Zinc in PDB 4rqu: Alcohol Dehydrogenase Crystal Structure in Complex with Nad

All present enzymatic activity of Alcohol Dehydrogenase Crystal Structure in Complex with Nad:
1.1.1.1;

The structure of Alcohol Dehydrogenase Crystal Structure in Complex with Nad, PDB code: 4rqu was solved by Y.W.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.37 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.150, 101.150, 165.640, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 19.8

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

Zinc binding site 1 out of 4 in the Alcohol Dehydrogenase Crystal Structure in Complex with Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alcohol Dehydrogenase Crystal Structure in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:26.6 occ:1.00 SG A:CYS113 2.0 45.8 1.0 SG A:CYS99 2.1 43.0 1.0 SG A:CYS105 2.2 28.2 1.0 SG A:CYS102 2.2 34.1 1.0 H A:CYS99 2.6 40.0 1.0 HA A:CYS113 2.8 44.4 1.0 HB2 A:CYS113 2.8 35.9 1.0 CB A:CYS113 2.9 29.9 1.0 HB3 A:CYS102 3.0 45.8 1.0 H A:GLY100 3.1 45.4 1.0 HB2 A:CYS105 3.1 41.3 1.0 H A:CYS102 3.2 46.2 1.0 CB A:CYS102 3.2 38.2 1.0 H A:ASP114 3.2 45.4 1.0 CA A:CYS113 3.3 37.0 1.0 CB A:CYS105 3.3 34.5 1.0 CB A:CYS99 3.3 39.6 1.0 HB3 A:CYS99 3.3 47.5 1.0 N A:CYS99 3.3 33.3 1.0 H A:CYS105 3.4 41.4 1.0 H A:LEU115 3.6 49.2 1.0 N A:GLY100 3.7 37.9 1.0 N A:ASP114 3.8 37.9 1.0 HB3 A:CYS113 3.8 35.9 1.0 CA A:CYS99 3.8 39.0 1.0 H A:GLU101 3.8 31.1 1.0 N A:CYS102 3.9 38.5 1.0 C A:CYS113 4.0 42.6 1.0 HA A:GLU98 4.0 38.6 1.0 HB3 A:CYS105 4.0 41.3 1.0 HB2 A:CYS102 4.0 45.8 1.0 HB3 A:LEU115 4.0 33.6 1.0 N A:CYS105 4.1 34.5 1.0 CA A:CYS102 4.1 31.3 1.0 HB2 A:CYS99 4.1 47.5 1.0 C A:CYS99 4.2 41.6 1.0 CA A:CYS105 4.3 36.0 1.0 HB2 A:HIS104 4.3 37.3 1.0 C A:GLU98 4.3 30.7 1.0 HB2 A:LEU115 4.4 33.6 1.0 N A:LEU115 4.4 41.0 1.0 N A:CYS113 4.5 36.0 1.0 N A:GLU101 4.5 25.9 1.0 HB2 A:ASP114 4.6 52.4 1.0 HA A:CYS105 4.6 43.2 1.0 H A:LEU116 4.6 32.9 1.0 CB A:LEU115 4.6 28.0 1.0 CA A:GLU98 4.6 32.2 1.0 HA A:CYS99 4.7 46.8 1.0 C A:CYS102 4.7 28.2 1.0 HB2 A:LEU116 4.7 44.0 1.0 H A:CYS113 4.8 43.2 1.0 CA A:GLY100 4.8 35.9 1.0 H A:HIS104 4.8 34.6 1.0 HA2 A:GLY100 4.9 43.0 1.0 HA A:CYS102 4.9 37.6 1.0 CA A:ASP114 4.9 35.1 1.0 O A:CYS102 5.0 27.8 1.0

Zinc binding site 2 out of 4 in the Alcohol Dehydrogenase Crystal Structure in Complex with Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alcohol Dehydrogenase Crystal Structure in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:38.0 occ:1.00 SG A:CYS47 1.9 27.4 1.0 NE2 A:HIS69 2.1 27.7 1.0 SG A:CYS177 2.3 50.2 1.0 CB A:CYS47 2.8 31.2 1.0 HB2 A:CYS47 2.8 37.4 1.0 CE1 A:HIS69 2.8 26.0 1.0 HE1 A:HIS69 2.9 31.2 1.0 HB3 A:CYS47 2.9 37.4 1.0 HB3 A:CYS177 3.1 53.0 1.0 CD2 A:HIS69 3.2 29.3 1.0 HB A:THR49 3.2 38.5 1.0 CB A:CYS177 3.3 44.2 1.0 HD2 A:HIS69 3.5 35.1 1.0 HB2 A:CYS177 3.6 53.0 1.0 HG3 A:GLU70 3.6 42.7 1.0 HH21 A:ARG372 3.8 35.5 1.0 OE2 A:GLU70 3.9 44.5 1.0 H A:GLY178 3.9 43.2 1.0 H A:THR49 4.0 34.4 1.0 ND1 A:HIS69 4.0 27.3 1.0 HG1 A:THR49 4.1 50.2 1.0 CB A:THR49 4.1 32.1 1.0 CG A:HIS69 4.2 30.0 1.0 CA A:CYS47 4.3 29.1 1.0 OG1 A:THR49 4.3 41.9 1.0 HH22 A:ARG372 4.3 35.5 1.0 N A:GLY178 4.3 36.0 1.0 NH2 A:ARG372 4.3 29.6 1.0 CG A:GLU70 4.4 35.6 1.0 CD A:GLU70 4.4 37.1 1.0 HA A:CYS47 4.6 34.9 1.0 HA3 A:GLY178 4.7 50.6 1.0 H A:ASP50 4.7 38.0 1.0 HG2 A:GLU70 4.7 42.7 1.0 HA2 A:GLY178 4.7 50.6 1.0 CA A:CYS177 4.7 37.2 1.0 N A:THR49 4.8 28.6 1.0 HD1 A:HIS69 4.8 32.8 1.0 C A:CYS47 4.8 33.7 1.0 HG21 A:THR49 4.8 50.9 1.0 CA A:GLY178 4.8 42.2 1.0 C A:CYS177 4.9 30.9 1.0 H A:HIS48 5.0 44.3 1.0

Zinc binding site 3 out of 4 in the Alcohol Dehydrogenase Crystal Structure in Complex with Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alcohol Dehydrogenase Crystal Structure in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:36.6 occ:1.00 SG B:CYS102 2.1 35.0 1.0 SG B:CYS105 2.2 42.8 1.0 SG B:CYS113 2.2 33.7 1.0 SG B:CYS99 2.3 35.4 1.0 HB3 B:CYS102 2.8 42.4 1.0 HA B:CYS113 2.9 28.8 1.0 H B:CYS99 3.0 37.4 1.0 CB B:CYS102 3.0 35.4 1.0 H B:CYS102 3.1 36.4 1.0 HB2 B:CYS105 3.1 47.6 1.0 CB B:CYS113 3.1 21.4 1.0 HB2 B:CYS113 3.2 25.7 1.0 CB B:CYS105 3.3 39.6 1.0 H B:ASP114 3.3 31.9 1.0 H B:CYS105 3.3 42.2 1.0 CA B:CYS113 3.4 24.0 1.0 CB B:CYS99 3.5 25.8 1.0 H B:GLY100 3.5 36.3 1.0 HB3 B:CYS99 3.6 31.0 1.0 N B:CYS99 3.7 31.1 1.0 N B:CYS102 3.7 30.3 1.0 H B:LEU115 3.7 26.0 1.0 HB2 B:CYS102 3.8 42.4 1.0 N B:ASP114 3.8 26.6 1.0 CA B:CYS102 3.9 30.1 1.0 H B:GLU101 3.9 44.2 1.0 N B:CYS105 3.9 35.2 1.0 HB3 B:CYS105 4.0 47.6 1.0 HB3 B:CYS113 4.0 25.7 1.0 CA B:CYS99 4.0 33.1 1.0 C B:CYS113 4.0 29.6 1.0 N B:GLY100 4.1 30.2 1.0 CA B:CYS105 4.2 33.3 1.0 HB2 B:HIS104 4.2 32.1 1.0 HA B:GLU98 4.2 37.9 1.0 HB2 B:CYS99 4.3 31.0 1.0 HB3 B:LEU115 4.3 17.8 1.0 C B:CYS99 4.4 26.0 1.0 HA B:CYS105 4.5 40.0 1.0 N B:LEU115 4.6 21.7 1.0 C B:CYS102 4.7 28.1 1.0 N B:GLU101 4.7 36.8 1.0 HA B:CYS102 4.7 36.2 1.0 H B:LEU116 4.7 31.1 1.0 C B:GLU98 4.7 27.5 1.0 N B:CYS113 4.8 31.0 1.0 O B:CYS102 4.8 27.3 1.0 HB2 B:ASP114 4.8 48.8 1.0 HB2 B:LEU115 4.9 17.8 1.0 HB2 B:LEU116 4.9 26.1 1.0 C B:GLU101 4.9 28.4 1.0 HA B:CYS99 4.9 39.7 1.0 H B:HIS104 5.0 39.6 1.0 CA B:GLU98 5.0 31.6 1.0 CB B:LEU115 5.0 14.8 1.0 O B:CYS113 5.0 25.5 1.0

Zinc binding site 4 out of 4 in the Alcohol Dehydrogenase Crystal Structure in Complex with Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alcohol Dehydrogenase Crystal Structure in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:32.2 occ:1.00 NE2 B:HIS69 2.0 29.0 1.0 O B:HOH506 2.0 27.2 1.0 SG B:CYS177 2.1 28.2 1.0 SG B:CYS47 2.3 21.9 1.0 CE1 B:HIS69 2.7 28.0 1.0 HE1 B:HIS69 2.8 33.6 1.0 HG1 B:THR49 2.8 37.8 1.0 H5N B:NAD403 2.8 29.6 1.0 OG1 B:THR49 3.2 31.5 1.0 HB3 B:CYS47 3.2 30.4 1.0 C5N B:NAD403 3.2 24.6 1.0 CD2 B:HIS69 3.2 31.0 1.0 CB B:CYS47 3.2 25.4 1.0 HB2 B:CYS47 3.5 30.4 1.0 HD2 B:HIS69 3.5 37.1 1.0 H6N B:NAD403 3.5 21.5 1.0 CB B:CYS177 3.6 26.9 1.0 HB B:THR49 3.6 26.2 1.0 HB3 B:CYS177 3.7 32.2 1.0 C6N B:NAD403 3.7 17.9 1.0 C4N B:NAD403 3.8 25.4 1.0 HB2 B:CYS177 3.8 32.2 1.0 ND1 B:HIS69 3.9 24.8 1.0 CB B:THR49 4.0 21.8 1.0 H4N B:NAD403 4.0 30.5 1.0 H B:THR49 4.0 42.0 1.0 CG B:HIS69 4.2 29.1 1.0 HG3 B:GLU70 4.3 44.7 1.0 HG21 B:THR49 4.6 38.9 1.0 N1N B:NAD403 4.6 16.1 1.0 HH21 B:ARG372 4.6 38.0 1.0 CA B:CYS47 4.6 26.3 1.0 HD1 B:HIS69 4.7 29.7 1.0 C3N B:NAD403 4.7 33.5 1.0 OE2 B:GLU70 4.7 25.7 1.0 H B:GLY178 4.7 43.8 1.0 N B:THR49 4.8 35.0 1.0 H2D B:NAD403 4.8 25.3 1.0 CA B:CYS177 4.8 27.4 1.0 N B:GLY178 4.9 36.5 1.0 CG2 B:THR49 4.9 32.4 1.0 HH22 B:ARG372 4.9 38.0 1.0 HA B:CYS177 5.0 32.8 1.0 HA2 B:GLY178 5.0 46.6 1.0

F.Chen, P.Wang, Y.An, J.Huang, Y.Xu. Structural Insight Into the Conformational Change of Alcohol Dehydrogenase From Arabidopsis Thalianal During Coenzyme Binding. Biochimie V.108C 33 2014.
ISSN: ISSN 0300-9084
PubMed: 25447145
DOI: 10.1016/J.BIOCHI.2014.10.023