Zinc in PDB 6ffx: Crystal Structure of R. Ruber Adh-A, Mutant F43H

The structure of Crystal Structure of R. Ruber Adh-A, Mutant F43H, PDB code: 6ffx 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)	29.30 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.647, 103.162, 111.187, 90.00, 90.74, 90.00
R / Rfree (%)	22.1 / 25.3

The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant F43H (pdb code 6ffx). 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 F43H, PDB code: 6ffx:
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 F43H


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 F43H within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:57.6 occ:1.00 SG A:CYS98 2.2 60.0 1.0 SG A:CYS92 2.3 61.8 1.0 SG A:CYS106 2.3 68.4 1.0 SG A:CYS95 2.4 62.4 1.0 CB A:CYS98 3.3 59.8 1.0 CB A:CYS95 3.3 61.8 1.0 CB A:CYS106 3.3 64.5 1.0 N A:CYS92 3.5 63.5 1.0 CB A:CYS92 3.5 65.2 1.0 N A:CYS95 3.8 62.9 1.0 N A:GLY93 3.8 63.6 1.0 CA A:CYS106 3.9 65.5 1.0 CA A:CYS92 3.9 65.0 1.0 CA A:CYS95 4.1 62.4 1.0 C A:CYS92 4.3 65.0 1.0 N A:CYS98 4.3 56.2 1.0 CA A:CYS98 4.3 56.9 1.0 N A:ALA94 4.5 65.4 1.0 N A:THR107 4.5 74.7 1.0 C A:GLY91 4.5 62.3 1.0 C A:CYS106 4.6 69.7 1.0 CA A:GLY91 4.7 60.0 1.0 N A:ARG108 4.8 82.6 1.0 C A:CYS95 4.8 61.1 1.0 CA A:GLY93 4.9 63.0 1.0 O A:CYS95 4.9 60.6 1.0 C A:ALA94 5.0 64.8 1.0

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


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 F43H within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:81.2 occ:1.00 OD2 A:ASP153 2.0 61.3 1.0 NE2 A:HIS62 2.2 77.4 1.0 SG A:CYS38 2.5 85.0 1.0 CD2 A:HIS62 3.1 75.1 1.0 CG A:ASP153 3.1 57.1 1.0 CB A:CYS38 3.1 82.3 1.0 CE1 A:HIS62 3.2 78.2 1.0 C5N A:NAD503 3.4 75.2 1.0 CB A:SER40 3.6 73.8 1.0 OD1 A:ASP153 3.7 54.3 1.0 OG A:SER40 3.7 72.6 1.0 C6N A:NAD503 4.1 76.6 1.0 C4N A:NAD503 4.1 74.4 1.0 ND1 A:HIS62 4.2 78.6 1.0 CG A:HIS62 4.2 75.2 1.0 CB A:ASP153 4.3 56.9 1.0 NH2 A:ARG340 4.5 72.2 1.0 CA A:CYS38 4.6 83.0 1.0 N A:SER40 4.6 76.7 1.0 CA A:SER40 4.7 76.5 1.0

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


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 F43H within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:58.9 occ:1.00 SG B:CYS98 2.2 58.0 1.0 SG B:CYS92 2.3 60.9 1.0 SG B:CYS106 2.3 63.6 1.0 SG B:CYS95 2.4 59.0 1.0 CB B:CYS98 3.2 58.3 1.0 CB B:CYS95 3.3 61.8 1.0 CB B:CYS106 3.3 61.6 1.0 N B:CYS92 3.5 61.8 1.0 CB B:CYS92 3.5 63.6 1.0 N B:CYS95 3.8 64.2 1.0 N B:GLY93 3.8 62.3 1.0 CA B:CYS106 3.9 61.4 1.0 CA B:CYS92 3.9 63.4 1.0 CA B:CYS95 4.1 62.1 1.0 N B:CYS98 4.2 54.4 1.0 C B:CYS92 4.3 62.6 1.0 CA B:CYS98 4.3 55.6 1.0 N B:ALA94 4.5 66.4 1.0 N B:THR107 4.5 69.9 1.0 C B:GLY91 4.5 63.0 1.0 C B:CYS106 4.6 64.8 1.0 CA B:GLY91 4.7 61.6 1.0 C B:CYS95 4.8 59.0 1.0 N B:ARG108 4.8 81.4 1.0 O B:CYS95 4.9 57.3 1.0 CA B:GLY93 4.9 62.1 1.0 C B:ALA94 5.0 65.9 1.0

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


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 F43H within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:86.8 occ:1.00 OD2 B:ASP153 1.9 62.7 1.0 NE2 B:HIS62 2.2 82.8 1.0 SG B:CYS38 2.4 89.0 1.0 CG B:ASP153 3.0 57.7 1.0 CD2 B:HIS62 3.1 81.2 1.0 CB B:CYS38 3.2 85.4 1.0 CE1 B:HIS62 3.2 85.5 1.0 C5N B:NAD503 3.4 84.0 1.0 OD1 B:ASP153 3.6 55.4 1.0 CB B:SER40 3.6 82.8 1.0 OG B:SER40 3.7 84.6 1.0 C6N B:NAD503 4.1 84.5 1.0 C4N B:NAD503 4.2 81.9 1.0 CB B:ASP153 4.2 56.7 1.0 CG B:HIS62 4.3 82.8 1.0 ND1 B:HIS62 4.3 86.5 1.0 NH2 B:ARG340 4.5 74.1 1.0 CA B:CYS38 4.6 86.6 1.0 N B:SER40 4.7 85.2 1.0 CA B:SER40 4.7 84.8 1.0

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


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 F43H within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:60.2 occ:1.00 SG C:CYS98 2.2 56.7 1.0 SG C:CYS106 2.3 59.3 1.0 SG C:CYS92 2.4 59.3 1.0 SG C:CYS95 2.4 61.8 1.0 CB C:CYS106 3.3 61.2 1.0 CB C:CYS98 3.3 56.1 1.0 CB C:CYS95 3.3 61.2 1.0 N C:CYS92 3.5 62.0 1.0 CB C:CYS92 3.6 63.1 1.0 CA C:CYS106 3.8 62.4 1.0 N C:GLY93 3.9 58.3 1.0 N C:CYS95 3.9 61.3 1.0 CA C:CYS92 3.9 63.4 1.0 CA C:CYS95 4.2 61.4 1.0 N C:CYS98 4.3 54.9 1.0 C C:CYS92 4.3 61.9 1.0 CA C:CYS98 4.3 55.6 1.0 N C:THR107 4.4 76.3 1.0 C C:CYS106 4.5 69.5 1.0 C C:GLY91 4.5 64.0 1.0 N C:ALA94 4.6 60.6 1.0 CA C:GLY91 4.7 63.3 1.0 N C:ARG108 4.8 87.2 1.0 C C:CYS95 4.8 58.5 1.0 O C:CYS95 4.9 57.2 1.0 CA C:GLY93 4.9 59.1 1.0

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


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 F43H within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:0.9 occ:1.00 OD2 C:ASP153 2.1 72.4 1.0 NE2 C:HIS62 2.2 86.1 1.0 SG C:CYS38 2.5 0.9 1.0 CD2 C:HIS62 3.1 84.9 1.0 CE1 C:HIS62 3.1 90.7 1.0 CB C:CYS38 3.2 0.9 1.0 CG C:ASP153 3.2 70.6 1.0 C5N C:NAD503 3.2 0.8 1.0 CB C:SER40 3.5 97.1 1.0 OG C:SER40 3.6 94.1 1.0 OD1 C:ASP153 3.8 70.2 1.0 C4N C:NAD503 3.8 0.4 1.0 C6N C:NAD503 4.1 0.7 1.0 ND1 C:HIS62 4.2 90.6 1.0 CG C:HIS62 4.3 88.0 1.0 CB C:ASP153 4.4 70.1 1.0 N C:SER40 4.6 0.7 1.0 CA C:SER40 4.6 0.6 1.0 NH2 C:ARG340 4.6 89.2 1.0 CA C:CYS38 4.7 0.0 1.0 C3N C:NAD503 5.0 0.3 1.0

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


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 F43H within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:63.9 occ:1.00 SG D:CYS98 2.2 60.6 1.0 SG D:CYS95 2.3 64.5 1.0 SG D:CYS106 2.3 62.4 1.0 SG D:CYS92 2.4 59.1 1.0 CB D:CYS95 3.2 62.8 1.0 CB D:CYS98 3.3 59.0 1.0 CB D:CYS106 3.3 62.9 1.0 N D:CYS92 3.6 62.7 1.0 CB D:CYS92 3.6 63.8 1.0 CA D:CYS106 3.8 62.1 1.0 N D:CYS95 3.8 64.3 1.0 N D:GLY93 3.9 61.7 1.0 CA D:CYS92 4.0 64.4 1.0 CA D:CYS95 4.1 62.8 1.0 N D:CYS98 4.2 54.9 1.0 CA D:CYS98 4.3 57.2 1.0 C D:CYS92 4.3 64.2 1.0 N D:THR107 4.4 71.8 1.0 C D:CYS106 4.5 66.4 1.0 N D:ALA94 4.5 66.0 1.0 C D:GLY91 4.6 63.7 1.0 C D:CYS95 4.8 60.2 1.0 N D:ARG108 4.8 85.0 1.0 CA D:GLY91 4.8 62.3 1.0 O D:CYS95 4.9 58.4 1.0 CA D:GLY93 4.9 62.7 1.0 C D:ALA94 5.0 65.3 1.0

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


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 F43H within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:0.0 occ:1.00 OD2 D:ASP153 2.0 71.0 1.0 NE2 D:HIS62 2.4 87.4 1.0 SG D:CYS38 2.4 96.4 1.0 CG D:ASP153 3.1 69.1 1.0 CB D:CYS38 3.2 99.1 1.0 CD2 D:HIS62 3.3 87.7 1.0 C5N D:NAD503 3.4 90.7 1.0 CE1 D:HIS62 3.4 92.4 1.0 CB D:SER40 3.5 0.2 1.0 OG D:SER40 3.6 97.7 1.0 OD1 D:ASP153 3.6 68.9 1.0 C4N D:NAD503 4.1 88.3 1.0 C6N D:NAD503 4.1 92.8 1.0 CB D:ASP153 4.3 69.6 1.0 ND1 D:HIS62 4.5 93.9 1.0 CG D:HIS62 4.5 91.5 1.0 NH2 D:ARG340 4.5 94.4 1.0 N D:SER40 4.6 0.3 1.0 CA D:SER40 4.7 0.6 1.0 CA D:CYS38 4.7 0.0 1.0

E.Hamnevik, D.Maurer, T.R.Enugala, T.Chu, R.Lofgren, D.Dobritzsch, M.Widersten. Directed Evolution of Alcohol Dehydrogenase For Improved Stereoselective Redox Transformations of 1-Phenylethane-1,2-Diol and Its Corresponding Acyloin. Biochemistry V. 57 1059 2018.
ISSN: ISSN 1520-4995
PubMed: 29384657
DOI: 10.1021/ACS.BIOCHEM.8B00055