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Zinc in PDB 6fg0: Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W

Protein crystallography data

The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W, PDB code: 6fg0 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 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.706, 105.463, 108.977, 90.00, 91.40, 90.00
R / Rfree (%) 16.3 / 18.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W (pdb code 6fg0). 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, F43T, L119Y, F282W, PDB code: 6fg0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6fg0

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Zinc binding site 1 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W


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, F43T, L119Y, F282W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.4
occ:1.00
SG A:CYS92 2.3 24.7 1.0
SG A:CYS95 2.3 22.2 1.0
SG A:CYS98 2.3 21.6 1.0
SG A:CYS106 2.4 23.0 1.0
CB A:CYS98 3.3 21.3 1.0
CB A:CYS106 3.3 22.9 1.0
CB A:CYS95 3.4 23.5 1.0
N A:CYS92 3.4 22.8 1.0
CB A:CYS92 3.5 24.7 1.0
CA A:CYS106 3.8 23.0 1.0
N A:CYS95 3.8 23.8 1.0
CA A:CYS92 3.9 23.7 1.0
N A:GLY93 3.9 23.1 1.0
CA A:CYS95 4.2 24.0 1.0
N A:THR107 4.3 27.7 1.0
C A:CYS92 4.3 23.8 1.0
N A:CYS98 4.3 19.7 1.0
N A:ALA94 4.3 24.3 1.0
CA A:CYS98 4.4 20.1 1.0
C A:CYS106 4.4 25.3 1.0
C A:GLY91 4.5 22.1 1.0
N A:ARG108 4.6 32.3 1.0
CB A:ARG108 4.6 36.1 1.0
CA A:GLY91 4.7 21.4 1.0
C A:CYS95 4.9 23.2 1.0
CA A:GLY93 4.9 23.3 1.0
CG A:ARG108 4.9 38.5 1.0
C A:ALA94 4.9 24.6 1.0
O A:CYS95 5.0 22.4 1.0
C A:GLY93 5.0 24.3 1.0

Zinc binding site 2 out of 8 in 6fg0

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Zinc binding site 2 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W


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, F43T, L119Y, F282W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:24.3
occ:1.00
OD2 A:ASP153 1.9 20.0 1.0
NE2 A:HIS62 2.1 21.4 1.0
SG A:CYS38 2.3 22.2 1.0
CD2 A:HIS62 3.0 21.4 1.0
CB A:CYS38 3.1 22.3 1.0
CE1 A:HIS62 3.1 22.2 1.0
CG A:ASP153 3.1 19.6 1.0
C5N A:NAD503 3.4 19.8 1.0
OD1 A:ASP153 3.7 19.9 1.0
OG A:SER40 3.8 22.8 1.0
CB A:SER40 3.8 22.7 1.0
C6N A:NAD503 4.0 19.9 1.0
CG A:HIS62 4.1 21.6 1.0
ND1 A:HIS62 4.2 22.1 1.0
CB A:ASP153 4.2 18.8 1.0
C4N A:NAD503 4.3 19.5 1.0
NH2 A:ARG340 4.4 20.6 1.0
CA A:CYS38 4.6 22.6 1.0
N A:SER40 4.8 22.5 1.0
CA A:SER40 4.9 23.2 1.0

Zinc binding site 3 out of 8 in 6fg0

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Zinc binding site 3 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W


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, F43T, L119Y, F282W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:22.0
occ:1.00
SG B:CYS92 2.3 23.7 1.0
SG B:CYS98 2.3 21.2 1.0
SG B:CYS95 2.3 21.5 1.0
SG B:CYS106 2.4 22.7 1.0
CB B:CYS106 3.3 21.8 1.0
CB B:CYS98 3.3 21.0 1.0
CB B:CYS95 3.4 22.5 1.0
N B:CYS92 3.4 22.2 1.0
CB B:CYS92 3.5 24.2 1.0
CA B:CYS106 3.8 22.1 1.0
N B:CYS95 3.8 23.1 1.0
CA B:CYS92 3.9 23.1 1.0
N B:GLY93 3.9 22.3 1.0
CA B:CYS95 4.2 22.9 1.0
C B:CYS92 4.3 23.1 1.0
N B:THR107 4.3 27.1 1.0
N B:CYS98 4.3 19.6 1.0
N B:ALA94 4.4 23.6 1.0
CA B:CYS98 4.4 19.9 1.0
C B:CYS106 4.4 24.3 1.0
C B:GLY91 4.5 21.8 1.0
N B:ARG108 4.6 31.4 1.0
CB B:ARG108 4.7 33.9 1.0
CA B:GLY91 4.7 21.1 1.0
C B:CYS95 4.9 22.0 1.0
CA B:GLY93 4.9 22.7 1.0
C B:ALA94 4.9 24.0 1.0
CG B:ARG108 5.0 35.5 1.0
O B:CYS95 5.0 21.9 1.0

Zinc binding site 4 out of 8 in 6fg0

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Zinc binding site 4 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W


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, F43T, L119Y, F282W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:24.1
occ:1.00
OD2 B:ASP153 1.9 19.9 1.0
NE2 B:HIS62 2.1 20.7 1.0
SG B:CYS38 2.3 20.5 1.0
CD2 B:HIS62 3.0 20.6 1.0
CB B:CYS38 3.1 21.2 1.0
CE1 B:HIS62 3.1 21.3 1.0
CG B:ASP153 3.1 19.9 1.0
C5N B:NAD503 3.4 18.9 1.0
OD1 B:ASP153 3.7 20.6 1.0
OG B:SER40 3.8 21.1 1.0
CB B:SER40 3.8 21.8 1.0
C6N B:NAD503 4.0 19.3 1.0
CG B:HIS62 4.1 20.6 1.0
ND1 B:HIS62 4.2 21.2 1.0
CB B:ASP153 4.2 18.7 1.0
C4N B:NAD503 4.3 18.9 1.0
NH2 B:ARG340 4.4 18.7 1.0
CA B:CYS38 4.6 21.1 1.0
N B:SER40 4.8 21.1 1.0
CA B:SER40 5.0 22.2 1.0

Zinc binding site 5 out of 8 in 6fg0

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Zinc binding site 5 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W


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, F43T, L119Y, F282W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:21.8
occ:1.00
SG C:CYS95 2.3 21.8 1.0
SG C:CYS92 2.3 24.5 1.0
SG C:CYS98 2.4 22.1 1.0
SG C:CYS106 2.4 23.3 1.0
CB C:CYS106 3.3 23.9 1.0
CB C:CYS98 3.3 21.6 1.0
CB C:CYS95 3.4 21.9 1.0
N C:CYS92 3.5 24.1 1.0
CB C:CYS92 3.5 24.9 1.0
N C:CYS95 3.8 22.7 1.0
CA C:CYS106 3.8 23.8 1.0
CA C:CYS92 3.9 24.8 1.0
N C:GLY93 3.9 23.6 1.0
CA C:CYS95 4.1 22.2 1.0
N C:CYS98 4.3 19.7 1.0
N C:THR107 4.3 28.5 1.0
C C:CYS92 4.3 24.6 1.0
CA C:CYS98 4.4 20.5 1.0
N C:ALA94 4.4 23.7 1.0
C C:CYS106 4.4 26.5 1.0
C C:GLY91 4.5 24.3 1.0
N C:ARG108 4.5 33.4 1.0
CB C:ARG108 4.6 36.4 1.0
CA C:GLY91 4.7 23.5 1.0
C C:CYS95 4.8 21.2 1.0
CA C:GLY93 4.9 23.7 1.0
CG C:ARG108 4.9 38.0 1.0
C C:ALA94 4.9 23.6 1.0
O C:CYS95 5.0 20.9 1.0

Zinc binding site 6 out of 8 in 6fg0

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Zinc binding site 6 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W


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, F43T, L119Y, F282W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:30.0
occ:1.00
OD2 C:ASP153 1.9 27.9 1.0
NE2 C:HIS62 2.1 28.1 1.0
SG C:CYS38 2.3 28.4 1.0
CD2 C:HIS62 3.0 28.2 1.0
CB C:CYS38 3.1 28.6 1.0
CG C:ASP153 3.1 26.1 1.0
CE1 C:HIS62 3.1 29.6 1.0
C5N C:NAD503 3.4 24.8 1.0
OD1 C:ASP153 3.7 27.4 1.0
OG C:SER40 3.8 28.7 1.0
CB C:SER40 3.9 29.4 1.0
C6N C:NAD503 3.9 25.1 1.0
CG C:HIS62 4.2 28.9 1.0
ND1 C:HIS62 4.2 30.0 1.0
CB C:ASP153 4.2 25.3 1.0
C4N C:NAD503 4.2 24.6 1.0
NH2 C:ARG340 4.4 26.6 1.0
CA C:CYS38 4.6 29.8 1.0
N C:SER40 4.9 29.8 1.0
CA C:SER40 5.0 30.3 1.0

Zinc binding site 7 out of 8 in 6fg0

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Zinc binding site 7 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W


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, F43T, L119Y, F282W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:21.8
occ:1.00
SG D:CYS98 2.3 22.0 1.0
SG D:CYS92 2.3 24.4 1.0
SG D:CYS95 2.3 21.5 1.0
SG D:CYS106 2.4 23.5 1.0
CB D:CYS98 3.3 21.4 1.0
CB D:CYS106 3.3 23.9 1.0
CB D:CYS95 3.4 21.9 1.0
N D:CYS92 3.5 24.1 1.0
CB D:CYS92 3.5 25.2 1.0
N D:CYS95 3.8 22.8 1.0
CA D:CYS106 3.8 24.4 1.0
N D:GLY93 3.9 24.1 1.0
CA D:CYS92 3.9 25.2 1.0
CA D:CYS95 4.2 22.2 1.0
N D:CYS98 4.2 19.3 1.0
C D:CYS92 4.3 25.0 1.0
N D:THR107 4.3 30.8 1.0
CA D:CYS98 4.3 20.5 1.0
N D:ALA94 4.4 24.1 1.0
C D:CYS106 4.5 26.9 1.0
C D:GLY91 4.5 24.4 1.0
N D:ARG108 4.6 36.1 1.0
CB D:ARG108 4.7 39.5 1.0
CA D:GLY91 4.7 23.8 1.0
C D:CYS95 4.8 21.1 1.0
CA D:GLY93 4.9 24.3 1.0
C D:ALA94 4.9 23.7 1.0
CG D:ARG108 5.0 41.0 1.0
O D:CYS95 5.0 20.5 1.0

Zinc binding site 8 out of 8 in 6fg0

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Zinc binding site 8 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W


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, F43T, L119Y, F282W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:34.8
occ:1.00
OD2 D:ASP153 1.9 31.3 1.0
NE2 D:HIS62 2.1 34.5 1.0
SG D:CYS38 2.3 33.3 1.0
CD2 D:HIS62 3.0 34.5 1.0
CG D:ASP153 3.1 29.1 1.0
CB D:CYS38 3.1 34.1 1.0
CE1 D:HIS62 3.1 36.3 1.0
C5N D:NAD503 3.3 26.0 1.0
OD1 D:ASP153 3.6 29.9 1.0
OG D:SER40 3.8 35.4 1.0
CB D:SER40 3.8 36.5 1.0
C6N D:NAD503 3.9 26.2 1.0
CG D:HIS62 4.2 35.3 1.0
ND1 D:HIS62 4.2 36.1 1.0
C4N D:NAD503 4.2 25.9 1.0
CB D:ASP153 4.2 28.0 1.0
NH2 D:ARG340 4.5 31.2 1.0
CA D:CYS38 4.6 35.1 1.0
N D:SER40 4.8 36.3 1.0
CA D:SER40 5.0 37.3 1.0

Reference:

D.Maurer, T.R.Enugala, E.Hamnevik, P.Bauer, M.Luking, 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 7526 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B01762
Page generated: Wed Dec 16 11:48:02 2020

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