Zinc in PDB 1ykf: Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii

All present enzymatic activity of Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii:
1.1.1.2;

The structure of Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii, PDB code: 1ykf was solved by Y.Korkhin, F.Frolow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.50
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	80.614, 80.614, 400.335, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 26.7

The binding sites of Zinc atom in the Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii (pdb code 1ykf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii, PDB code: 1ykf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn354 b:0.6 occ:1.00 OD2 A:ASP150 2.0 47.2 1.0 NE2 A:HIS59 2.0 36.5 1.0 SG A:CYS37 2.6 61.6 1.0 CE1 A:HIS59 3.0 33.6 1.0 CG A:ASP150 3.1 29.2 1.0 CD2 A:HIS59 3.1 32.2 1.0 CB A:CYS37 3.3 45.7 1.0 OG A:SER39 3.6 65.1 1.0 OE2 A:GLU60 3.8 29.4 1.0 OD1 A:ASP150 3.8 42.2 1.0 O7N A:NAP353 3.9 96.8 1.0 CE A:MET151 4.0 8.3 1.0 C4N A:NAP353 4.0 0.2 1.0 CD A:GLU60 4.1 24.1 1.0 CB A:ASP150 4.1 15.5 1.0 C3N A:NAP353 4.2 0.7 1.0 ND1 A:HIS59 4.2 13.0 1.0 C7N A:NAP353 4.2 0.4 1.0 CG A:HIS59 4.3 18.8 1.0 CG A:GLU60 4.4 18.9 1.0 CB A:SER39 4.5 62.2 1.0 O A:HOH357 4.6 18.5 1.0 C5N A:NAP353 4.6 0.9 1.0 OE1 A:GLU60 4.7 23.4 1.0 CA A:CYS37 4.8 42.2 1.0 C2N A:NAP353 4.9 0.4 1.0

Zinc binding site 2 out of 4 in the Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn354 b:0.4 occ:1.00 NE2 B:HIS59 2.0 33.7 1.0 OD2 B:ASP150 2.3 37.2 1.0 CG B:ASP150 2.8 40.6 1.0 CD2 B:HIS59 2.9 25.7 1.0 SG B:CYS37 2.9 56.7 1.0 CE1 B:HIS59 3.1 32.2 1.0 OD1 B:ASP150 3.3 67.3 1.0 O7N B:NAP353 3.4 96.3 1.0 CB B:CYS37 3.7 61.0 1.0 CB B:ASP150 3.8 40.5 1.0 OE2 B:GLU60 3.9 37.9 1.0 OG B:SER39 3.9 70.5 1.0 C7N B:NAP353 3.9 0.7 1.0 C4N B:NAP353 4.0 0.1 1.0 C3N B:NAP353 4.1 0.6 1.0 CG B:HIS59 4.1 19.9 1.0 ND1 B:HIS59 4.2 31.6 1.0 CD B:GLU60 4.2 40.5 1.0 CG B:GLU60 4.2 32.2 1.0 CE B:MET151 4.6 12.2 1.0 CB B:SER39 4.7 66.2 1.0 C5N B:NAP353 4.8 0.6 1.0 N7N B:NAP353 4.8 97.9 1.0 C2N B:NAP353 5.0 1.0 1.0 O B:HOH357 5.0 35.0 1.0 OE1 B:GLU60 5.0 33.1 1.0

Zinc binding site 3 out of 4 in the Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn354 b:78.8 occ:1.00 NE2 C:HIS59 2.0 30.6 1.0 OD2 C:ASP150 2.5 26.7 1.0 SG C:CYS37 2.9 43.6 1.0 O7N C:NAP353 2.9 88.4 1.0 OG C:SER39 3.0 68.4 1.0 CE1 C:HIS59 3.0 33.8 1.0 CG C:ASP150 3.1 20.4 1.0 C7N C:NAP353 3.1 96.2 1.0 CD2 C:HIS59 3.1 21.2 1.0 C3N C:NAP353 3.2 0.1 1.0 OD1 C:ASP150 3.3 39.1 1.0 C4N C:NAP353 3.3 0.5 1.0 CB C:CYS37 3.8 35.1 1.0 N7N C:NAP353 3.9 95.7 1.0 CB C:SER39 3.9 46.2 1.0 C2N C:NAP353 4.0 0.8 1.0 ND1 C:HIS59 4.2 23.6 1.0 C5N C:NAP353 4.2 0.3 1.0 CB C:ASP150 4.2 20.5 1.0 CG C:HIS59 4.2 21.0 1.0 CE C:MET151 4.6 18.7 1.0 N1N C:NAP353 4.7 0.4 1.0 C6N C:NAP353 4.8 0.7 1.0

Zinc binding site 4 out of 4 in the Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn354 b:92.0 occ:1.00 NE2 D:HIS59 2.2 38.4 1.0 OD2 D:ASP150 2.5 51.1 1.0 SG D:CYS37 2.7 36.0 1.0 OG D:SER39 3.0 72.0 1.0 CG D:ASP150 3.1 30.9 1.0 CD2 D:HIS59 3.2 31.1 1.0 CE1 D:HIS59 3.3 34.9 1.0 OD1 D:ASP150 3.4 37.6 1.0 O7N D:NAP353 3.5 92.9 1.0 CB D:CYS37 3.6 38.9 1.0 C7N D:NAP353 3.7 98.5 1.0 C3N D:NAP353 3.8 0.7 1.0 C4N D:NAP353 3.8 0.7 1.0 CB D:SER39 4.0 53.0 1.0 CB D:ASP150 4.2 30.8 1.0 OE2 D:GLU60 4.3 14.9 1.0 CG D:HIS59 4.4 36.6 1.0 ND1 D:HIS59 4.4 33.4 1.0 C2N D:NAP353 4.4 0.5 1.0 C5N D:NAP353 4.5 0.1 1.0 N7N D:NAP353 4.5 95.7 1.0 CE D:MET151 4.6 5.0 1.0 CD D:GLU60 4.6 24.3 1.0 CG D:GLU60 4.9 29.4 1.0

Y.Korkhin, A.J.Kalb(Gilboa), M.Peretz, O.Bogin, Y.Burstein, F.Frolow. Nadp-Dependent Bacterial Alcohol Dehydrogenases: Crystal Structure, Cofactor-Binding and Cofactor Specificity of the Adhs of Clostridium Beijerinckii and Thermoanaerobacter Brockii. J.Mol.Biol. V. 278 967 1998.
ISSN: ISSN 0022-2836
PubMed: 9836873
DOI: 10.1006/JMBI.1998.1750