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Zinc in PDB 5od3: Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y

Protein crystallography data

The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y, PDB code: 5od3 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) 29.56 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.555, 105.969, 108.076, 90.00, 91.37, 90.00
R / Rfree (%) 16.8 / 19.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y (pdb code 5od3). 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 Y54G, L119Y, PDB code: 5od3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5od3

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Zinc binding site 1 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y


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 Y54G, L119Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.9
occ:1.00
 SG A:CYS106 2.3 22.2 1.0
SG A:CYS92 2.3 24.2 1.0
SG A:CYS95 2.3 21.7 1.0
SG A:CYS98 2.3 22.6 1.0
CB A:CYS106 3.3 23.3 1.0
CB A:CYS98 3.4 20.5 1.0
CB A:CYS95 3.4 21.5 1.0
CB A:CYS92 3.4 25.1 1.0
N A:CYS92 3.5 21.8 1.0
CA A:CYS106 3.8 22.1 1.0
N A:GLY93 3.8 23.6 1.0
N A:CYS95 3.9 22.6 1.0
CA A:CYS92 3.9 23.2 1.0
CA A:CYS95 4.2 22.9 1.0
C A:CYS92 4.3 23.7 1.0
N A:CYS98 4.3 19.2 1.0
N A:THR107 4.3 27.9 1.0
CA A:CYS98 4.4 20.4 1.0
N A:ALA94 4.4 25.1 1.0
C A:CYS106 4.4 23.5 1.0
C A:GLY91 4.5 22.2 1.0
N A:ARG108 4.6 31.2 1.0
CB A:ARG108 4.6 34.9 1.0
CA A:GLY91 4.7 21.6 1.0
CA A:GLY93 4.9 23.5 1.0
C A:CYS95 4.9 21.5 1.0
C A:ALA94 5.0 25.6 1.0

Zinc binding site 2 out of 8 in 5od3

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Zinc binding site 2 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y


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 Y54G, L119Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:40.2
occ:1.00
 OD2 A:ASP153 1.9 32.0 1.0
NE2 A:HIS62 2.0 30.7 1.0
SG A:CYS38 2.3 26.6 1.0
CE1 A:HIS62 3.0 30.9 1.0
CD2 A:HIS62 3.0 30.1 1.0
CG A:ASP153 3.1 26.5 1.0
CB A:CYS38 3.1 26.0 1.0
C5N A:NAD503 3.3 23.9 1.0
OD1 A:ASP153 3.6 28.6 1.0
CB A:SER40 3.7 25.5 1.0
OG A:SER40 3.8 26.8 1.0
C6N A:NAD503 3.9 23.0 1.0
ND1 A:HIS62 4.1 27.4 1.0
CG A:HIS62 4.1 28.0 1.0
CB A:ASP153 4.2 22.1 1.0
C4N A:NAD503 4.3 23.5 1.0
NH2 A:ARG340 4.5 23.2 1.0
CA A:CYS38 4.6 23.8 1.0
N A:SER40 4.7 21.8 1.0
CA A:SER40 4.8 23.3 1.0

Zinc binding site 3 out of 8 in 5od3

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Zinc binding site 3 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y


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 Y54G, L119Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:22.5
occ:1.00
 SG B:CYS106 2.3 19.9 1.0
SG B:CYS95 2.3 22.6 1.0
SG B:CYS98 2.3 22.0 1.0
SG B:CYS92 2.4 23.6 1.0
CB B:CYS98 3.3 20.7 1.0
CB B:CYS106 3.3 21.9 1.0
CB B:CYS95 3.3 22.1 1.0
CB B:CYS92 3.4 25.6 1.0
N B:CYS92 3.5 23.5 1.0
N B:CYS95 3.8 21.1 1.0
CA B:CYS106 3.8 22.7 1.0
N B:GLY93 3.8 22.9 1.0
CA B:CYS92 3.9 24.3 1.0
CA B:CYS95 4.1 22.2 1.0
N B:CYS98 4.2 20.2 1.0
C B:CYS92 4.3 26.2 1.0
N B:THR107 4.3 29.1 1.0
N B:ALA94 4.4 24.6 1.0
CA B:CYS98 4.4 20.1 1.0
C B:CYS106 4.5 25.1 1.0
C B:GLY91 4.5 23.4 1.0
N B:ARG108 4.6 32.2 1.0
CB B:ARG108 4.6 34.0 1.0
CA B:GLY91 4.7 22.2 1.0
C B:CYS95 4.8 22.1 1.0
CA B:GLY93 4.8 23.7 1.0
C B:ALA94 4.9 23.7 1.0
O B:CYS95 4.9 20.4 1.0

Zinc binding site 4 out of 8 in 5od3

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Zinc binding site 4 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y


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 Y54G, L119Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:40.2
occ:1.00
 OD2 B:ASP153 1.9 31.8 1.0
NE2 B:HIS62 2.0 30.8 1.0
O B:HOH791 2.3 39.8 1.0
SG B:CYS38 2.3 26.6 1.0
CE1 B:HIS62 3.0 28.9 1.0
CD2 B:HIS62 3.0 30.4 1.0
CG B:ASP153 3.0 25.6 1.0
CB B:CYS38 3.1 27.1 1.0
C5N B:NAD503 3.3 24.9 1.0
OD1 B:ASP153 3.6 27.9 1.0
CB B:SER40 3.7 29.1 1.0
O B:HOH768 3.7 39.8 1.0
OG B:SER40 3.8 33.7 1.0
C6N B:NAD503 3.9 23.8 1.0
ND1 B:HIS62 4.1 29.3 1.0
CG B:HIS62 4.1 27.7 1.0
CB B:ASP153 4.2 23.1 1.0
C4N B:NAD503 4.3 24.4 1.0
NH2 B:ARG340 4.5 26.1 1.0
CA B:CYS38 4.6 25.5 1.0
N B:SER40 4.7 24.4 1.0
CA B:SER40 4.8 25.8 1.0

Zinc binding site 5 out of 8 in 5od3

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Zinc binding site 5 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y


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 Y54G, L119Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:21.8
occ:1.00
 SG C:CYS106 2.3 21.4 1.0
SG C:CYS98 2.3 23.1 1.0
SG C:CYS95 2.3 23.6 1.0
SG C:CYS92 2.3 21.7 1.0
CB C:CYS106 3.3 21.8 1.0
CB C:CYS98 3.3 22.6 1.0
CB C:CYS95 3.4 24.2 1.0
CB C:CYS92 3.4 25.0 1.0
N C:CYS92 3.5 23.7 1.0
CA C:CYS106 3.8 21.4 1.0
N C:GLY93 3.8 23.1 1.0
N C:CYS95 3.8 23.0 1.0
CA C:CYS92 3.9 23.8 1.0
CA C:CYS95 4.2 22.8 1.0
N C:CYS98 4.2 18.8 1.0
C C:CYS92 4.2 24.9 1.0
N C:THR107 4.3 30.1 1.0
CA C:CYS98 4.3 20.1 1.0
N C:ALA94 4.4 21.9 1.0
C C:CYS106 4.5 24.4 1.0
C C:GLY91 4.5 22.1 1.0
N C:ARG108 4.6 36.3 1.0
CB C:ARG108 4.7 37.6 1.0
CA C:GLY91 4.7 21.9 1.0
CA C:GLY93 4.8 23.1 1.0
C C:CYS95 4.8 23.7 1.0
O C:CYS95 5.0 23.8 1.0
C C:ALA94 5.0 23.4 1.0

Zinc binding site 6 out of 8 in 5od3

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Zinc binding site 6 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y


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 Y54G, L119Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:45.6
occ:1.00
 OD2 C:ASP153 1.9 35.6 1.0
NE2 C:HIS62 2.0 33.6 1.0
SG C:CYS38 2.3 34.4 1.0
CD2 C:HIS62 3.0 32.4 1.0
CE1 C:HIS62 3.0 34.8 1.0
CG C:ASP153 3.0 31.1 1.0
CB C:CYS38 3.1 34.7 1.0
C5N C:NAD503 3.3 27.3 1.0
OD1 C:ASP153 3.6 33.0 1.0
CB C:SER40 3.7 34.3 1.0
OG C:SER40 3.9 35.6 1.0
C6N C:NAD503 3.9 26.2 1.0
ND1 C:HIS62 4.1 33.1 1.0
CG C:HIS62 4.1 31.8 1.0
CB C:ASP153 4.2 27.5 1.0
C4N C:NAD503 4.3 26.6 1.0
NH2 C:ARG340 4.4 27.4 1.0
CA C:CYS38 4.6 31.5 1.0
N C:SER40 4.8 31.8 1.0
CA C:SER40 4.8 34.0 1.0

Zinc binding site 7 out of 8 in 5od3

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Zinc binding site 7 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y


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 Y54G, L119Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:21.5
occ:1.00
 SG D:CYS106 2.3 20.7 1.0
SG D:CYS92 2.3 23.7 1.0
SG D:CYS95 2.3 21.9 1.0
SG D:CYS98 2.3 21.9 1.0
CB D:CYS106 3.3 21.2 1.0
CB D:CYS98 3.3 20.1 1.0
CB D:CYS95 3.4 22.9 1.0
CB D:CYS92 3.5 25.2 1.0
N D:CYS92 3.5 22.9 1.0
CA D:CYS106 3.8 21.6 1.0
N D:GLY93 3.8 23.7 1.0
N D:CYS95 3.9 22.7 1.0
CA D:CYS92 3.9 24.0 1.0
CA D:CYS95 4.2 22.9 1.0
N D:CYS98 4.2 19.9 1.0
C D:CYS92 4.3 24.9 1.0
N D:THR107 4.3 27.9 1.0
CA D:CYS98 4.4 20.4 1.0
N D:ALA94 4.4 22.5 1.0
C D:CYS106 4.4 24.2 1.0
C D:GLY91 4.5 23.7 1.0
N D:ARG108 4.6 31.2 1.0
CB D:ARG108 4.6 31.7 1.0
CA D:GLY91 4.7 22.9 1.0
C D:CYS95 4.8 23.1 1.0
CA D:GLY93 4.9 22.9 1.0
O D:CYS95 5.0 22.6 1.0
C D:ALA94 5.0 24.7 1.0

Zinc binding site 8 out of 8 in 5od3

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Zinc binding site 8 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, L119Y


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 Y54G, L119Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:41.7
occ:1.00
 OD2 D:ASP153 1.9 34.4 1.0
NE2 D:HIS62 2.0 32.3 1.0
O D:HOH744 2.3 38.2 1.0
SG D:CYS38 2.3 29.9 1.0
CE1 D:HIS62 3.0 30.4 1.0
CD2 D:HIS62 3.0 31.8 1.0
CG D:ASP153 3.1 29.8 1.0
CB D:CYS38 3.1 31.3 1.0
C5N D:NAD503 3.4 26.5 1.0
OD1 D:ASP153 3.6 30.4 1.0
CB D:SER40 3.7 30.7 1.0
OG D:SER40 3.8 33.0 1.0
C6N D:NAD503 4.0 26.4 1.0
ND1 D:HIS62 4.1 32.8 1.0
CG D:HIS62 4.1 29.3 1.0
CB D:ASP153 4.2 25.7 1.0
C4N D:NAD503 4.3 26.5 1.0
NH2 D:ARG340 4.4 24.9 1.0
CA D:CYS38 4.6 31.3 1.0
N D:SER40 4.7 26.6 1.0
CA D:SER40 4.8 29.3 1.0

Reference:

D.Maurer, T.R.Enugala, E.Hamnevik, P.Bauer, M.Luking, D.Petrovic, H.Hillier, S.C.L.Kamerlin, D.Dobritzsch, M.Widersten. Stereo- and Regioselectivity in Catalyzed Transformation of A 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone By Wild Type and Laboratory Evolved Alcohol Dehydrogenases Acs Catalysis V. 8 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B01762
Page generated: Sun Oct 27 23:24:38 2024

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