Iodine in PDB 4xq4: X-Ray Structure Analysis of Xylanase - N44D

All present enzymatic activity of X-Ray Structure Analysis of Xylanase - N44D:
3.2.1.8;

The structure of X-Ray Structure Analysis of Xylanase - N44D, PDB code: 4xq4 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)	27.20 / 1.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.940, 69.750, 78.281, 90.00, 117.45, 90.00
R / Rfree (%)	14.1 / 16.8

The binding sites of Iodine atom in the X-Ray Structure Analysis of Xylanase - N44D (pdb code 4xq4). 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 - N44D, PDB code: 4xq4:
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 - N44D


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 - N44D within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:8.6 occ:1.00 H A:ASN82 3.0 8.1 1.0 HB3 A:ARG81 3.3 11.2 1.0 HB2 A:LEU84 3.4 9.1 1.0 HG12 A:ILE129 3.5 11.4 1.0 HG21 A:ILE129 3.5 12.7 1.0 HA A:ARG81 3.5 10.1 1.0 O A:HOH341 3.6 18.7 1.0 N A:ASN82 3.7 6.7 1.0 HG2 A:ARG81 3.7 12.3 1.0 HD13 A:LEU84 3.8 9.9 1.0 CB A:ARG81 4.0 9.4 1.0 CA A:ARG81 4.1 8.4 1.0 HB2 A:ASN82 4.2 11.0 1.0 CB A:LEU84 4.3 7.6 1.0 HA A:ASN82 4.3 9.7 1.0 CG A:ARG81 4.3 10.3 1.0 O A:HOH403 4.4 23.1 1.0 H A:LEU84 4.4 9.1 1.0 C A:ARG81 4.4 7.5 1.0 CG2 A:ILE129 4.4 10.5 1.0 HA A:LEU84 4.4 8.8 1.0 CG1 A:ILE129 4.5 9.5 1.0 CA A:ASN82 4.5 8.1 1.0 HD3 A:ARG81 4.6 13.6 1.0 N A:LEU84 4.6 7.6 1.0 CD1 A:LEU84 4.6 8.3 1.0 HG23 A:ILE129 4.6 12.7 1.0 HD22 A:LEU84 4.7 10.9 1.0 CA A:LEU84 4.7 7.3 1.0 HG13 A:ILE129 4.7 11.4 1.0 HH11 A:ARG81 4.7 15.5 1.0 HD12 A:LEU84 4.8 9.9 1.0 HB2 A:ARG81 4.9 11.2 1.0 HB3 A:LEU84 4.9 9.1 1.0 CB A:ASN82 4.9 9.2 1.0 CG A:LEU84 5.0 8.2 1.0

Iodine binding site 2 out of 5 in the X-Ray Structure Analysis of Xylanase - N44D


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 - N44D within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:18.4 occ:0.44 HG A:SER65 2.6 12.3 0.2 HG A:SER184 2.7 14.7 1.0 HD21 A:ASN67 2.9 14.3 1.0 OG A:SER65 3.1 10.3 0.2 HB2 A:SER65 3.3 12.6 0.8 OG A:SER184 3.3 12.2 1.0 HA A:ALA185 3.3 8.5 1.0 HB3 A:SER65 3.5 12.6 0.8 HB2 A:SER184 3.6 12.4 1.0 HB2 A:SER65 3.7 11.5 0.2 ND2 A:ASN67 3.7 11.9 1.0 N A:ALA185 3.8 7.0 1.0 CB A:SER65 3.9 10.5 0.8 CA A:ALA185 3.9 7.1 1.0 C A:SER184 3.9 7.0 1.0 CB A:SER184 3.9 10.3 1.0 H A:SER186 4.0 8.8 1.0 CB A:SER65 4.0 9.6 0.2 HB2 A:ASN67 4.0 10.3 1.0 HD22 A:ASN67 4.0 14.3 1.0 C A:ALA185 4.0 7.6 1.0 O A:SER184 4.1 7.6 1.0 O A:HOH549 4.1 28.8 1.0 HB3 A:SER186 4.1 12.7 1.0 N A:SER186 4.1 7.3 1.0 HB2 A:SER186 4.1 12.7 1.0 H A:ALA185 4.1 8.4 1.0 O A:SER65 4.2 9.7 1.0 O A:HOH505 4.5 33.3 1.0 C A:SER65 4.5 8.6 1.0 CB A:SER186 4.5 10.6 1.0 CA A:SER184 4.6 7.5 1.0 O A:HOH334 4.6 28.5 1.0 HB3 A:SER65 4.6 11.5 0.2 O A:ALA185 4.7 7.8 1.0 CG A:ASN67 4.8 10.3 1.0 H A:ASN67 4.8 7.5 1.0 HB3 A:SER184 4.8 12.4 1.0 CB A:ASN67 4.8 8.6 1.0 OG A:SER65 4.8 12.0 0.8 CA A:SER65 4.9 9.3 0.8 CA A:SER65 4.9 8.9 0.2 CA A:SER186 5.0 7.8 1.0

Iodine binding site 3 out of 5 in the X-Ray Structure Analysis of Xylanase - N44D


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 - N44D within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:7.9 occ:1.00 H B:SER146 2.7 8.8 1.0 HB2 B:ARG145 3.4 7.7 1.0 HA B:ARG145 3.5 7.8 1.0 O B:HOH308 3.6 7.8 1.0 N B:SER146 3.6 7.3 1.0 HG B:SER146 3.6 11.7 1.0 H B:SER147 3.6 9.5 1.0 OG B:SER146 3.9 9.7 1.0 CA B:ARG145 4.1 6.5 1.0 CB B:ARG145 4.2 6.4 1.0 N B:SER147 4.2 7.9 1.0 O B:HOH334 4.2 15.2 1.0 HB2 B:SER147 4.3 11.0 1.0 C B:ARG145 4.4 6.2 1.0 HB3 B:ARG145 4.4 7.7 1.0 CA B:SER146 4.5 7.5 1.0 HG B:SER147 4.5 10.8 1.0 C B:SER146 4.7 7.6 1.0 CB B:SER146 4.8 8.7 1.0

Iodine binding site 4 out of 5 in the X-Ray Structure Analysis of Xylanase - N44D


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 - N44D within 5.0Å range: probe atom residue distance (Å) B Occ B:I202 b:20.2 occ:0.49 HG B:SER184 2.7 15.1 1.0 HD21 B:ASN67 2.9 14.8 1.0 O B:HOH371 3.1 37.6 1.0 HB2 B:SER65 3.3 12.2 1.0 HA B:ALA185 3.3 7.4 1.0 OG B:SER184 3.4 12.6 1.0 HB3 B:SER65 3.5 12.2 1.0 HB2 B:SER184 3.6 12.0 1.0 ND2 B:ASN67 3.7 12.4 1.0 CB B:SER65 3.8 10.2 1.0 N B:ALA185 3.8 6.6 1.0 CA B:ALA185 3.9 6.1 1.0 HB2 B:ASN67 3.9 10.5 1.0 C B:SER184 3.9 7.1 1.0 H B:SER186 4.0 8.3 1.0 CB B:SER184 4.0 10.0 1.0 HD22 B:ASN67 4.0 14.8 1.0 O B:SER184 4.0 7.0 1.0 C B:ALA185 4.0 6.8 1.0 N B:SER186 4.1 6.9 1.0 HB3 B:SER186 4.2 13.3 1.0 H B:ALA185 4.2 7.9 1.0 HB2 B:SER186 4.2 13.3 1.0 O B:SER65 4.2 8.5 1.0 O B:HOH586 4.3 31.6 1.0 C B:SER65 4.5 6.8 1.0 HG B:SER65 4.6 15.8 1.0 CB B:SER186 4.6 11.1 1.0 CA B:SER184 4.6 7.3 1.0 CG B:ASN67 4.7 11.2 1.0 H B:ASN67 4.7 7.4 1.0 O B:ALA185 4.7 7.7 1.0 CB B:ASN67 4.7 8.7 1.0 O B:HOH326 4.7 23.5 1.0 OG B:SER65 4.8 13.2 1.0 HB3 B:SER184 4.8 12.0 1.0 CA B:SER65 4.8 8.1 1.0

Iodine binding site 5 out of 5 in the X-Ray Structure Analysis of Xylanase - N44D


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 - N44D within 5.0Å range: probe atom residue distance (Å) B Occ B:I203 b:20.6 occ:0.30 HG1 B:THR26 2.9 18.9 1.0 O B:HOH514 3.0 26.8 1.0 HA B:TRP39 3.2 8.6 1.0 O B:GLY24 3.5 15.0 1.0 O B:ASN38 3.5 9.5 1.0 HA B:VAL25 3.6 14.4 0.1 OG1 B:THR26 3.6 15.8 1.0 C B:GLY24 3.7 13.4 1.0 HA B:VAL25 3.7 14.0 0.8 HA2 B:GLY24 3.8 16.0 1.0 H B:THR26 3.8 13.5 1.0 HB2 B:SER40 3.8 9.8 0.2 HB3 B:SER40 3.8 10.7 0.8 H B:SER40 3.9 9.2 0.8 H B:SER40 3.9 9.2 0.2 N B:VAL25 3.9 12.2 1.0 N B:THR26 4.0 11.2 1.0 HG B:SER40 4.0 10.9 0.2 CA B:TRP39 4.1 7.2 1.0 CA B:VAL25 4.1 12.0 0.1 HB B:THR26 4.1 17.2 1.0 CA B:VAL25 4.1 11.7 0.8 C B:VAL25 4.1 11.8 1.0 C B:ASN38 4.2 7.9 1.0 N B:SER40 4.2 7.7 1.0 CA B:GLY24 4.3 13.3 1.0 CB B:THR26 4.4 14.3 1.0 H B:VAL25 4.4 14.6 0.8 H B:VAL25 4.4 14.6 0.1 N B:TRP39 4.4 6.9 1.0 C B:TRP39 4.4 7.5 1.0 HB2 B:SER40 4.5 10.7 0.8 CB B:SER40 4.6 8.2 0.2 CB B:SER40 4.6 8.9 0.8 OG B:SER40 4.6 9.1 0.2 O B:VAL25 4.8 13.4 1.0 HB2 B:ASN38 4.8 14.8 1.0 CA B:THR26 4.8 12.5 1.0 HB3 B:ASN38 4.8 14.8 1.0 HA3 B:GLY24 4.9 16.0 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