Zinc in PDB 5o8q: Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A

The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, PDB code: 5o8q 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)	29.64 / 2.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.689, 109.458, 256.653, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A (pdb code 5o8q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, PDB code: 5o8q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:74.5 occ:1.00 OD2 A:ASP153 1.9 40.3 1.0 CE1 A:HIS62 2.6 50.9 1.0 SG A:CYS38 2.7 56.6 1.0 OG A:SER40 2.8 62.3 1.0 NE2 A:HIS62 2.8 51.8 1.0 CG A:ASP153 3.1 37.5 1.0 C5N A:NAD503 3.2 26.3 1.0 CB A:CYS38 3.3 50.2 1.0 ND1 A:HIS62 3.9 48.8 1.0 C6N A:NAD503 3.9 26.6 1.0 CB A:ASP153 4.0 34.5 1.0 C4N A:NAD503 4.0 25.8 1.0 OD1 A:ASP153 4.0 38.8 1.0 CB A:SER40 4.1 60.4 1.0 CD2 A:HIS62 4.2 49.5 1.0 N A:SER40 4.6 58.5 1.0 NH2 A:ARG340 4.7 35.0 1.0 CG A:HIS62 4.7 47.1 1.0 CA A:CYS38 4.8 49.6 1.0 OE2 A:GLU63 4.9 45.2 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:27.9 occ:1.00 SG A:CYS106 2.3 32.9 1.0 SG A:CYS98 2.3 27.1 1.0 SG A:CYS92 2.3 32.7 1.0 SG A:CYS95 2.4 30.8 1.0 CB A:CYS106 3.3 33.6 1.0 CB A:CYS98 3.3 27.2 1.0 CB A:CYS95 3.4 32.8 1.0 N A:CYS92 3.4 31.2 1.0 CB A:CYS92 3.5 33.7 1.0 N A:CYS95 3.8 32.4 1.0 CA A:CYS106 3.9 34.5 1.0 CA A:CYS92 3.9 32.4 1.0 N A:GLY93 3.9 30.3 1.0 CA A:CYS95 4.2 32.7 1.0 N A:CYS98 4.3 26.4 1.0 C A:CYS92 4.3 31.9 1.0 CA A:CYS98 4.4 26.2 1.0 N A:ALA94 4.4 31.8 1.0 N A:THR107 4.4 44.3 1.0 C A:GLY91 4.5 30.4 1.0 C A:CYS106 4.5 39.3 1.0 CB A:ARG108 4.7 57.4 1.0 CA A:GLY91 4.7 29.4 1.0 N A:ARG108 4.7 53.3 1.0 C A:CYS95 4.9 31.4 1.0 CA A:GLY93 4.9 29.9 1.0 C A:ALA94 4.9 33.2 1.0 O A:CYS95 5.0 30.4 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:84.0 occ:1.00 OD2 B:ASP153 2.1 39.5 1.0 NE2 B:HIS62 2.4 47.2 1.0 SG B:CYS38 2.8 55.0 1.0 CB B:CYS38 3.0 48.7 1.0 CD2 B:HIS62 3.0 45.6 1.0 CG B:ASP153 3.2 35.9 1.0 CE1 B:HIS62 3.5 47.2 1.0 OG B:SER40 3.7 48.9 1.0 CB B:ASP153 3.9 33.1 1.0 C5N B:NAD503 3.9 24.1 1.0 CB B:SER40 4.1 50.0 1.0 OD1 B:ASP153 4.2 37.2 1.0 CG B:HIS62 4.3 43.9 1.0 ND1 B:HIS62 4.5 46.0 1.0 CA B:CYS38 4.5 47.2 1.0 OE2 B:GLU63 4.6 44.0 1.0 O B:HOH678 4.6 36.5 1.0 NH2 B:ARG340 4.6 35.2 1.0 N B:SER40 4.7 49.9 1.0 C6N B:NAD503 4.7 24.1 1.0 C4N B:NAD503 4.7 23.6 1.0 CG B:GLU63 4.8 40.3 1.0 C B:CYS38 5.0 47.7 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:28.2 occ:1.00 SG B:CYS98 2.3 26.9 1.0 SG B:CYS95 2.3 28.8 1.0 SG B:CYS106 2.4 31.9 1.0 SG B:CYS92 2.4 31.9 1.0 CB B:CYS98 3.2 26.6 1.0 CB B:CYS106 3.3 32.1 1.0 CB B:CYS95 3.4 31.0 1.0 N B:CYS92 3.5 31.0 1.0 CB B:CYS92 3.5 33.2 1.0 N B:CYS95 3.8 31.1 1.0 CA B:CYS106 3.9 32.8 1.0 N B:GLY93 3.9 30.0 1.0 CA B:CYS92 4.0 32.2 1.0 CA B:CYS95 4.1 31.2 1.0 N B:CYS98 4.2 25.8 1.0 CA B:CYS98 4.3 25.5 1.0 C B:CYS92 4.3 31.5 1.0 N B:ALA94 4.4 30.9 1.0 N B:THR107 4.4 42.5 1.0 C B:GLY91 4.6 30.4 1.0 C B:CYS106 4.6 37.5 1.0 CB B:ARG108 4.8 56.7 1.0 CA B:GLY91 4.8 29.1 1.0 N B:ARG108 4.8 51.6 1.0 C B:CYS95 4.8 29.9 1.0 CA B:GLY93 4.9 29.5 1.0 C B:ALA94 4.9 32.0 1.0 O B:CYS95 4.9 28.8 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:86.6 occ:1.00 OD2 C:ASP153 2.2 42.9 1.0 NE2 C:HIS62 2.7 59.7 1.0 SG C:CYS38 2.8 54.6 1.0 CB C:CYS38 3.3 52.2 1.0 C5N C:NAD503 3.3 26.7 1.0 CG C:ASP153 3.4 39.2 1.0 CD2 C:HIS62 3.4 58.0 1.0 CE1 C:HIS62 3.7 59.4 1.0 OG C:SER40 3.8 56.0 1.0 CB C:SER40 3.9 58.0 1.0 C6N C:NAD503 4.0 25.8 1.0 C4N C:NAD503 4.1 26.2 1.0 OD1 C:ASP153 4.2 40.8 1.0 O C:HOH630 4.3 33.7 1.0 CB C:ASP153 4.3 37.1 1.0 N C:SER40 4.5 59.5 1.0 CG C:HIS62 4.7 56.4 1.0 CA C:CYS38 4.8 53.0 1.0 ND1 C:HIS62 4.8 58.1 1.0 NH2 C:ARG340 4.8 39.4 1.0 CA C:SER40 4.8 60.4 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:27.0 occ:1.00 SG C:CYS98 2.3 27.1 1.0 SG C:CYS106 2.3 29.8 1.0 SG C:CYS95 2.3 27.8 1.0 SG C:CYS92 2.4 30.7 1.0 CB C:CYS106 3.3 28.6 1.0 CB C:CYS98 3.3 26.8 1.0 CB C:CYS95 3.4 30.1 1.0 N C:CYS92 3.5 31.5 1.0 CB C:CYS92 3.5 33.2 1.0 CA C:CYS106 3.8 28.2 1.0 N C:CYS95 3.8 31.4 1.0 N C:GLY93 3.9 31.2 1.0 CA C:CYS92 4.0 32.7 1.0 CA C:CYS95 4.2 30.4 1.0 N C:CYS98 4.2 24.6 1.0 CA C:CYS98 4.3 25.1 1.0 C C:CYS92 4.3 32.4 1.0 N C:THR107 4.4 32.8 1.0 N C:ALA94 4.4 31.8 1.0 C C:CYS106 4.5 30.8 1.0 C C:GLY91 4.5 31.3 1.0 CA C:GLY91 4.7 30.1 1.0 N C:ARG108 4.7 41.2 1.0 CB C:ARG108 4.8 45.6 1.0 C C:CYS95 4.9 29.0 1.0 CA C:GLY93 4.9 31.0 1.0 O C:CYS95 5.0 27.7 1.0 C C:ALA94 5.0 32.1 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:75.8 occ:1.00 OD2 D:ASP153 2.0 41.2 1.0 CE1 D:HIS62 2.5 47.4 1.0 O D:HOH697 2.5 42.7 1.0 SG D:CYS38 2.7 53.5 1.0 NE2 D:HIS62 2.7 48.0 1.0 CG D:ASP153 3.2 37.1 1.0 CB D:CYS38 3.3 46.6 1.0 C5N D:NAD503 3.3 25.0 1.0 ND1 D:HIS62 3.8 45.6 1.0 OG D:SER40 3.8 50.6 1.0 CB D:SER40 3.9 53.0 1.0 C6N D:NAD503 4.0 25.2 1.0 O D:HOH690 4.0 38.3 1.0 CB D:ASP153 4.1 34.1 1.0 OD1 D:ASP153 4.1 38.2 1.0 CD2 D:HIS62 4.1 45.8 1.0 C4N D:NAD503 4.1 24.9 1.0 N D:SER40 4.5 53.2 1.0 CG D:HIS62 4.6 43.4 1.0 O D:HOH695 4.6 38.8 1.0 CA D:CYS38 4.7 45.4 1.0 NH2 D:ARG340 4.8 32.7 1.0 CA D:SER40 4.9 54.6 1.0 OE2 D:GLU63 4.9 41.3 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:24.8 occ:1.00 SG D:CYS92 2.3 27.6 1.0 SG D:CYS98 2.3 25.4 1.0 SG D:CYS106 2.3 29.1 1.0 SG D:CYS95 2.4 25.7 1.0 CB D:CYS98 3.3 24.2 1.0 CB D:CYS106 3.3 29.3 1.0 CB D:CYS95 3.4 27.4 1.0 N D:CYS92 3.5 27.0 1.0 CB D:CYS92 3.5 28.6 1.0 N D:CYS95 3.8 27.0 1.0 N D:GLY93 3.9 25.6 1.0 CA D:CYS92 3.9 27.8 1.0 CA D:CYS106 3.9 29.9 1.0 CA D:CYS95 4.2 27.3 1.0 C D:CYS92 4.3 26.9 1.0 N D:CYS98 4.3 23.3 1.0 N D:ALA94 4.3 26.4 1.0 CA D:CYS98 4.4 23.0 1.0 N D:THR107 4.4 37.2 1.0 C D:GLY91 4.5 26.9 1.0 C D:CYS106 4.6 33.5 1.0 CB D:ARG108 4.7 49.0 1.0 CA D:GLY91 4.7 26.2 1.0 N D:ARG108 4.8 45.5 1.0 CA D:GLY93 4.9 25.2 1.0 C D:CYS95 4.9 26.1 1.0 C D:ALA94 4.9 27.4 1.0 O D:CYS95 5.0 24.8 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:71.0 occ:1.00 OD2 E:ASP153 2.2 38.7 1.0 CE1 E:HIS62 2.6 47.2 1.0 SG E:CYS38 2.7 54.2 1.0 NE2 E:HIS62 2.9 47.7 1.0 C5N E:NAD503 3.1 24.3 1.0 CB E:CYS38 3.3 49.6 1.0 CG E:ASP153 3.4 35.7 1.0 C6N E:NAD503 3.7 24.7 1.0 OG E:SER40 3.8 59.2 1.0 CB E:SER40 3.9 60.3 1.0 C4N E:NAD503 3.9 25.4 1.0 ND1 E:HIS62 3.9 45.2 1.0 O E:HOH653 4.0 38.1 1.0 OD1 E:ASP153 4.2 36.7 1.0 CD2 E:HIS62 4.2 45.5 1.0 CB E:ASP153 4.3 33.8 1.0 N E:SER40 4.4 60.4 1.0 CG E:HIS62 4.7 43.7 1.0 CA E:CYS38 4.7 49.5 1.0 O E:HOH636 4.7 41.0 1.0 CA E:SER40 4.8 61.8 1.0 NH2 E:ARG340 4.8 34.4 1.0 N1N E:NAD503 4.8 25.3 1.0 N E:HIS39 5.0 55.0 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:22.6 occ:1.00 SG E:CYS106 2.3 24.4 1.0 SG E:CYS98 2.3 23.3 1.0 SG E:CYS92 2.4 26.6 1.0 SG E:CYS95 2.4 23.4 1.0 CB E:CYS106 3.3 24.9 1.0 CB E:CYS98 3.3 23.2 1.0 CB E:CYS95 3.4 25.3 1.0 N E:CYS92 3.5 26.5 1.0 CB E:CYS92 3.5 28.0 1.0 N E:CYS95 3.8 26.1 1.0 CA E:CYS106 3.8 25.3 1.0 CA E:CYS92 3.9 27.2 1.0 N E:GLY93 3.9 25.3 1.0 CA E:CYS95 4.2 25.7 1.0 N E:CYS98 4.3 22.5 1.0 C E:CYS92 4.3 26.9 1.0 CA E:CYS98 4.4 22.5 1.0 N E:THR107 4.4 31.8 1.0 N E:ALA94 4.4 26.1 1.0 C E:GLY91 4.5 26.2 1.0 C E:CYS106 4.5 28.3 1.0 N E:ARG108 4.7 38.8 1.0 CB E:ARG108 4.7 43.2 1.0 CA E:GLY91 4.7 25.4 1.0 C E:CYS95 4.9 24.9 1.0 CA E:GLY93 4.9 25.2 1.0 C E:ALA94 4.9 27.0 1.0 O E:CYS95 5.0 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