Iodine in PDB 6zgq: Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A

The structure of Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A, PDB code: 6zgq was solved by S.Hoffmann, H.D.Mootz, D.Kuemmel, R.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.96 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.504, 45.060, 46.281, 65.45, 77.51, 69.35
R / Rfree (%)	22.6 / 25.3

The binding sites of Iodine atom in the Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A (pdb code 6zgq). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A, PDB code: 6zgq:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:45.9 occ:1.00 O A:GLY148 3.3 10.3 1.0 CA A:ALA127 3.4 9.5 1.0 CB A:ALA127 3.4 9.5 1.0 N A:LEU128 3.5 9.2 1.0 CE1 A:HIS68 3.5 7.4 1.0 O A:GLU0 3.6 30.0 1.0 CZ A:PHE135 3.9 11.3 1.0 O A:LEU128 3.9 9.6 1.0 ND1 A:HIS68 3.9 7.6 1.0 N A:SER150 4.0 12.3 1.0 C A:ALA127 4.0 9.2 1.0 CE2 A:PHE135 4.0 11.1 1.0 CA A:ALA149 4.1 8.3 1.0 CD1 A:LEU2 4.1 13.7 1.0 C A:ALA149 4.2 9.8 1.0 CG A:LEU2 4.2 13.4 1.0 C A:GLY148 4.3 7.6 1.0 O A:HIS126 4.4 10.4 1.0 OG A:SER150 4.5 18.7 1.0 CA A:LEU128 4.6 9.1 1.0 N A:ALA127 4.6 9.6 1.0 N A:ALA149 4.7 8.4 1.0 C A:LEU128 4.7 9.7 1.0 CA A:ALA1 4.7 14.9 1.0 C A:GLU0 4.7 27.5 1.0 NE2 A:HIS68 4.8 7.5 1.0 CB A:SER150 4.8 16.9 1.0 CA A:SER150 4.9 15.1 1.0 N A:LEU2 4.9 13.4 1.0 C A:HIS126 5.0 9.7 1.0

Iodine binding site 2 out of 7 in the Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:58.5 occ:1.00 OG1 A:THR44 3.2 9.8 1.0 O A:HOH313 3.5 0.1 1.0 O A:THR44 3.5 11.9 1.0 C A:THR44 3.8 11.5 1.0 N A:LYS46 4.0 10.6 1.0 N A:GLN45 4.0 11.1 1.0 C A:GLN45 4.0 11.0 1.0 CB A:THR44 4.1 9.8 1.0 CA A:GLN45 4.1 11.3 1.0 CB A:LYS46 4.2 14.6 1.0 CA A:THR44 4.6 10.3 1.0 O A:GLN45 4.6 11.3 1.0 CA A:LYS46 4.7 11.7 1.0 CE A:LYS46 4.9 24.2 1.0 O A:HOH339 5.0 18.3 1.0

Iodine binding site 3 out of 7 in the Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:72.4 occ:1.00 O A:HOH378 3.5 81.2 1.0 CD A:LYS63 3.8 14.0 1.0 CB A:HIS54 3.9 8.2 1.0 ND1 A:HIS54 4.0 9.4 1.0 CG A:HIS54 4.0 8.8 1.0 CG1 A:ILE52 4.0 10.2 0.3 CE A:LYS63 4.1 15.0 1.0 CG2 A:ILE52 4.1 10.0 0.7 CG A:LYS63 4.3 11.4 1.0 CD1 A:ILE52 4.5 10.0 0.7 CD1 A:ILE52 4.6 9.9 0.3 O A:HOH341 4.7 0.9 1.0 CE1 A:HIS54 4.7 10.4 1.0 CD2 A:HIS54 4.8 9.3 1.0 CB A:LYS63 5.0 10.8 1.0 CG1 A:ILE52 5.0 9.7 0.7

Iodine binding site 4 out of 7 in the Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:30.3 occ:1.00 O B:GLU0 3.4 23.5 1.0 N B:LEU128 3.5 9.2 1.0 CA B:ALA127 3.5 8.8 1.0 O B:GLY148 3.6 11.4 1.0 CE1 B:HIS68 3.6 7.7 1.0 CB B:ALA127 3.7 8.2 1.0 N B:SER150 3.8 14.5 1.0 ND1 B:HIS68 3.9 8.0 1.0 O B:LEU128 3.9 10.2 1.0 C B:ALA127 4.1 8.7 1.0 CA B:ALA149 4.1 10.6 1.0 CZ B:PHE135 4.1 7.2 1.0 C B:ALA149 4.1 12.4 1.0 CG B:LEU2 4.2 11.5 1.0 CE2 B:PHE135 4.2 7.6 1.0 CD1 B:LEU2 4.3 11.6 1.0 O B:HIS126 4.5 9.0 1.0 CB B:SER150 4.5 18.8 1.0 CA B:ALA1 4.5 13.6 1.0 C B:GLU0 4.5 20.9 1.0 C B:GLY148 4.5 10.6 1.0 OG B:SER150 4.6 20.3 1.0 CA B:SER150 4.6 16.3 1.0 CA B:LEU128 4.6 9.1 1.0 C B:LEU128 4.7 9.6 1.0 N B:ALA127 4.8 8.7 1.0 C B:ALA1 4.8 11.9 1.0 N B:ALA149 4.8 10.1 1.0 NE2 B:HIS68 4.8 7.8 1.0 N B:LEU2 4.9 11.8 1.0 O B:ALA149 5.0 13.0 1.0 N B:ALA1 5.0 14.8 1.0

Iodine binding site 5 out of 7 in the Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A within 5.0Å range: probe atom residue distance (Å) B Occ B:I202 b:27.2 occ:1.00 O B:HOH303 2.8 19.8 1.0 O A:HOH322 3.1 18.9 1.0 CB B:LYS15 3.9 8.7 1.0 CB A:LYS15 4.0 9.1 1.0 O A:ASP14 4.1 10.1 1.0 O B:ASP14 4.1 9.9 1.0 CA B:LYS15 4.1 8.8 1.0 C B:ASP14 4.1 9.0 1.0 CA A:LYS15 4.2 9.1 1.0 C A:ASP14 4.2 9.6 1.0 CE B:LYS15 4.2 10.4 1.0 N B:ASP14 4.2 9.2 1.0 N B:LYS15 4.2 8.8 1.0 N A:ASP14 4.2 9.4 1.0 N A:LYS15 4.3 9.6 1.0 CG A:LYS15 4.4 9.4 1.0 C B:GLY13 4.4 9.1 1.0 C A:GLY13 4.4 9.7 1.0 CG B:LYS15 4.4 9.5 1.0 CA A:GLY13 4.4 9.6 1.0 CA B:GLY13 4.5 8.7 1.0 N A:GLY13 4.6 9.8 1.0 N B:GLY13 4.6 9.0 1.0 CD A:LYS15 4.7 10.3 1.0 OG1 B:THR10 4.8 10.2 1.0 CA B:ASP14 4.8 9.2 1.0 CD B:LYS15 4.8 10.5 1.0 C B:ALA12 4.9 10.1 1.0 CA A:ASP14 4.9 9.7 1.0 O B:GLY13 4.9 9.5 1.0 CB B:ALA12 4.9 11.1 1.0 OG1 A:THR10 4.9 8.8 1.0

Iodine binding site 6 out of 7 in the Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A within 5.0Å range: probe atom residue distance (Å) B Occ B:I203 b:52.0 occ:1.00 O B:HOH354 3.1 16.9 1.0 OG1 B:THR44 3.2 9.6 1.0 O B:THR44 3.6 11.0 1.0 C B:THR44 3.8 10.6 1.0 N B:GLN45 3.9 10.3 1.0 CB B:THR44 4.0 9.6 1.0 N B:LYS46 4.1 9.8 1.0 CA B:GLN45 4.1 10.8 1.0 C B:GLN45 4.1 10.5 1.0 CB B:LYS46 4.2 11.0 1.0 CA B:THR44 4.5 10.2 1.0 O B:HOH305 4.6 11.4 1.0 O B:GLN45 4.7 10.1 1.0 CA B:LYS46 4.8 10.1 1.0 O B:HOH319 4.8 17.3 1.0

Iodine binding site 7 out of 7 in the Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Acel Nrdhf Class 3 Split Intein Gsh Linked Splice Inactive Variant - C124A, N146A within 5.0Å range: probe atom residue distance (Å) B Occ B:I204 b:74.5 occ:1.00 O B:HOH366 2.8 29.9 1.0 O B:HOH302 3.6 23.5 1.0 CD B:LYS63 4.0 17.2 1.0 CB B:HIS54 4.1 10.3 1.0 CG2 B:ILE52 4.1 13.4 1.0 ND1 B:HIS54 4.1 10.9 1.0 CG B:HIS54 4.2 11.3 1.0 CE B:LYS63 4.3 19.8 1.0 CD1 B:ILE52 4.5 14.7 1.0 CG B:LYS63 4.5 13.8 1.0 NZ B:LYS63 4.8 22.9 1.0 CE1 B:HIS54 4.9 12.1 1.0 CG1 B:ILE52 5.0 13.6 1.0 CD2 B:HIS54 5.0 12.3 1.0

S.Hoffmann, T.M.E.Terhorst, R.K.Singh, D.Kummel, S.Pietrokovski, H.D.Mootz. Biochemical and Structural Characterization of An Unusual and Naturally Split Class 3 Intein. Chembiochem 2020.
ISSN: ESSN 1439-7633
PubMed: 32813312
DOI: 10.1002/CBIC.202000509