Iodine in PDB 9b7c: High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide

All present enzymatic activity of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide:
3.2.1.17;

The structure of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide, PDB code: 9b7c was solved by H.K.Wang, J.B.Greisman, D.R.Hekstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.15 / 1.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.405, 79.405, 37.837, 90, 90, 90
R / Rfree (%)	11.1 / 12.3

The structure of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iodine atom in the High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide (pdb code 9b7c). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide, PDB code: 9b7c:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:21.7 occ:0.31 HH A:TYR23 2.7 18.2 1.0 OH A:TYR23 3.1 15.2 1.0 HE2 A:TYR23 3.2 15.6 1.0 O A:HOH344 3.2 23.3 0.6 HA3 A:GLY104 3.5 18.0 1.0 CE2 A:TYR23 3.8 13.0 1.0 CZ A:TYR23 3.8 13.0 1.0 HA2 A:GLY104 4.2 18.0 1.0 CA A:GLY104 4.3 15.0 1.0 O A:ARG21 4.5 19.6 0.5 O A:ARG21 4.5 19.1 0.6 HB3 A:ARG21 4.6 24.3 0.5 HB3 A:ARG21 4.6 24.9 0.6 O A:HOH344 4.7 22.3 0.4 NH2 A:ARG21 4.7 32.0 0.5 HH21 A:ARG21 4.8 38.4 0.5 N A:GLY104 4.8 14.8 1.0 CZ A:ARG21 4.9 31.1 0.5 HH22 A:ARG21 4.9 38.4 0.5 H A:MET105 4.9 14.1 1.0

Iodine binding site 2 out of 3 in the High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:29.1 occ:0.29 H A:GLY26 2.6 14.8 1.0 HA A:GLN121 2.9 25.3 0.5 HA A:GLN121 2.9 25.5 0.5 HG A:SER24 2.9 23.1 1.0 HB2 A:SER24 3.0 19.9 1.0 HG2 A:GLN121 3.2 34.9 0.5 HD11 A:ILE124 3.2 34.0 1.0 OG A:SER24 3.2 19.2 1.0 HA3 A:GLY26 3.2 15.2 1.0 HB2 A:GLN121 3.4 31.3 0.5 N A:GLY26 3.4 12.4 1.0 HD13 A:ILE124 3.5 34.0 1.0 CB A:SER24 3.6 16.6 1.0 HB2 A:GLN121 3.6 30.2 0.5 HG3 A:GLN121 3.6 37.0 0.5 CA A:GLN121 3.7 21.3 0.5 CA A:GLN121 3.7 21.1 0.5 HG12 A:ILE124 3.7 27.3 1.0 CD1 A:ILE124 3.7 28.3 1.0 HG23 A:VAL120 3.7 24.9 1.0 CA A:GLY26 3.8 12.6 1.0 CB A:GLN121 3.9 26.1 0.5 CG A:GLN121 3.9 29.1 0.5 CB A:GLN121 3.9 25.2 0.5 HE21 A:GLN121 4.0 43.2 0.5 HG3 A:GLN121 4.0 34.9 0.5 CG A:GLN121 4.1 30.8 0.5 N A:GLN121 4.1 19.6 0.5 N A:GLN121 4.1 19.5 0.5 HB3 A:SER24 4.2 19.9 1.0 H A:LEU25 4.2 16.4 1.0 CG1 A:ILE124 4.2 22.7 1.0 NE2 A:GLN121 4.2 36.0 0.5 N A:LEU25 4.3 13.6 1.0 CD A:GLN121 4.3 34.9 0.5 HB3 A:LEU25 4.4 17.0 1.0 H A:GLN121 4.4 23.5 0.5 H A:GLN121 4.4 23.4 0.5 HA2 A:GLY26 4.4 15.2 1.0 C A:SER24 4.5 13.2 1.0 H A:ASN27 4.5 13.2 1.0 O A:VAL120 4.6 18.3 1.0 C A:LEU25 4.6 12.1 1.0 C A:VAL120 4.6 17.8 1.0 HD12 A:ILE124 4.6 34.0 1.0 HG13 A:ILE124 4.7 27.3 1.0 CG2 A:VAL120 4.7 20.8 1.0 HE22 A:GLN121 4.7 43.2 0.5 CA A:SER24 4.7 14.7 1.0 HB3 A:GLN121 4.8 31.3 0.5 CA A:LEU25 4.9 13.1 1.0 HB3 A:GLN121 4.9 30.2 0.5 C A:GLN121 4.9 19.2 0.5 C A:GLN121 4.9 19.4 0.5 C A:GLY26 4.9 11.8 1.0 HG21 A:VAL120 4.9 24.9 1.0 O A:SER24 5.0 13.6 1.0

Iodine binding site 3 out of 3 in the High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:25.7 occ:0.14 O A:HOH338 3.5 30.6 1.0 HD3 A:ARG14 3.6 33.1 0.5 HB1 A:ALA10 3.6 20.8 1.0 HE A:ARG14 3.7 35.9 0.5 HA A:ALA11 3.8 18.0 1.0 HD3 A:ARG14 3.9 35.2 0.5 HB3 A:ALA10 4.0 20.8 1.0 O A:HOH350 4.2 35.5 1.0 HB2 A:ARG14 4.2 25.9 0.5 HB2 A:ARG14 4.2 26.8 0.5 CB A:ALA10 4.3 17.3 1.0 NE A:ARG14 4.3 29.9 0.5 O A:ALA10 4.3 16.2 1.0 C A:ALA10 4.3 14.9 1.0 CD A:ARG14 4.4 27.6 0.5 N A:ALA11 4.4 14.5 1.0 HD2 A:ARG14 4.4 35.2 0.5 CA A:ALA11 4.5 15.0 1.0 HB2 A:ALA11 4.6 19.9 1.0 CD A:ARG14 4.6 29.3 0.5 HB3 A:ARG14 4.6 25.9 0.5 HB3 A:ARG14 4.7 26.8 0.5 H A:ALA11 4.8 17.4 1.0 CB A:ARG14 4.9 21.6 0.5 CB A:ARG14 4.9 22.4 0.5 CA A:ALA10 5.0 15.2 1.0 HD2 A:ARG14 5.0 33.1 0.5

D.R.Hekstra, H.K.Wang. Bayesian Priors For Comparative Crystallography To Be Published.