Iodine in PDB 6mry: NOD173 Plant Defensin

The structure of NOD173 Plant Defensin, PDB code: 6mry was solved by S.Caria, M.Kvansakul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.37 / 2.30
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.107, 69.318, 107.662, 90.00, 108.08, 90.00
R / Rfree (%)	18.9 / 23.2

The structure of NOD173 Plant Defensin also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the NOD173 Plant Defensin (pdb code 6mry). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the NOD173 Plant Defensin, PDB code: 6mry:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ C:I101 b:81.3 occ:1.00 I3 C:I3C101 0.0 81.3 1.0 C6 C:I3C101 2.1 72.4 1.0 C1 C:I3C101 3.0 70.3 1.0 C5 C:I3C101 3.1 64.8 1.0 C7 C:I3C101 3.2 52.7 1.0 N13 C:I3C101 3.3 40.8 1.0 CZ C:PHE30 3.3 30.1 1.0 CE2 C:PHE30 3.5 30.6 1.0 CE1 C:PHE30 3.6 22.1 1.0 O9 C:I3C101 3.6 45.4 1.0 O8 C:I3C101 3.7 53.5 1.0 O C:GLU28 3.9 44.4 1.0 CD2 C:PHE30 4.0 22.9 1.0 CD1 C:PHE30 4.1 25.2 1.0 O C:LYS29 4.2 43.6 1.0 CG C:PHE30 4.2 32.8 1.0 CB J:CYS48 4.3 55.4 1.0 CD C:LYS46 4.4 56.9 1.0 C2 C:I3C101 4.4 97.7 1.0 C4 C:I3C101 4.4 0.3 1.0 C C:LYS29 4.6 42.7 1.0 CE C:LYS46 4.8 58.7 1.0 CG J:ARG2 4.9 42.4 1.0 C3 C:I3C101 4.9 81.5 1.0 SG J:CYS48 4.9 53.3 1.0 N C:PHE30 5.0 41.3 1.0

Iodine binding site 2 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ C:I101 b:0.8 occ:1.00 I2 C:I3C101 0.0 0.8 1.0 C4 C:I3C101 2.1 0.3 1.0 C5 C:I3C101 3.0 64.8 1.0 C3 C:I3C101 3.1 81.5 1.0 N13 C:I3C101 3.2 40.8 1.0 C10 C:I3C101 3.3 61.2 1.0 O12 C:I3C101 3.6 58.1 1.0 O11 C:I3C101 3.9 62.0 1.0 C6 C:I3C101 4.4 72.4 1.0 C2 C:I3C101 4.4 97.7 1.0 C1 C:I3C101 4.9 70.3 1.0 CB C:LYS29 5.0 45.4 1.0

Iodine binding site 3 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ C:I101 b:1.0 occ:1.00 I1 C:I3C101 0.0 1.0 1.0 C2 C:I3C101 2.1 97.7 1.0 C1 C:I3C101 3.1 70.3 1.0 C3 C:I3C101 3.1 81.5 1.0 C7 C:I3C101 3.2 52.7 1.0 C10 C:I3C101 3.3 61.2 1.0 O11 C:I3C101 3.6 62.0 1.0 O8 C:I3C101 3.6 53.5 1.0 O9 C:I3C101 3.7 45.4 1.0 NH1 J:ARG47 3.9 88.4 1.0 O12 C:I3C101 3.9 58.1 1.0 N J:ALA1 3.9 64.9 1.0 C6 C:I3C101 4.4 72.4 1.0 C4 C:I3C101 4.4 0.3 1.0 C5 C:I3C101 4.9 64.8 1.0

Iodine binding site 4 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ F:I101 b:53.9 occ:1.00 I3 F:I3C101 0.0 53.9 1.0 C6 F:I3C101 2.1 45.8 1.0 C1 F:I3C101 3.0 38.4 1.0 C5 F:I3C101 3.1 36.8 1.0 O F:GLN3 3.1 46.4 1.0 C7 F:I3C101 3.2 35.7 1.0 N13 F:I3C101 3.2 34.6 1.0 CD F:LYS5 3.5 35.3 1.0 O9 F:I3C101 3.6 46.3 1.0 C F:GLN3 3.6 42.9 1.0 O8 F:I3C101 3.6 47.6 1.0 CG F:LYS5 3.7 44.9 1.0 CB F:GLN3 3.8 50.2 1.0 N F:CYS4 4.1 42.3 1.0 CA F:CYS4 4.3 46.7 1.0 C2 F:I3C101 4.3 47.5 1.0 CA F:GLN3 4.3 52.7 1.0 C4 F:I3C101 4.4 52.9 1.0 C F:CYS4 4.4 48.4 1.0 CB I:ALA6 4.5 33.8 1.0 N F:LYS5 4.6 38.4 1.0 CA I:ALA6 4.8 37.7 1.0 C3 F:I3C101 4.9 29.4 1.0 CB F:LYS5 4.9 35.0 1.0 O F:HOH203 4.9 44.0 1.0 O I:LYS5 4.9 47.0 1.0 O F:CYS4 4.9 48.0 1.0 CE F:LYS5 5.0 44.5 1.0

Iodine binding site 5 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ F:I101 b:75.4 occ:1.00 I2 F:I3C101 0.0 75.4 1.0 C4 F:I3C101 2.1 52.9 1.0 C3 F:I3C101 3.1 29.4 1.0 C5 F:I3C101 3.1 36.8 1.0 C10 F:I3C101 3.2 21.5 1.0 N13 F:I3C101 3.3 34.6 1.0 O12 F:I3C101 3.6 45.3 1.0 NE2 F:HIS34 3.6 29.8 1.0 CE1 F:HIS34 3.7 27.3 1.0 CD2 F:HIS34 3.7 26.3 1.0 O11 F:I3C101 3.8 30.1 1.0 ND1 F:HIS34 3.9 30.1 1.0 CG F:HIS34 3.9 23.5 1.0 C2 F:I3C101 4.4 47.5 1.0 C6 F:I3C101 4.4 45.8 1.0 CB F:HIS34 4.8 27.8 1.0 C1 F:I3C101 4.9 38.4 1.0

Iodine binding site 6 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ F:I101 b:55.1 occ:1.00 I1 F:I3C101 0.0 55.1 1.0 C2 F:I3C101 2.1 47.5 1.0 CE H:LYS37 2.4 63.0 1.0 C3 F:I3C101 3.0 29.4 1.0 NZ H:LYS37 3.0 72.2 1.0 C1 F:I3C101 3.1 38.4 1.0 C10 F:I3C101 3.2 21.5 1.0 C7 F:I3C101 3.3 35.7 1.0 O11 F:I3C101 3.5 30.1 1.0 OE1 I:GLU7 3.5 38.1 1.0 CD I:GLU7 3.6 33.1 1.0 CD H:LYS37 3.7 40.6 1.0 O8 F:I3C101 3.7 47.6 1.0 O I:HOH201 3.7 36.2 1.0 OE2 I:GLU7 3.7 35.9 1.0 O12 F:I3C101 3.7 45.3 1.0 O9 F:I3C101 3.8 46.3 1.0 CG H:LYS37 4.2 37.5 1.0 CG I:GLU7 4.3 36.2 1.0 CB H:LYS37 4.3 33.8 1.0 C4 F:I3C101 4.3 52.9 1.0 C6 F:I3C101 4.4 45.8 1.0 NZ F:LYS5 4.4 36.8 1.0 CB I:GLU7 4.6 37.0 1.0 OA2 I:FLC102 4.8 68.5 1.0 C5 F:I3C101 4.9 36.8 1.0 O I:HOH202 5.0 35.5 1.0

Iodine binding site 7 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ G:I101 b:48.8 occ:1.00 I3 G:I3C101 0.0 48.8 1.0 C6 G:I3C101 2.1 41.5 1.0 C1 G:I3C101 3.1 34.7 1.0 C5 G:I3C101 3.1 31.4 1.0 N13 G:I3C101 3.2 16.5 1.0 O G:LYS29 3.3 30.2 1.0 C7 G:I3C101 3.3 33.1 1.0 O G:HOH216 3.7 45.8 1.0 O8 G:I3C101 3.7 43.4 1.0 O9 G:I3C101 3.9 49.4 1.0 CE G:LYS46 3.9 44.0 1.0 CG2 G:THR31 4.0 21.6 1.0 C G:LYS29 4.2 39.4 1.0 C2 G:I3C101 4.4 38.7 1.0 C4 G:I3C101 4.4 68.2 1.0 CA G:PHE30 4.4 30.6 1.0 N G:THR31 4.5 26.4 1.0 C G:PHE30 4.5 30.1 1.0 CB G:LYS46 4.5 26.9 1.0 NZ G:LYS46 4.6 58.1 1.0 N G:PHE30 4.7 39.5 1.0 O G:HOH201 4.8 49.2 1.0 C3 G:I3C101 4.9 40.3 1.0

Iodine binding site 8 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ G:I101 b:0.6 occ:1.00 I2 G:I3C101 0.0 0.6 1.0 C4 G:I3C101 2.1 68.2 1.0 C3 G:I3C101 3.0 40.3 1.0 C5 G:I3C101 3.1 31.4 1.0 C10 G:I3C101 3.2 35.0 1.0 N13 G:I3C101 3.3 16.5 1.0 O G:HOH212 3.5 26.9 1.0 O12 G:I3C101 3.6 33.0 1.0 O11 G:I3C101 3.7 38.2 1.0 C2 G:I3C101 4.3 38.7 1.0 C6 G:I3C101 4.4 41.5 1.0 C1 G:I3C101 4.9 34.7 1.0

Iodine binding site 9 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ G:I101 b:49.1 occ:1.00 I1 G:I3C101 0.0 49.1 1.0 C2 G:I3C101 2.1 38.7 1.0 C3 G:I3C101 3.0 40.3 1.0 C1 G:I3C101 3.1 34.7 1.0 C10 G:I3C101 3.2 35.0 1.0 C7 G:I3C101 3.2 33.1 1.0 O9 G:I3C101 3.6 49.4 1.0 O11 G:I3C101 3.6 38.2 1.0 CZ G:ARG47 3.6 50.8 1.0 NE G:ARG47 3.6 51.6 1.0 O12 G:I3C101 3.6 33.0 1.0 O8 G:I3C101 3.7 43.4 1.0 NH1 G:ARG47 3.7 49.5 1.0 O G:HOH201 4.1 49.2 1.0 NH2 G:ARG47 4.1 48.7 1.0 O G:HOH209 4.2 46.9 1.0 CD G:ARG47 4.2 51.7 1.0 CB G:ARG47 4.2 35.7 1.0 C4 G:I3C101 4.3 68.2 1.0 C6 G:I3C101 4.4 41.5 1.0 C5 G:I3C101 4.9 31.4 1.0 CG G:ARG47 4.9 44.4 1.0

Iodine binding site 10 out of 15 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of NOD173 Plant Defensin within 5.0Å range: probe atom residue distance (Å) B Occ H:I101 b:0.6 occ:1.00 I3 H:I3C101 0.0 0.6 1.0 C6 H:I3C101 2.1 76.0 1.0 C1 H:I3C101 3.1 55.7 1.0 C5 H:I3C101 3.1 51.7 1.0 C7 H:I3C101 3.2 47.6 1.0 N13 H:I3C101 3.4 54.2 1.0 NE2 H:HIS34 3.5 42.3 1.0 O8 H:I3C101 3.5 64.2 1.0 CE1 H:HIS34 3.6 41.4 1.0 O9 H:I3C101 3.8 47.7 1.0 CD2 H:HIS34 3.8 38.6 1.0 ND1 H:HIS34 3.9 42.4 1.0 CG H:HIS34 4.1 40.0 1.0 C4 H:I3C101 4.4 58.5 1.0 C2 H:I3C101 4.4 64.3 1.0 C3 H:I3C101 4.9 48.1 1.0

F.T.Lay, G.F.Ryan, S.Caria, T.K.Phan, P.K.Veneer, J.A.White, M.Kvansakul, M.D.Hulett. Structural and Functional Characterization of the Membrane-Permeabilizing Activity Ofnicotiana Occidentalisdefensin NOD173 and Protein Engineering to Enhance Oncolysis. Faseb J. V. 33 6470 2019.
ISSN: ESSN 1530-6860
PubMed: 30794440
DOI: 10.1096/FJ.201802540R