Zinc in PDB 1bi3: Structure of Apo-and Holo-Diphtheria Toxin Repressor

The structure of Structure of Apo-and Holo-Diphtheria Toxin Repressor, PDB code: 1bi3 was solved by E.Pohl, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.40
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	63.400, 63.400, 213.200, 90.00, 90.00, 120.00
R / Rfree (%)	25.3 / 33.3

The binding sites of Zinc atom in the Structure of Apo-and Holo-Diphtheria Toxin Repressor (pdb code 1bi3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Apo-and Holo-Diphtheria Toxin Repressor, PDB code: 1bi3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Apo-and Holo-Diphtheria Toxin Repressor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Apo-and Holo-Diphtheria Toxin Repressor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn291 b:38.6 occ:1.00 ND1 A:HIS98 1.8 11.3 1.0 NE2 A:HIS79 1.9 7.4 1.0 O4 A:SO4292 2.1 46.5 1.0 OE2 A:GLU83 2.2 23.0 1.0 CE1 A:HIS98 2.5 10.0 1.0 CE1 A:HIS79 2.8 5.6 1.0 CD A:GLU83 3.0 16.7 1.0 CG A:HIS98 3.1 6.2 1.0 CD2 A:HIS79 3.1 13.6 1.0 OE1 A:GLU83 3.3 17.7 1.0 S A:SO4292 3.4 34.2 1.0 O3 A:SO4292 3.6 38.4 1.0 CB A:HIS98 3.7 19.4 1.0 NE2 A:HIS98 3.7 4.6 1.0 O A:HOH318 3.8 16.2 1.0 CA A:HIS98 3.9 18.2 1.0 ND1 A:HIS79 4.0 11.6 1.0 CD2 A:HIS98 4.0 4.2 1.0 O2 A:SO4292 4.0 39.4 1.0 CG A:HIS79 4.1 9.5 1.0 CD2 A:PHE128 4.1 20.0 1.0 CG A:GLU83 4.2 17.2 1.0 CE2 A:PHE128 4.2 24.0 1.0 O A:HIS98 4.3 16.1 1.0 O1 A:SO4292 4.5 43.4 1.0 C A:HIS98 4.5 16.6 1.0 CB A:ALA101 4.9 16.0 1.0 NH2 A:ARG13 4.9 22.3 1.0

Zinc binding site 2 out of 2 in the Structure of Apo-and Holo-Diphtheria Toxin Repressor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Apo-and Holo-Diphtheria Toxin Repressor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1291 b:35.2 occ:1.00 ND1 B:HIS98 1.8 7.9 1.0 O4 B:SO41292 1.9 38.4 1.0 OE2 B:GLU83 2.0 21.3 1.0 NE2 B:HIS79 2.1 15.2 1.0 CD B:GLU83 2.8 14.3 1.0 CE1 B:HIS98 2.8 8.2 1.0 CG B:HIS98 2.9 13.1 1.0 CE1 B:HIS79 3.0 12.2 1.0 OE1 B:GLU83 3.1 16.6 1.0 S B:SO41292 3.2 35.9 1.0 CD2 B:HIS79 3.2 16.8 1.0 CB B:HIS98 3.4 21.6 1.0 O3 B:SO41292 3.6 28.6 1.0 CA B:HIS98 3.7 15.7 1.0 O2 B:SO41292 3.7 35.6 1.0 CD2 B:PHE128 3.9 16.1 1.0 CE2 B:PHE128 3.9 17.8 1.0 NE2 B:HIS98 3.9 6.1 1.0 CG B:GLU83 4.0 12.8 1.0 CD2 B:HIS98 4.0 6.5 1.0 O B:HOH335 4.1 15.2 1.0 ND1 B:HIS79 4.2 12.4 1.0 CG B:HIS79 4.3 12.0 1.0 O1 B:SO41292 4.4 39.3 1.0 O B:HIS98 4.4 16.2 1.0 C B:HIS98 4.5 17.4 1.0 N B:HIS98 4.8 21.1 1.0 CB B:ALA101 4.9 11.8 1.0

E.Pohl, R.K.Holmes, W.G.Hol. Motion of the Dna-Binding Domain with Respect to the Core of the Diphtheria Toxin Repressor (Dtxr) Revealed in the Crystal Structures of Apo- and Holo-Dtxr. J.Biol.Chem. V. 273 22420 1998.
ISSN: ISSN 0021-9258
PubMed: 9712865
DOI: 10.1074/JBC.273.35.22420