Zinc in PDB 1kev: Structure of Nadp-Dependent Alcohol Dehydrogenase

All present enzymatic activity of Structure of Nadp-Dependent Alcohol Dehydrogenase:
1.1.1.2;

The structure of Structure of Nadp-Dependent Alcohol Dehydrogenase, PDB code: 1kev 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)	50.00 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.450, 151.420, 127.870, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.9

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

Zinc binding site 1 out of 4 in the Structure of Nadp-Dependent Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Nadp-Dependent Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn353 b:53.0 occ:1.00 NE2 A:HIS59 2.0 31.0 1.0 OD2 A:ASP150 2.1 32.4 1.0 SG A:CYS37 2.2 22.1 1.0 CE1 A:HIS59 2.9 29.4 1.0 CB A:CYS37 3.1 27.2 1.0 CD2 A:HIS59 3.1 28.9 1.0 C4N A:NDP352 3.1 67.8 1.0 OG A:SER39 3.2 43.5 1.0 CG A:ASP150 3.3 30.9 1.0 OE2 A:GLU60 3.6 36.7 1.0 C3N A:NDP352 3.8 65.9 1.0 C5N A:NDP352 3.8 67.1 1.0 OD1 A:ASP150 3.9 32.6 1.0 C7N A:NDP352 4.0 58.5 1.0 O7N A:NDP352 4.1 56.6 1.0 ND1 A:HIS59 4.1 30.7 1.0 CG A:HIS59 4.2 25.8 1.0 CE A:MET151 4.3 12.3 1.0 CB A:ASP150 4.3 29.6 1.0 CD A:GLU60 4.3 26.7 1.0 CB A:SER39 4.4 34.2 1.0 O A:HOH374 4.5 41.3 1.0 CA A:CYS37 4.6 27.5 1.0 O A:HOH370 4.7 28.1 1.0 CG A:GLU60 4.7 26.6 1.0 N7N A:NDP352 4.8 52.4 1.0 C2N A:NDP352 4.8 70.6 1.0 C6N A:NDP352 4.9 71.9 1.0

Zinc binding site 2 out of 4 in the Structure of Nadp-Dependent Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Nadp-Dependent Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn353 b:48.5 occ:1.00 OD2 B:ASP150 1.9 31.1 1.0 NE2 B:HIS59 2.0 31.3 1.0 SG B:CYS37 2.4 26.8 1.0 OE2 B:GLU60 2.4 28.9 1.0 CE1 B:HIS59 2.8 37.3 1.0 CD2 B:HIS59 3.1 31.0 1.0 CB B:CYS37 3.1 30.5 1.0 CG B:ASP150 3.1 27.4 1.0 CD B:GLU60 3.5 19.7 1.0 C4N B:NDP352 3.5 82.6 1.0 CG B:GLU60 3.9 21.5 1.0 OG B:SER39 3.9 50.5 1.0 CB B:ASP150 4.0 24.1 1.0 ND1 B:HIS59 4.0 35.9 1.0 OD1 B:ASP150 4.0 24.6 1.0 CG B:HIS59 4.1 29.4 1.0 C5N B:NDP352 4.1 83.0 1.0 CE B:MET151 4.2 11.9 1.0 C3N B:NDP352 4.4 82.0 1.0 OE1 B:GLU60 4.5 20.2 1.0 O B:HOH377 4.5 29.5 1.0 O7N B:NDP352 4.5 75.1 1.0 CA B:CYS37 4.5 29.3 1.0 C7N B:NDP352 4.6 76.6 1.0 O B:HOH381 4.9 33.6 1.0

Zinc binding site 3 out of 4 in the Structure of Nadp-Dependent Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Nadp-Dependent Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn353 b:62.6 occ:1.00 NE2 C:HIS59 1.9 37.2 1.0 OD2 C:ASP150 2.2 36.6 1.0 SG C:CYS37 2.3 28.6 1.0 CE1 C:HIS59 2.7 33.8 1.0 CD2 C:HIS59 3.1 29.2 1.0 C4N C:NDP352 3.1 79.4 1.0 CB C:CYS37 3.2 24.6 1.0 CG C:ASP150 3.4 29.5 1.0 OG C:SER39 3.5 42.3 1.0 C3N C:NDP352 3.6 77.8 1.0 OE2 C:GLU60 3.8 31.5 1.0 C7N C:NDP352 3.8 72.3 1.0 O7N C:NDP352 3.9 71.1 1.0 C5N C:NDP352 3.9 78.0 1.0 OD1 C:ASP150 3.9 24.9 1.0 ND1 C:HIS59 3.9 32.5 1.0 CG C:HIS59 4.1 32.1 1.0 CB C:SER39 4.2 41.4 1.0 N7N C:NDP352 4.5 68.3 1.0 CD C:GLU60 4.5 24.5 1.0 CB C:ASP150 4.6 24.9 1.0 C2N C:NDP352 4.7 80.0 1.0 CA C:CYS37 4.7 25.9 1.0 CE C:MET151 4.7 16.7 1.0 O C:HOH381 4.8 40.9 1.0 C6N C:NDP352 4.9 79.8 1.0 CG C:GLU60 4.9 25.3 1.0 O C:HOH377 4.9 26.3 1.0

Zinc binding site 4 out of 4 in the Structure of Nadp-Dependent Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Nadp-Dependent Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn353 b:46.8 occ:1.00 NE2 D:HIS59 1.9 29.1 1.0 OD2 D:ASP150 2.2 28.1 1.0 SG D:CYS37 2.3 25.6 1.0 CE1 D:HIS59 2.8 24.6 1.0 CD2 D:HIS59 3.1 20.8 1.0 C4N D:NDP352 3.1 76.8 1.0 OG D:SER39 3.2 50.3 1.0 CB D:CYS37 3.3 29.4 1.0 CG D:ASP150 3.3 23.3 1.0 C3N D:NDP352 3.6 74.2 1.0 C5N D:NDP352 3.8 76.1 1.0 C7N D:NDP352 3.8 67.8 1.0 O7N D:NDP352 3.9 65.0 1.0 OE2 D:GLU60 3.9 24.8 1.0 OD1 D:ASP150 4.0 24.5 1.0 ND1 D:HIS59 4.0 22.4 1.0 CB D:SER39 4.1 39.9 1.0 CG D:HIS59 4.2 19.2 1.0 CE D:MET151 4.4 16.5 1.0 CB D:ASP150 4.5 22.7 1.0 CD D:GLU60 4.5 26.6 1.0 N7N D:NDP352 4.6 59.8 1.0 C2N D:NDP352 4.7 77.8 1.0 CA D:CYS37 4.7 25.6 1.0 C6N D:NDP352 4.8 78.8 1.0 O D:HOH389 4.9 30.7 1.0 CG D:GLU60 4.9 24.6 1.0 O D:HOH385 5.0 21.9 1.0

Y.Korkhin, F.Frolow, O.Bogin, M.Peretz, A.J.Kalb, Y.Burstein. Crystalline Alcohol Dehydrogenases From the Mesophilic Bacterium Clostridium Beijerinckii and the Thermophilic Bacterium Thermoanaerobium Brockii: Preparation, Characterization and Molecular Symmetry. Acta Crystallogr.,Sect.D V. 52 882 1996.
ISSN: ISSN 0907-4449
PubMed: 15299659
DOI: 10.1107/S0907444996001461