Iodine in PDB 4tjv: Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1

The structure of Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1, PDB code: 4tjv was solved by F.Luo, Y.H.Fong, L.W.Jiang, K.B.Wong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.78 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.600, 62.680, 35.810, 90.00, 109.39, 90.00
R / Rfree (%)	16.6 / 19

The binding sites of Iodine atom in the Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1 (pdb code 4tjv). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1, PDB code: 4tjv:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:26.6 occ:0.86 N A:LYS64 3.7 15.5 1.0 O A:HOH311 3.8 43.2 1.0 CA A:PRO63 4.0 13.9 1.0 O A:HOH404 4.0 25.9 0.9 CG A:LYS64 4.1 25.2 1.0 CG2 A:ILE78 4.1 16.1 1.0 O A:HOH344 4.2 22.0 1.0 CG1 A:ILE78 4.2 13.7 1.0 CD1 A:ILE78 4.3 15.5 1.0 CB A:LYS64 4.3 18.8 1.0 C A:PRO63 4.4 11.6 1.0 CB A:PRO63 4.6 13.8 1.0 CD A:LYS64 4.6 24.6 1.0 CA A:LYS64 4.6 16.7 1.0 CG1 A:VAL61 4.8 19.2 1.0 CB A:ILE78 4.8 14.8 1.0

Iodine binding site 2 out of 6 in the Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:48.7 occ:0.41 N A:HIS181 3.3 17.6 1.0 ND2 A:ASN26 3.4 37.4 1.0 CB A:ASN26 3.5 26.0 1.0 CA A:PRO180 3.7 17.6 1.0 O A:HIS181 3.8 19.7 1.0 CB A:PRO180 3.9 19.9 1.0 CG A:ASN26 3.9 39.8 1.0 C A:PRO180 4.0 15.7 1.0 CA A:HIS181 4.3 17.3 1.0 C A:HIS181 4.5 17.4 1.0 CB A:HIS181 4.6 17.2 1.0 CA A:ASN26 4.9 24.6 1.0 CG A:HIS181 4.9 23.7 1.0 ND1 A:HIS181 5.0 27.9 1.0

Iodine binding site 3 out of 6 in the Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:35.0 occ:0.33 O A:HOH415 3.0 24.1 0.7 O A:HOH422 3.0 23.1 0.8 OG1 A:THR152 3.2 13.0 1.0 O A:HOH378 3.3 12.4 1.0 CG A:GLU41 3.7 25.5 1.0 CG2 A:THR152 3.8 14.2 1.0 OE1 A:GLU41 3.8 39.3 1.0 CD2 A:TYR40 3.9 16.6 1.0 CB A:THR152 4.1 11.8 1.0 CD A:GLU41 4.3 39.3 1.0 CB A:TYR40 4.4 14.2 1.0 N A:GLU41 4.4 13.9 1.0 CB A:LEU155 4.5 12.7 1.0 CG A:TYR40 4.6 14.2 1.0 O A:GLU41 4.6 15.5 1.0 CE2 A:TYR40 4.8 18.9 1.0 N A:LEU155 4.9 12.9 1.0 CB A:GLU41 4.9 18.2 1.0 CA A:TYR40 4.9 13.8 1.0

Iodine binding site 4 out of 6 in the Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:51.3 occ:0.53 O A:HOH359 3.2 30.4 1.0 O A:HOH369 3.8 36.3 1.0 O A:HOH401 3.9 31.5 1.0

Iodine binding site 5 out of 6 in the Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:63.9 occ:0.35 O A:HOH398 3.2 35.3 1.0 N A:GLU177 3.5 21.4 1.0 N A:GLY53 3.8 27.6 1.0 CA A:THR176 3.8 20.8 1.0 C A:TYR52 3.9 31.1 1.0 CA A:GLY53 4.1 22.1 1.0 O A:HOH306 4.1 17.4 1.0 O A:GLN51 4.1 57.6 1.0 O A:TRP175 4.1 28.5 1.0 CG2 A:THR176 4.2 20.9 1.0 CG A:GLU177 4.2 42.1 1.0 C A:THR176 4.2 21.4 1.0 O A:TYR52 4.3 35.6 1.0 CA A:TYR52 4.3 36.4 1.0 CB A:GLU177 4.3 28.7 1.0 OE1 A:GLU177 4.5 58.9 1.0 CA A:GLU177 4.5 24.1 1.0 C A:GLN51 4.5 44.3 1.0 CB A:THR176 4.6 22.4 1.0 CD1 A:TRP175 4.6 24.5 1.0 N A:TYR52 4.7 34.1 1.0 CD A:GLU177 4.7 62.0 1.0 N A:THR176 4.7 19.9 1.0 C A:TRP175 4.8 23.9 1.0

Iodine binding site 6 out of 6 in the Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Protease-Associated Domain of Arabidopsis Vacuolar Sorting Receptor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:42.6 occ:0.36 O A:HOH344 3.1 22.0 1.0 O A:HOH323 3.4 25.9 0.8 O A:HOH343 4.0 37.9 0.9 CB A:SER79 4.0 19.1 1.0 N A:SER79 4.1 15.2 1.0 O A:ASP77 4.3 18.6 1.0 O A:SER79 4.4 18.0 1.0 CA A:SER79 4.6 13.8 1.0 C A:SER79 4.9 16.0 1.0 OG A:SER79 5.0 22.2 1.0 C A:ILE78 5.0 14.3 1.0

F.Luo, Y.H.Fong, Y.Zeng, J.Shen, L.Jiang, K.B.Wong. How Vacuolar Sorting Receptor Proteins Interact with Their Cargo Proteins: Crystal Structures of Apo and Cargo-Bound Forms of the Protease-Associated Domain From An Arabidopsis Vacuolar Sorting Receptor. Plant Cell V. 26 3693 2014.
ISSN: ESSN 1532-298X
PubMed: 25271241
DOI: 10.1105/TPC.114.129940