Iodine in PDB 1gwd: Tri-Iodide Derivative of Hen Egg-White Lysozyme

All present enzymatic activity of Tri-Iodide Derivative of Hen Egg-White Lysozyme:
3.2.1.17;

The structure of Tri-Iodide Derivative of Hen Egg-White Lysozyme, PDB code: 1gwd was solved by G.Evans, G.Bricogne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.09 / 1.77
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.050, 79.050, 36.820, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 21.1

The structure of Tri-Iodide Derivative of Hen Egg-White Lysozyme also contains other interesting chemical elements:

Chlorine	(Cl)	7 atoms
Sodium	(Na)	3 atoms

The binding sites of Iodine atom in the Tri-Iodide Derivative of Hen Egg-White Lysozyme (pdb code 1gwd). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Tri-Iodide Derivative of Hen Egg-White Lysozyme, PDB code: 1gwd:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:I1130 b:27.9 occ:0.36 I A:IOD1147 2.7 25.6 0.2 CA A:ARG14 3.7 11.3 1.0 N A:ARG14 3.8 11.4 1.0 CB A:ARG14 3.8 11.4 1.0 CG A:LYS13 3.9 16.8 1.0 NE A:ARG14 4.0 30.2 1.0 CD A:LYS13 4.1 23.0 1.0 C A:LYS13 4.2 14.1 1.0 O A:ALA10 4.4 8.7 1.0 CE A:LYS13 4.4 33.6 1.0 CB A:LYS13 4.5 11.1 1.0 O A:LYS13 4.5 14.3 1.0 NH1 A:ARG14 4.5 34.5 1.0 CZ A:ARG14 4.7 45.3 1.0 CD A:ARG14 4.9 25.7 1.0 CG A:ARG14 5.0 21.2 1.0

Iodine binding site 2 out of 5 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:I1131 b:14.2 occ:0.25 O A:HOH2021 3.1 26.0 1.0 ND2 A:ASN65 3.1 11.0 1.0 CA A:GLY67 3.7 6.8 1.0 N A:GLY67 4.1 6.8 1.0 O A:HOH2052 4.2 19.6 1.0 CG A:ASN65 4.2 18.1 1.0 OD1 A:ASN65 4.4 10.8 1.0 C A:ASP66 4.7 8.8 1.0 O A:ASP66 4.9 7.9 1.0 C A:GLY67 5.0 11.4 1.0

Iodine binding site 3 out of 5 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:I1132 b:13.2 occ:0.18 N A:LEU25 3.0 6.9 1.0 CA A:SER24 3.6 6.7 1.0 N A:ASN19 3.6 12.2 1.0 CB A:ASP18 3.6 15.1 1.0 CB A:LEU25 3.7 6.3 1.0 C A:SER24 3.8 9.9 1.0 C A:ASP18 3.9 16.1 1.0 CB A:SER24 3.9 9.3 1.0 CA A:LEU25 3.9 6.3 1.0 CA A:ASP18 3.9 12.6 1.0 CB A:ASN19 4.3 13.9 1.0 CA A:ASN19 4.4 11.0 1.0 O A:ASP18 4.7 15.8 1.0 CG A:ASP18 4.8 27.5 1.0 OD1 A:ASP18 4.8 30.3 1.0 N A:SER24 4.9 6.9 1.0

Iodine binding site 4 out of 5 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:I1133 b:19.8 occ:0.20 ND2 A:ASN74 3.3 8.8 1.0 O A:HOH2061 3.5 23.2 1.0 CB A:ASN74 3.7 7.7 1.0 CB A:ASN65 3.8 6.3 1.0 CG A:ASN65 3.9 18.1 1.0 CG A:ASN74 4.0 16.4 1.0 OD1 A:ASN65 4.2 10.8 1.0 O A:HOH2051 4.3 9.6 1.0 ND2 A:ASN65 4.4 11.0 1.0 O A:HOH2065 4.8 15.3 1.0 O A:HOH2052 5.0 19.6 1.0

Iodine binding site 5 out of 5 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:I1147 b:25.6 occ:0.23 I A:IOD1130 2.7 27.9 0.4 OXT A:LEU129 3.7 30.8 1.0 C A:LEU129 4.3 25.6 1.0 CD A:LYS13 4.4 23.0 1.0 CA A:LEU129 4.5 16.2 1.0 CB A:ALA10 4.5 7.0 1.0 O A:ALA10 4.6 8.7 1.0 CA A:ALA10 4.8 6.2 1.0 CE A:LYS13 5.0 33.6 1.0 C A:CMO1135 5.0 16.6 1.0

G.Evans, G.Bricogne. Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods For Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment Acta Crystallogr.,Sect.D V. 58 976 2002.
ISSN: ISSN 0907-4449
PubMed: 12037300
DOI: 10.1107/S0907444902005486