Zinc in PDB 5o8h: Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y

The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y, PDB code: 5o8h was solved by D.Dobritzsch, D.Maurer, E.Hamnevik, T.Reddy Enugala, M.Widersten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.63 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.702, 105.678, 109.623, 90.00, 91.51, 90.00
R / Rfree (%)	17.6 / 20.4

The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y (pdb code 5o8h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y, PDB code: 5o8h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:25.2 occ:1.00 SG A:CYS95 2.3 24.5 1.0 SG A:CYS106 2.3 25.4 1.0 SG A:CYS92 2.3 23.4 1.0 SG A:CYS98 2.3 23.2 1.0 CB A:CYS106 3.3 25.4 1.0 CB A:CYS98 3.3 21.4 1.0 CB A:CYS95 3.4 23.4 1.0 CB A:CYS92 3.4 26.2 1.0 N A:CYS92 3.5 26.2 1.0 N A:GLY93 3.8 23.1 1.0 N A:CYS95 3.8 24.9 1.0 CA A:CYS92 3.8 26.7 1.0 CA A:CYS106 3.9 25.9 1.0 CA A:CYS95 4.2 24.7 1.0 C A:CYS92 4.2 25.4 1.0 N A:CYS98 4.3 21.5 1.0 N A:ALA94 4.4 25.1 1.0 CA A:CYS98 4.4 22.4 1.0 C A:GLY91 4.5 26.0 1.0 CB A:ARG108 4.6 34.8 0.5 CB A:ARG108 4.6 35.3 0.5 C A:CYS106 4.7 28.9 1.0 N A:THR107 4.7 35.2 1.0 N A:ARG108 4.8 36.0 1.0 CA A:GLY91 4.8 25.1 1.0 CA A:GLY93 4.8 25.5 1.0 C A:CYS95 4.9 24.4 1.0 CG A:ARG108 4.9 36.6 0.5 C A:ALA94 5.0 26.9 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:52.9 occ:1.00 NE2 A:HIS62 2.1 26.4 0.5 OD2 A:ASP153 2.1 32.0 1.0 O A:HOH846 2.5 40.9 1.0 SG A:CYS38 2.6 30.7 1.0 CD2 A:HIS62 2.8 26.3 0.5 CE1 A:HIS62 3.2 25.6 0.5 CB A:CYS38 3.2 31.8 1.0 CG A:ASP153 3.3 28.1 1.0 C5N A:NAD503 3.5 22.8 1.0 CB A:SER40 3.6 31.4 1.0 OG A:SER40 3.6 34.1 1.0 CG A:HIS62 4.0 26.1 0.5 CD2 A:HIS62 4.0 29.3 0.5 OD1 A:ASP153 4.1 32.5 1.0 C6N A:NAD503 4.1 21.1 1.0 ND1 A:HIS62 4.2 27.0 0.5 CB A:ASP153 4.2 26.3 1.0 C4N A:NAD503 4.3 22.5 1.0 CA A:CYS38 4.7 31.1 1.0 O A:HOH834 4.8 34.4 1.0 N A:SER40 4.8 28.9 1.0 CA A:SER40 4.8 30.1 1.0 NH2 A:ARG340 4.9 29.3 1.0 CG A:HIS62 4.9 30.2 0.5 NE2 A:HIS62 5.0 29.2 0.5

Zinc binding site 3 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:24.3 occ:1.00 SG B:CYS95 2.3 25.9 1.0 SG B:CYS106 2.3 23.3 1.0 SG B:CYS92 2.3 24.6 1.0 SG B:CYS98 2.3 24.9 1.0 CB B:CYS106 3.3 23.8 1.0 CB B:CYS98 3.3 21.9 1.0 CB B:CYS95 3.4 25.2 1.0 CB B:CYS92 3.4 25.4 1.0 N B:CYS92 3.5 26.7 1.0 N B:GLY93 3.9 25.1 1.0 N B:CYS95 3.9 23.9 1.0 CA B:CYS92 3.9 25.2 1.0 CA B:CYS106 3.9 24.8 1.0 CA B:CYS95 4.2 24.7 1.0 C B:CYS92 4.3 26.9 1.0 N B:CYS98 4.3 21.8 1.0 N B:ALA94 4.4 24.5 1.0 CA B:CYS98 4.4 22.8 1.0 C B:GLY91 4.5 26.2 1.0 CG B:ARG108 4.6 48.0 1.0 CB B:ARG108 4.6 42.1 1.0 C B:CYS106 4.7 27.9 1.0 N B:THR107 4.7 33.3 1.0 N B:ARG108 4.8 36.1 1.0 CA B:GLY91 4.8 25.1 1.0 CA B:GLY93 4.9 23.6 1.0 C B:CYS95 4.9 22.9 1.0 C B:ALA94 5.0 25.6 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:57.0 occ:1.00 OD2 B:ASP153 2.1 34.2 1.0 NE2 B:HIS62 2.1 31.0 0.5 O B:HOH849 2.6 37.7 1.0 SG B:CYS38 2.7 31.4 1.0 CD2 B:HIS62 2.9 31.7 0.5 CE1 B:HIS62 3.2 30.1 0.5 CG B:ASP153 3.3 28.9 1.0 C5N B:NAD503 3.4 21.2 1.0 CB B:CYS38 3.4 30.8 1.0 OG B:SER40 3.6 29.8 1.0 CB B:SER40 3.6 28.6 1.0 OD1 B:ASP153 4.0 31.6 1.0 C6N B:NAD503 4.0 21.7 1.0 CG B:HIS62 4.1 31.3 0.5 C4N B:NAD503 4.1 22.5 1.0 ND1 B:HIS62 4.2 32.2 0.5 CD2 B:HIS62 4.2 25.2 0.5 CB B:ASP153 4.2 24.9 1.0 O B:HOH791 4.6 42.2 1.0 CA B:SER40 4.8 28.3 1.0 CA B:CYS38 4.9 28.7 1.0 N B:SER40 4.9 26.0 1.0 NH2 B:ARG340 5.0 28.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:23.3 occ:1.00 SG C:CYS95 2.3 24.1 1.0 SG C:CYS92 2.3 24.3 1.0 SG C:CYS106 2.3 23.6 1.0 SG C:CYS98 2.4 22.0 1.0 CB C:CYS106 3.3 24.6 1.0 CB C:CYS98 3.3 21.5 1.0 CB C:CYS95 3.3 22.3 1.0 CB C:CYS92 3.5 26.5 1.0 N C:CYS92 3.5 24.7 1.0 N C:CYS95 3.8 24.0 1.0 N C:GLY93 3.9 24.9 1.0 CA C:CYS106 3.9 25.1 1.0 CA C:CYS92 3.9 25.5 1.0 CA C:CYS95 4.2 22.8 1.0 N C:CYS98 4.3 20.1 1.0 C C:CYS92 4.3 27.7 1.0 CA C:CYS98 4.4 20.9 1.0 N C:ALA94 4.4 25.8 1.0 C C:GLY91 4.6 23.4 1.0 CB C:ARG108 4.6 43.7 1.0 C C:CYS106 4.7 28.0 1.0 N C:THR107 4.7 34.9 1.0 N C:ARG108 4.8 41.2 1.0 CA C:GLY91 4.8 23.9 1.0 C C:CYS95 4.8 21.6 1.0 CA C:GLY93 4.9 24.6 1.0 C C:ALA94 5.0 25.9 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:61.2 occ:1.00 OD2 C:ASP153 2.1 39.9 1.0 NE2 C:HIS62 2.2 52.1 1.0 SG C:CYS38 2.7 37.5 1.0 CD2 C:HIS62 2.9 49.6 1.0 O C:HOH813 3.1 42.7 1.0 CE1 C:HIS62 3.2 50.0 1.0 C5N C:NAD503 3.3 25.6 1.0 CG C:ASP153 3.3 33.5 1.0 CB C:CYS38 3.3 36.3 1.0 OG C:SER40 3.6 34.4 1.0 CB C:SER40 3.6 37.7 1.0 C6N C:NAD503 3.9 26.3 1.0 C4N C:NAD503 4.0 26.6 1.0 OD1 C:ASP153 4.0 36.9 1.0 CG C:HIS62 4.1 47.2 1.0 ND1 C:HIS62 4.2 51.6 1.0 CB C:ASP153 4.3 29.6 1.0 CA C:CYS38 4.8 35.0 1.0 CA C:SER40 4.8 38.7 1.0 N C:SER40 4.8 37.5 1.0 O C:HOH723 4.9 35.1 1.0 NH2 C:ARG340 4.9 29.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:24.6 occ:1.00 SG D:CYS98 2.3 24.6 1.0 SG D:CYS95 2.3 23.4 1.0 SG D:CYS106 2.3 25.6 1.0 SG D:CYS92 2.4 27.8 1.0 CB D:CYS106 3.2 27.5 1.0 CB D:CYS98 3.3 22.9 1.0 CB D:CYS95 3.4 24.4 1.0 CB D:CYS92 3.5 27.8 1.0 N D:CYS92 3.5 24.8 1.0 N D:GLY93 3.9 24.7 1.0 N D:CYS95 3.9 24.1 1.0 CA D:CYS106 3.9 26.5 1.0 CA D:CYS92 3.9 26.4 1.0 CA D:CYS95 4.2 23.9 1.0 N D:CYS98 4.2 20.1 1.0 C D:CYS92 4.3 26.7 1.0 CA D:CYS98 4.3 21.8 1.0 N D:ALA94 4.4 24.5 1.0 C D:GLY91 4.5 25.7 1.0 CG D:ARG108 4.6 49.6 1.0 CB D:ARG108 4.7 44.7 1.0 C D:CYS106 4.7 29.7 1.0 N D:THR107 4.8 34.8 1.0 CA D:GLY91 4.8 25.4 1.0 N D:ARG108 4.9 39.2 1.0 CA D:GLY93 4.9 25.0 1.0 C D:CYS95 4.9 23.1 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, F43H, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:81.7 occ:1.00 OD2 D:ASP153 2.1 46.2 1.0 SG D:CYS38 2.7 38.1 0.5 O D:HOH776 3.1 48.4 1.0 CB D:CYS38 3.2 46.6 0.5 CB D:CYS38 3.2 44.1 0.5 C5N D:NAD503 3.3 25.3 1.0 SG D:CYS38 3.4 43.9 0.5 CG D:ASP153 3.4 37.4 1.0 CB D:SER40 3.5 52.7 1.0 OG D:SER40 3.6 44.3 1.0 C6N D:NAD503 4.0 26.9 1.0 ND1 D:HIS62 4.1 66.8 1.0 C4N D:NAD503 4.1 26.7 1.0 OD1 D:ASP153 4.2 40.2 1.0 CB D:ASP153 4.3 32.7 1.0 CA D:CYS38 4.6 48.5 0.5 CA D:CYS38 4.7 47.2 0.5 CA D:SER40 4.7 54.4 1.0 N D:SER40 4.8 55.5 1.0 NH1 D:ARG340 4.9 37.6 1.0 CE1 D:HIS62 4.9 68.7 1.0 O D:HOH750 5.0 42.9 1.0

E.Hamnevik, T.R.Enugala, D.Maurer, S.Ntuku, A.Oliveira, D.Dobritzsch, M.Widersten. Relaxation of Nonproductive Binding and Increased Rate of Coenzyme Release in An Alcohol Dehydrogenase Increases Turnover with A Nonpreferred Alcohol Enantiomer. Febs J. V. 284 3895 2017.
ISSN: ISSN 1742-4658
PubMed: 28963762
DOI: 10.1111/FEBS.14279