Zinc in PDB 5o9f: Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, H39Y

The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, H39Y, PDB code: 5o9f was solved by D.Dobritzsch, D.Maurer, E.Hamnevik, T.R.Enugala, M.Widersten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.50 / 1.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.842, 105.293, 109.287, 90.00, 91.36, 90.00
R / Rfree (%)	16.8 / 18.6

The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, H39Y (pdb code 5o9f). 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, Y54F, F43S, H39Y, PDB code: 5o9f:
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, Y54F, F43S, 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, Y54F, F43S, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.9 occ:1.00 SG A:CYS106 2.3 20.3 1.0 SG A:CYS95 2.3 19.7 1.0 SG A:CYS92 2.3 20.6 1.0 SG A:CYS98 2.3 18.1 1.0 CB A:CYS106 3.2 20.8 1.0 CB A:CYS98 3.3 17.9 1.0 CB A:CYS95 3.4 20.7 1.0 N A:CYS92 3.5 19.6 1.0 CB A:CYS92 3.5 21.1 1.0 N A:CYS95 3.8 21.0 1.0 CA A:CYS92 3.9 20.4 1.0 N A:GLY93 3.9 20.0 1.0 CA A:CYS106 3.9 21.5 1.0 CA A:CYS95 4.2 21.1 1.0 N A:CYS98 4.3 17.0 1.0 C A:CYS92 4.3 20.4 1.0 CA A:CYS98 4.4 17.1 1.0 N A:ALA94 4.4 21.5 1.0 C A:GLY91 4.5 19.5 1.0 CB A:ARG108 4.5 34.9 1.0 O A:HOH616 4.6 39.1 1.0 CG A:ARG108 4.7 37.5 1.0 CA A:GLY91 4.7 18.8 1.0 C A:CYS106 4.8 24.3 1.0 N A:ARG108 4.8 32.0 1.0 N A:THR107 4.8 28.4 1.0 C A:CYS95 4.9 20.2 1.0 CA A:GLY93 4.9 20.5 1.0 C A:ALA94 5.0 21.8 1.0 O A:CYS95 5.0 19.7 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, 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, Y54F, F43S, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:20.8 occ:1.00 O9 A:9ON504 2.0 24.1 1.0 OD2 A:ASP153 2.0 20.8 1.0 NE2 A:HIS62 2.0 17.5 1.0 SG A:CYS38 2.3 18.5 1.0 CD2 A:HIS62 3.0 18.2 1.0 C1 A:9ON504 3.0 31.9 1.0 CE1 A:HIS62 3.0 18.7 1.0 CB A:CYS38 3.1 17.9 1.0 CG A:ASP153 3.2 19.9 1.0 O8 A:9ON504 3.4 29.6 1.0 C5N A:NAD503 3.4 15.6 1.0 OG A:SER40 3.8 16.7 1.0 OD1 A:ASP153 3.9 21.4 1.0 CB A:SER40 3.9 17.2 1.0 O A:HOH603 4.0 22.2 1.0 C6N A:NAD503 4.0 15.4 1.0 CG A:HIS62 4.1 18.4 1.0 ND1 A:HIS62 4.1 18.7 1.0 CB A:ASP153 4.1 18.1 1.0 C4N A:NAD503 4.2 15.7 1.0 C2 A:9ON504 4.3 35.9 1.0 CA A:CYS38 4.6 18.0 1.0 NH2 A:ARG340 4.7 17.2 1.0 N A:SER40 4.9 17.0 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, 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, Y54F, F43S, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:18.0 occ:1.00 SG B:CYS106 2.3 18.9 1.0 SG B:CYS92 2.3 20.2 1.0 SG B:CYS95 2.3 19.1 1.0 SG B:CYS98 2.4 18.2 1.0 CB B:CYS106 3.2 19.5 1.0 CB B:CYS98 3.4 17.4 1.0 CB B:CYS95 3.4 19.9 1.0 N B:CYS92 3.5 19.5 1.0 CB B:CYS92 3.5 20.7 1.0 N B:CYS95 3.8 19.6 1.0 N B:GLY93 3.9 19.5 1.0 CA B:CYS92 3.9 20.3 1.0 CA B:CYS106 3.9 20.2 1.0 CA B:CYS95 4.2 19.9 1.0 C B:CYS92 4.3 20.4 1.0 N B:CYS98 4.3 16.4 1.0 N B:ALA94 4.4 20.0 1.0 CA B:CYS98 4.4 16.5 1.0 O B:HOH606 4.5 35.1 1.0 C B:GLY91 4.5 19.1 1.0 CB B:ARG108 4.5 32.1 1.0 CG B:ARG108 4.7 35.1 1.0 CA B:GLY91 4.8 18.9 1.0 C B:CYS106 4.8 22.4 1.0 N B:THR107 4.8 25.7 1.0 N B:ARG108 4.8 28.8 1.0 C B:CYS95 4.9 19.1 1.0 CA B:GLY93 4.9 19.6 1.0 C B:ALA94 5.0 20.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, 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, Y54F, F43S, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:21.3 occ:1.00 O8 B:9ON504 1.9 26.4 1.0 OD2 B:ASP153 2.0 21.5 1.0 NE2 B:HIS62 2.0 19.4 1.0 SG B:CYS38 2.3 19.6 1.0 CD2 B:HIS62 3.0 19.8 1.0 C1 B:9ON504 3.0 32.5 1.0 CE1 B:HIS62 3.0 20.3 1.0 CB B:CYS38 3.1 18.6 1.0 CG B:ASP153 3.2 19.6 1.0 O9 B:9ON504 3.4 30.4 1.0 C5N B:NAD503 3.4 16.2 1.0 OG B:SER40 3.8 17.6 1.0 OD1 B:ASP153 3.9 21.1 1.0 CB B:SER40 3.9 17.5 1.0 O B:HOH601 4.0 24.4 1.0 C6N B:NAD503 4.0 15.6 1.0 CG B:HIS62 4.1 19.7 1.0 ND1 B:HIS62 4.1 20.8 1.0 CB B:ASP153 4.2 17.9 1.0 C4N B:NAD503 4.2 16.8 1.0 C2 B:9ON504 4.3 35.9 1.0 CA B:CYS38 4.6 18.6 1.0 NH2 B:ARG340 4.7 17.6 1.0 N B:SER40 4.9 17.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, 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, Y54F, F43S, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:17.9 occ:1.00 SG C:CYS92 2.3 20.3 1.0 SG C:CYS106 2.3 18.3 1.0 SG C:CYS95 2.3 17.6 1.0 SG C:CYS98 2.4 18.2 1.0 CB C:CYS106 3.2 18.4 1.0 CB C:CYS98 3.4 17.5 1.0 CB C:CYS95 3.4 18.4 1.0 N C:CYS92 3.5 19.5 1.0 CB C:CYS92 3.5 21.2 1.0 N C:CYS95 3.8 18.7 1.0 CA C:CYS92 3.9 20.9 1.0 N C:GLY93 3.9 19.1 1.0 CA C:CYS106 4.0 19.1 1.0 CA C:CYS95 4.2 18.4 1.0 N C:CYS98 4.3 15.8 1.0 C C:CYS92 4.3 20.5 1.0 O C:HOH704 4.3 25.5 1.0 CA C:CYS98 4.4 16.6 1.0 N C:ALA94 4.4 19.4 1.0 C C:GLY91 4.5 20.1 1.0 CB C:ARG108 4.6 31.8 1.0 CG C:ARG108 4.6 34.0 1.0 CA C:GLY91 4.8 19.4 1.0 C C:CYS106 4.8 21.4 1.0 C C:CYS95 4.9 17.7 1.0 N C:ARG108 4.9 28.0 1.0 CA C:GLY93 4.9 19.1 1.0 N C:THR107 4.9 23.7 1.0 C C:ALA94 5.0 19.9 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, 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, Y54F, F43S, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:21.9 occ:0.50 O C:HOH643 1.8 34.7 1.0 OD2 C:ASP153 2.0 31.9 1.0 NE2 C:HIS62 2.2 42.9 1.0 SG C:CYS38 2.2 32.7 0.5 CD2 C:HIS62 3.1 42.7 1.0 CB C:CYS38 3.1 33.4 0.5 CB C:CYS38 3.1 33.2 0.5 CG C:ASP153 3.1 28.6 1.0 CE1 C:HIS62 3.2 43.5 1.0 C5N C:NAD503 3.3 21.1 1.0 SG C:CYS38 3.4 31.5 0.5 O C:HOH809 3.5 39.7 1.0 OG C:SER40 3.7 36.7 1.0 OD1 C:ASP153 3.8 30.0 1.0 C6N C:NAD503 3.9 21.2 1.0 CB C:SER40 3.9 37.0 1.0 O C:HOH603 4.1 32.1 1.0 CB C:ASP153 4.1 27.2 1.0 C4N C:NAD503 4.1 21.5 1.0 ND1 C:HIS62 4.3 43.4 1.0 CG C:HIS62 4.3 42.4 1.0 CA C:CYS38 4.6 34.6 0.5 CA C:CYS38 4.6 34.7 0.5 NH2 C:ARG340 4.7 34.8 1.0 N C:SER40 4.8 37.3 1.0 CA C:SER40 5.0 37.6 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, 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, Y54F, F43S, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:17.4 occ:1.00 SG D:CYS106 2.3 18.5 1.0 SG D:CYS92 2.3 19.2 1.0 SG D:CYS95 2.3 17.7 1.0 SG D:CYS98 2.3 17.6 1.0 CB D:CYS106 3.2 19.1 1.0 CB D:CYS98 3.4 17.0 1.0 CB D:CYS95 3.4 18.2 1.0 N D:CYS92 3.5 19.4 1.0 CB D:CYS92 3.5 20.5 1.0 N D:CYS95 3.8 18.4 1.0 CA D:CYS92 3.9 20.1 1.0 N D:GLY93 3.9 19.4 1.0 CA D:CYS106 3.9 19.7 1.0 CA D:CYS95 4.2 18.4 1.0 O D:HOH780 4.3 32.0 1.0 C D:CYS92 4.3 20.0 1.0 N D:CYS98 4.3 15.8 1.0 N D:ALA94 4.4 19.8 1.0 CA D:CYS98 4.4 16.3 1.0 C D:GLY91 4.5 19.5 1.0 CB D:ARG108 4.5 31.3 1.0 CA D:GLY91 4.7 19.1 1.0 C D:CYS106 4.8 22.4 1.0 N D:ARG108 4.9 28.9 1.0 C D:CYS95 4.9 17.6 1.0 N D:THR107 4.9 25.1 1.0 CA D:GLY93 4.9 19.4 1.0 CG D:ARG108 4.9 33.4 1.0 C D:ALA94 5.0 19.4 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43S, 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, Y54F, F43S, H39Y within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:24.6 occ:1.00 OD2 D:ASP153 2.0 24.1 1.0 O8 D:9ON504 2.0 28.9 1.0 NE2 D:HIS62 2.0 25.8 1.0 SG D:CYS38 2.3 23.6 1.0 CD2 D:HIS62 3.0 25.9 1.0 C1 D:9ON504 3.0 37.0 1.0 CE1 D:HIS62 3.1 26.7 1.0 CB D:CYS38 3.1 23.9 1.0 CG D:ASP153 3.2 22.5 1.0 C5N D:NAD503 3.3 18.5 1.0 O9 D:9ON504 3.3 34.4 1.0 OG D:SER40 3.8 22.7 1.0 OD1 D:ASP153 3.9 22.6 1.0 CB D:SER40 4.0 24.0 1.0 C6N D:NAD503 4.0 18.2 1.0 O D:HOH604 4.0 26.6 1.0 CG D:HIS62 4.1 25.9 1.0 ND1 D:HIS62 4.1 26.9 1.0 CB D:ASP153 4.1 21.2 1.0 C4N D:NAD503 4.2 18.6 1.0 C2 D:9ON504 4.3 40.0 1.0 CA D:CYS38 4.6 24.5 1.0 NH2 D:ARG340 4.7 21.8 1.0 N D:SER40 4.9 24.0 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