:MET169 4.4 17.9 1.0 CB A:THR168 4.5 20.4 1.0 CA A:MET169 4.6 16.8 1.0 CD A:LYS56 4.6 19.1 1.0 OG1 A:THR168 4.9 22.8 1.0 CG A:LYS56 4.9 19.3 1.0 N A:THR168 4.9 16.7 1.0

Iodine binding site 4 out of 5 in the X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0


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-N44E with Mes at PH6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:30.1 occ:0.36 NE2 A:GLN125 3.4 27.1 1.0 N A:VAL123 3.5 16.4 1.0 CA A:ARG122 4.0 16.0 1.0 O A:HOH472 4.0 33.0 1.0 CG A:GLN125 4.1 18.1 1.0 NH1 A:ARG122 4.1 21.5 1.0 CD A:GLN125 4.2 21.1 1.0 O A:VAL123 4.2 19.7 1.0 C A:ARG122 4.3 17.1 1.0 O A:GLN121 4.3 16.9 1.0 O A:HOH499 4.4 29.4 1.0 CA A:VAL123 4.4 18.2 1.0 CB A:VAL123 4.4 18.8 1.0 CD A:ARG122 4.5 16.3 1.0 O A:HOH426 4.6 25.5 1.0 CZ A:ARG122 4.7 20.2 1.0 CB A:ARG122 4.7 16.8 1.0 C A:VAL123 4.8 18.1 1.0 CG2 A:VAL123 4.8 20.4 1.0 NE A:ARG122 4.8 18.1 1.0

Iodine binding site 5 out of 5 in the X-Ray Structure Analysis of Xylanase-N44E with Mes at PH6.0


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-N44E with Mes at PH6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:27.7 occ:0.28 O A:PRO68 3.3 19.6 1.0 N A:GLY70 3.6 16.5 1.0 CA A:GLY94 3.8 15.6 1.0 CG2 A:THR95 3.9 15.3 1.0 C A:PRO68 3.9 18.6 1.0 C A:GLY94 4.0 15.2 1.0 CA A:ASN69 4.0 20.2 1.0 N A:THR95 4.0 15.5 1.0 O A:GLY70 4.1 15.4 1.0 C A:ASN69 4.3 18.5 1.0 N A:ASN69 4.3 18.1 1.0 CA A:GLY70 4.5 16.0 1.0 O A:HOH311 4.5 30.6 1.0 CG A:PRO68 4.5 17.3 1.0 O A:GLY94 4.7 16.0 1.0 CB A:PRO68 4.7 16.8 1.0 CA A:THR95 4.7 15.5 1.0 C A:GLY70 4.8 16.0 1.0 CB A:THR95 4.9 15.9 1.0 CA A:PRO68 5.0 18.6 1.0 OD1 A:ASN69 5.0 22.8 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