Iodine in PDB 7rb4: Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila

The structure of Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila, PDB code: 7rb4 was solved by S.N.Sugiman-Marangos, S.K.Gill, R.A.Melnyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.29 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.653, 82.456, 91.815, 90, 90, 90
R / Rfree (%)	20.1 / 22.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila (pdb code 7rb4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 26 binding sites of Iodine where determined in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila, PDB code: 7rb4:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


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 Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I701 b:27.3 occ:0.63 OG1 A:THR512 3.4 25.2 1.0 O A:HOH1032 3.4 39.6 1.0 N A:THR512 3.8 25.1 1.0 O A:HOH974 3.8 41.4 1.0 CA A:GLN511 4.0 31.5 1.0 CG A:PRO494 4.1 18.9 1.0 C A:GLN511 4.1 31.7 1.0 CD2 A:LEU492 4.1 20.5 1.0 O A:LYS510 4.1 24.3 1.0 CB A:THR512 4.2 25.7 1.0 OD1 A:ASN79 4.2 30.6 1.0 N A:GLN511 4.4 30.3 1.0 CB A:PRO494 4.4 18.3 1.0 CD A:PRO494 4.4 18.9 1.0 C A:LYS510 4.4 23.9 1.0 O A:HOH936 4.5 28.5 1.0 CA A:THR512 4.6 25.4 1.0 CB A:LEU492 4.7 21.6 1.0 O A:HOH975 4.9 22.0 1.0 O A:GLN511 4.9 31.4 1.0 CG A:LEU492 5.0 21.0 1.0

Iodine binding site 2 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


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 Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I702 b:40.4 occ:0.62 CG2 A:VAL395 3.7 63.2 1.0 N A:ILE400 3.8 26.1 1.0 N A:VAL395 3.9 63.7 1.0 CA A:ILE400 4.0 25.9 1.0 CB A:ILE400 4.1 26.6 1.0 CB A:LEU399 4.1 24.8 1.0 C A:LEU399 4.1 24.7 1.0 CA A:VAL394 4.2 51.4 1.0 CB A:VAL394 4.4 51.1 1.0 O A:LEU399 4.5 23.6 1.0 C A:VAL394 4.5 52.2 1.0 O A:GLY396 4.6 32.6 1.0 CG1 A:VAL394 4.7 50.4 1.0 CA A:LEU399 4.8 25.2 1.0 N A:GLY396 4.8 34.6 1.0 CB A:VAL395 4.8 64.0 1.0 CA A:VAL395 4.9 64.1 1.0 O A:ASP393 4.9 76.4 1.0 CG1 A:ILE400 5.0 26.4 1.0

Iodine binding site 3 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


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 Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I703 b:45.5 occ:0.46 O A:HOH805 3.2 41.8 1.0 OH A:TYR74 3.3 45.9 1.0 NH1 A:ARG174 3.3 27.1 1.0 O A:HOH993 3.7 32.6 1.0 NE1 A:TRP498 3.8 25.0 1.0 CE2 A:TYR74 4.0 44.9 1.0 O A:HOH953 4.0 36.0 1.0 CD A:ARG174 4.0 27.2 1.0 CZ A:TYR74 4.1 45.2 1.0 CB A:HIS70 4.3 24.4 1.0 CG2 A:VAL505 4.3 23.1 1.0 CZ A:ARG174 4.4 27.4 1.0 ND1 A:HIS70 4.4 25.3 1.0 CG A:ARG174 4.4 27.7 1.0 CG A:HIS70 4.5 25.0 1.0 CE2 A:TRP498 4.6 24.7 1.0 NE A:ARG174 4.6 27.2 1.0 OE2 A:GLU176 4.6 25.3 1.0 O A:HOH1047 4.7 25.6 1.0 CB A:ALA65 4.7 18.2 1.0 CD1 A:TRP498 4.7 25.1 1.0 CZ2 A:TRP498 4.7 24.5 1.0 CD A:GLU176 4.9 25.4 1.0

Iodine binding site 4 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


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 Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I704 b:50.0 occ:0.51 N A:LYS199 3.4 47.2 1.0 CD1 A:LEU214 3.7 34.5 1.0 CB A:LYS199 3.9 49.1 1.0 N A:GLY200 4.0 40.6 1.0 CA A:LYS199 4.0 48.5 1.0 CD1 A:LEU218 4.2 33.6 1.0 C A:LYS199 4.2 49.6 1.0 O A:TRP197 4.2 28.4 1.0 C A:TYR198 4.4 31.5 1.0 CG A:LYS199 4.5 48.9 1.0 CA A:TYR198 4.5 30.3 1.0 CD2 A:LEU218 4.5 33.8 1.0 CD1 A:TYR198 4.6 30.4 1.0 CG A:LEU214 4.6 34.0 1.0 CA A:GLY200 4.7 41.5 1.0 CD2 A:LEU214 4.7 34.0 1.0 CG A:LEU218 4.7 33.7 1.0 O A:LYS199 5.0 50.6 1.0

Iodine binding site 5 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


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 Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I705 b:64.4 occ:0.49 O A:HOH1018 3.2 39.5 1.0 NE A:ARG119 3.4 39.6 1.0 CD A:ARG119 3.6 39.6 1.0 CG A:ARG116 3.7 40.9 1.0 I A:IOD715 3.7 60.6 0.4 O A:LEU132 3.8 31.4 1.0 CA A:ASN133 3.9 36.1 1.0 CB A:ASN133 4.0 36.3 1.0 CA A:ARG116 4.2 39.1 1.0 N A:ARG116 4.2 38.7 1.0 CG A:ARG119 4.3 39.1 1.0 C A:TYR115 4.4 32.5 1.0 O A:TYR115 4.4 32.6 1.0 CB A:ARG116 4.6 39.8 1.0 CB A:ALA129 4.6 30.2 1.0 CZ A:ARG119 4.6 39.6 1.0 CB A:TYR115 4.7 32.6 1.0 C A:LEU132 4.7 31.7 1.0 CD2 A:TYR115 4.7 32.9 1.0 CA A:ALA129 4.8 29.9 1.0 N A:ASN133 4.8 36.0 1.0 C A:ASN133 4.8 36.1 1.0 CD A:ARG116 4.8 41.5 1.0 N A:GLU134 5.0 59.8 1.0

Iodine binding site 6 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


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 Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I706 b:48.6 occ:0.36 O A:HOH1185 3.2 32.1 1.0 OE1 A:GLU271 3.3 54.4 1.0 CD A:GLU271 3.6 52.8 1.0 NE2 A:GLN267 3.6 40.4 1.0 OE2 A:GLU271 3.7 52.5 1.0 CA A:ILE268 4.1 36.9 1.0 CD1 A:LEU303 4.2 34.1 1.0 CG A:GLN267 4.2 39.2 1.0 CE1 A:HIS272 4.2 33.0 1.0 CG1 A:ILE268 4.2 38.6 1.0 CD A:GLN267 4.3 39.8 1.0 CB A:ILE268 4.4 37.5 1.0 CG A:GLU271 4.4 51.5 1.0 CB A:GLU271 4.5 50.4 1.0 N A:ILE268 4.6 36.1 1.0 O A:GLN267 4.6 37.9 1.0 C A:GLN267 4.8 37.8 1.0 CD1 A:ILE268 5.0 38.7 1.0 ND1 A:HIS272 5.0 32.7 1.0 CD2 A:LEU303 5.0 35.5 1.0

Iodine binding site 7 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I707 b:87.4 occ:0.39 CZ A:ARG263 3.5 36.5 1.0 NE A:ARG263 3.5 35.8 1.0 NH2 A:ARG263 3.8 36.8 1.0 NH1 A:ARG263 3.8 36.9 1.0 I A:IOD726 3.9 49.4 0.3 CD A:ARG263 4.0 35.4 1.0 OE1 A:GLU260 4.3 41.2 1.0 O A:HOH977 4.9 37.3 1.0 OE2 A:GLU260 4.9 41.5 1.0 CD A:GLU260 5.0 40.6 1.0

Iodine binding site 8 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I708 b:64.1 occ:0.44 CD A:PRO273 3.7 47.8 1.0 N A:GLU274 3.9 60.5 1.0 CB A:GLU274 3.9 60.6 1.0 N A:PRO273 4.0 45.3 1.0 CB A:HIS272 4.0 34.2 1.0 CA A:HIS272 4.0 35.8 1.0 C A:HIS272 4.2 36.6 1.0 OE1 A:GLU274 4.2 61.6 1.0 CD2 A:HIS272 4.3 35.1 1.0 OH A:TYR296 4.4 32.9 1.0 CG A:HIS272 4.5 34.0 1.0 CA A:GLU274 4.6 60.2 1.0 CG A:PRO273 4.8 50.5 1.0 C A:PRO273 4.9 46.6 1.0 CA A:PRO273 4.9 46.8 1.0

Iodine binding site 9 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I709 b:60.9 occ:0.43 CE A:LYS130 3.6 50.5 1.0 O A:HOH987 3.6 50.7 1.0 NZ A:LYS130 3.7 50.8 1.0 CD A:LYS130 4.6 49.4 1.0 CG A:LYS130 4.6 48.0 1.0

Iodine binding site 10 out of 26 in the Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Peptono Toxin, A Diphtheria Toxin Homolog, From Seinonella Peptonophila within 5.0Å range: probe atom residue distance (Å) B Occ A:I710 b:85.7 occ:0.49 O A:HOH1087 3.3 49.0 1.0 O A:ASN334 3.4 86.4 1.0 N A:ASN334 3.5 88.3 1.0 O A:GLY337 3.6 70.9 1.0 CB A:SER574 3.7 73.3 1.0 OG A:SER574 3.7 74.5 1.0 CB A:LYS333 3.8 72.3 1.0 CA A:LYS333 3.9 75.2 1.0 C A:GLY337 4.0 71.4 1.0 CG A:LYS333 4.0 71.4 1.0 C A:LYS333 4.2 76.9 1.0 C A:ASN334 4.3 88.1 1.0 CA A:ASN334 4.3 90.2 1.0 CB A:LEU338 4.3 53.7 1.0 N A:LEU338 4.4 56.0 1.0 CD A:LYS333 4.4 70.0 1.0 CA A:LEU338 4.4 54.7 1.0 CG A:LEU338 4.6 52.7 1.0 CD1 A:LEU338 4.6 52.5 1.0 CB A:ASN334 4.6 93.9 1.0 CA A:GLY337 4.7 75.2 1.0

S.N.Sugiman-Marangos, S.K.Gill, M.J.Mansfield, K.E.Orrell, A.C.Doxey, R.A.Melnyk. Structures of Distant Diphtheria Toxin Homologs Reveal Functional Determinants of An Evolutionarily Conserved Toxin Scaffold. Commun Biol V. 5 375 2022.
ISSN: ESSN 2399-3642
PubMed: 35440624
DOI: 10.1038/S42003-022-03333-9