Iodine in PDB 7sky: Pertussis Toxin S1 Bound to Nad+

All present enzymatic activity of Pertussis Toxin S1 Bound to Nad+:
2.4.2.30;

The structure of Pertussis Toxin S1 Bound to Nad+, PDB code: 7sky was solved by D.R.Littler, T.Beddoe, A.Pulliainen, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.60 / 1.37
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	34.6, 68.25, 71.67, 90.73, 90.27, 91.45
R / Rfree (%)	20.2 / 22.4

The binding sites of Iodine atom in the Pertussis Toxin S1 Bound to Nad+ (pdb code 7sky). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Pertussis Toxin S1 Bound to Nad+, PDB code: 7sky:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Pertussis Toxin S1 Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Pertussis Toxin S1 Bound to Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:57.8 occ:1.00 CD2 B:LEU131 2.6 16.9 1.0 O2D B:NAD202 3.4 15.7 1.0 OE1 B:GLU129 3.5 13.6 1.0 CB B:SER52 3.6 8.8 1.0 OG B:SER52 3.7 11.4 1.0 CB B:GLU129 3.7 9.6 1.0 CG B:LEU131 3.7 14.4 1.0 C6N B:NAD202 3.8 8.4 1.0 O B:TYR130 3.8 9.2 1.0 CA B:SER52 3.9 8.0 1.0 CD2 B:LEU36 3.9 12.0 1.0 NE2 B:HIS35 4.0 11.4 1.0 C5N B:NAD202 4.1 8.4 1.0 C B:TYR130 4.1 9.8 1.0 O B:THR53 4.1 7.6 1.0 N B:TYR130 4.2 6.5 1.0 N B:THR53 4.3 5.7 1.0 C2D B:NAD202 4.3 14.1 1.0 CD2 B:HIS35 4.3 12.4 1.0 CB B:ALA100 4.4 9.4 1.0 CD B:GLU129 4.4 10.8 1.0 N B:LEU131 4.5 8.8 1.0 CG B:GLU129 4.5 10.7 1.0 N1N B:NAD202 4.5 8.8 1.0 C B:GLU129 4.6 7.4 1.0 CA B:GLU129 4.6 8.0 1.0 CA B:LEU131 4.6 8.9 1.0 C B:SER52 4.6 5.9 1.0 CA B:TYR130 4.7 8.1 1.0 CB B:LEU131 4.7 14.6 1.0 CD1 B:LEU131 4.8 16.5 1.0 C1D B:NAD202 4.8 12.1 1.0 O B:HOH350 5.0 13.0 1.0

Iodine binding site 2 out of 4 in the Pertussis Toxin S1 Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Pertussis Toxin S1 Bound to Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:9.8 occ:1.00 CD2 A:LEU131 3.4 22.7 1.0 O2D A:NAD202 3.4 11.6 1.0 OE1 A:GLU129 3.7 15.7 1.0 CB A:SER52 3.8 6.2 1.0 NE2 A:HIS35 3.8 9.5 1.0 C6N A:NAD202 3.8 8.1 1.0 CA A:SER52 3.9 4.9 1.0 OG A:SER52 3.9 7.4 1.0 O A:TYR130 3.9 9.6 1.0 CD2 A:LEU36 4.0 11.1 1.0 CB A:GLU129 4.0 10.9 1.0 C A:TYR130 4.1 7.7 1.0 CD2 A:HIS35 4.1 8.3 1.0 C5N A:NAD202 4.1 10.2 1.0 O A:THR53 4.2 8.6 1.0 N A:THR53 4.2 7.1 1.0 N A:LEU131 4.2 7.9 1.0 C2D A:NAD202 4.3 8.6 1.0 N A:TYR130 4.3 9.1 1.0 CA A:LEU131 4.4 9.3 1.0 CG A:LEU131 4.4 18.7 1.0 N1N A:NAD202 4.5 7.4 1.0 C A:SER52 4.6 7.4 1.0 CB A:ALA100 4.6 13.1 1.0 CD A:GLU129 4.6 15.9 1.0 CG A:GLU129 4.7 13.9 1.0 CB A:LEU131 4.7 14.5 1.0 C A:GLU129 4.8 9.9 1.0 CA A:TYR130 4.8 8.7 1.0 CA A:GLU129 4.9 10.7 1.0 C1D A:NAD202 4.9 7.3 1.0

Iodine binding site 3 out of 4 in the Pertussis Toxin S1 Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Pertussis Toxin S1 Bound to Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ C:I201 b:10.5 occ:1.00 O2D C:NAD202 3.5 13.1 1.0 OE1 C:GLU129 3.7 16.1 1.0 NE2 C:HIS35 3.8 10.2 1.0 CB C:SER52 3.8 9.1 1.0 C6N C:NAD202 3.8 7.8 1.0 O C:TYR130 3.9 9.7 1.0 CA C:SER52 3.9 8.6 1.0 OG C:SER52 3.9 8.9 1.0 CD2 C:LEU36 3.9 10.0 1.0 CB C:GLU129 3.9 12.4 1.0 CG C:LEU131 4.0 15.6 1.0 C5N C:NAD202 4.0 11.2 1.0 CD2 C:HIS35 4.1 11.9 1.0 C C:TYR130 4.1 9.0 1.0 O C:THR53 4.2 8.8 1.0 N C:THR53 4.2 8.4 1.0 C2D C:NAD202 4.3 10.9 1.0 N C:LEU131 4.3 8.8 1.0 N C:TYR130 4.3 7.6 1.0 CA C:LEU131 4.4 8.9 1.0 CD1 C:LEU131 4.5 20.7 1.0 CG C:GLU129 4.6 11.3 1.0 CD C:GLU129 4.6 14.1 1.0 C C:SER52 4.6 8.0 1.0 CB C:ALA100 4.6 12.2 1.0 N1N C:NAD202 4.7 7.4 1.0 CB C:LEU131 4.7 14.0 1.0 C C:GLU129 4.7 7.8 1.0 CA C:GLU129 4.8 8.0 1.0 CA C:TYR130 4.8 7.2 1.0 C1D C:NAD202 4.9 9.5 1.0

Iodine binding site 4 out of 4 in the Pertussis Toxin S1 Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Pertussis Toxin S1 Bound to Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ D:I201 b:13.8 occ:1.00 O2D D:NAD202 3.4 19.3 1.0 NE2 D:HIS35 3.7 10.4 1.0 CB D:SER52 3.7 7.7 1.0 OE1 D:GLU129 3.8 21.8 1.0 C6N D:NAD202 3.8 12.1 1.0 OG D:SER52 3.8 10.6 1.0 CA D:SER52 3.9 8.5 1.0 CB D:GLU129 3.9 14.4 1.0 O D:TYR130 4.0 10.1 1.0 C5N D:NAD202 4.1 13.4 1.0 CD2 D:HIS35 4.1 14.4 1.0 CG D:LEU131 4.1 14.9 1.0 C2D D:NAD202 4.1 16.9 1.0 C D:TYR130 4.2 9.9 1.0 CD2 D:LEU36 4.2 16.6 1.0 O D:THR53 4.3 9.6 1.0 N D:THR53 4.3 7.3 1.0 CD1 D:LEU131 4.3 18.5 1.0 N D:TYR130 4.3 9.1 1.0 N D:LEU131 4.4 11.8 1.0 CA D:LEU131 4.5 11.4 1.0 CB D:ALA100 4.6 11.5 1.0 N1N D:NAD202 4.6 10.0 1.0 C D:SER52 4.6 8.2 1.0 CD D:GLU129 4.7 18.6 1.0 CG D:GLU129 4.7 16.9 1.0 C D:GLU129 4.7 9.7 1.0 CB D:LEU131 4.8 13.4 1.0 CA D:GLU129 4.8 10.9 1.0 CA D:TYR130 4.8 9.9 1.0 CE1 D:HIS35 4.9 9.9 1.0 C1D D:NAD202 4.9 12.9 1.0

M.Sakari, M.T.Tran, J.Rossjohn, A.T.Pulliainen, T.Beddoe, D.R.Littler. Crystal Structures of Pertussis Toxin with Nad + and Analogs Provide Structural Insights Into the Mechanism of Its Cytosolic Adp-Ribosylation Activity. J.Biol.Chem. V. 298 01892 2022.
ISSN: ESSN 1083-351X
PubMed: 35378130
DOI: 10.1016/J.JBC.2022.101892