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Zinc in PDB 5o9d: Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y

Protein crystallography data

The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y, PDB code: 5o9d 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) 28.30 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.492, 104.828, 109.009, 90.00, 91.13, 90.00
R / Rfree (%) 17 / 19.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y (pdb code 5o9d). 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, F43H, H39Y, PDB code: 5o9d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5o9d

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Zinc binding site 1 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, 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, F43H, H39Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:15.4
occ:1.00
 SG A:CYS106 2.3 17.6 1.0
SG A:CYS92 2.3 17.7 1.0
SG A:CYS95 2.3 16.4 1.0
SG A:CYS98 2.4 15.2 1.0
CB A:CYS106 3.3 17.7 1.0
CB A:CYS98 3.3 15.0 1.0
CB A:CYS95 3.4 17.9 1.0
N A:CYS92 3.4 17.2 1.0
CB A:CYS92 3.4 18.5 1.0
N A:CYS95 3.8 17.9 1.0
N A:GLY93 3.9 17.1 1.0
CA A:CYS92 3.9 17.9 1.0
CA A:CYS106 4.0 18.4 1.0
CA A:CYS95 4.2 17.9 1.0
C A:CYS92 4.2 17.8 1.0
N A:CYS98 4.3 14.2 1.0
O A:HOH604 4.3 35.6 1.0
N A:ALA94 4.4 18.1 1.0
CA A:CYS98 4.4 14.3 1.0
C A:GLY91 4.5 16.8 1.0
CB A:ARG108 4.5 31.8 1.0
CG A:ARG108 4.6 34.1 1.0
CA A:GLY91 4.7 16.3 1.0
C A:CYS106 4.8 20.8 1.0
N A:THR107 4.8 23.8 1.0
N A:ARG108 4.8 28.2 1.0
C A:CYS95 4.9 17.1 1.0
CA A:GLY93 4.9 17.1 1.0
C A:ALA94 5.0 18.6 1.0
O A:CYS95 5.0 16.3 1.0

Zinc binding site 2 out of 8 in 5o9d

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Zinc binding site 2 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, 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, F43H, H39Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:18.0
occ:1.00
 OD2 A:ASP153 1.9 20.0 1.0
NE2 A:HIS62 2.0 16.8 1.0
O9 A:9ON504 2.1 23.8 1.0
SG A:CYS38 2.3 16.4 1.0
C1 A:9ON504 3.0 28.6 1.0
CD2 A:HIS62 3.0 17.1 1.0
CE1 A:HIS62 3.1 17.2 1.0
CB A:CYS38 3.1 15.9 1.0
CG A:ASP153 3.1 18.3 1.0
O8 A:9ON504 3.2 25.1 1.0
C5N A:NAD503 3.5 13.6 1.0
OG A:SER40 3.8 17.3 1.0
CB A:SER40 3.8 16.6 1.0
OD1 A:ASP153 3.8 19.9 1.0
O A:HOH601 4.0 21.4 1.0
C6N A:NAD503 4.1 13.6 1.0
CB A:ASP153 4.1 16.6 1.0
CG A:HIS62 4.1 17.1 1.0
ND1 A:HIS62 4.1 17.0 1.0
C4N A:NAD503 4.3 13.9 1.0
C2 A:9ON504 4.4 32.1 1.0
CA A:CYS38 4.6 16.2 1.0
NH2 A:ARG340 4.7 15.3 1.0
N A:SER40 4.8 16.4 1.0
CA A:SER40 4.9 16.9 1.0

Zinc binding site 3 out of 8 in 5o9d

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Zinc binding site 3 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, 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, F43H, H39Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:16.1
occ:1.00
 SG B:CYS106 2.3 18.1 1.0
SG B:CYS92 2.3 18.1 1.0
SG B:CYS95 2.3 17.1 1.0
SG B:CYS98 2.4 15.4 1.0
CB B:CYS106 3.2 17.7 1.0
CB B:CYS98 3.3 15.4 1.0
CB B:CYS95 3.4 18.6 1.0
N B:CYS92 3.4 17.3 1.0
CB B:CYS92 3.5 18.8 1.0
N B:CYS95 3.8 18.6 1.0
CA B:CYS92 3.9 18.1 1.0
N B:GLY93 3.9 17.0 1.0
CA B:CYS106 3.9 18.4 1.0
CA B:CYS95 4.2 18.7 1.0
N B:CYS98 4.2 14.9 1.0
O B:HOH619 4.3 35.9 1.0
C B:CYS92 4.3 17.8 1.0
CA B:CYS98 4.3 14.8 1.0
N B:ALA94 4.4 18.6 1.0
C B:GLY91 4.5 16.9 1.0
CB B:ARG108 4.5 31.2 1.0
CG B:ARG108 4.6 33.2 1.0
CA B:GLY91 4.7 16.2 1.0
C B:CYS106 4.8 20.9 1.0
N B:ARG108 4.8 28.5 1.0
N B:THR107 4.8 23.8 1.0
C B:CYS95 4.8 17.8 1.0
CA B:GLY93 4.9 17.1 1.0
O B:CYS95 5.0 16.8 1.0
C B:ALA94 5.0 19.3 1.0

Zinc binding site 4 out of 8 in 5o9d

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Zinc binding site 4 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, 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, F43H, H39Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:16.4
occ:1.00
 OD2 B:ASP153 1.9 18.2 1.0
O8 B:9ON504 2.0 21.7 1.0
NE2 B:HIS62 2.1 16.7 1.0
SG B:CYS38 2.3 16.2 1.0
C1 B:9ON504 2.9 27.4 1.0
CD2 B:HIS62 3.0 16.3 1.0
CG B:ASP153 3.1 17.1 1.0
CE1 B:HIS62 3.1 16.6 1.0
CB B:CYS38 3.1 15.6 1.0
O9 B:9ON504 3.2 24.4 1.0
C5N B:NAD503 3.4 12.7 1.0
OD1 B:ASP153 3.8 19.1 1.0
CB B:SER40 3.8 16.2 1.0
OG B:SER40 3.8 16.9 1.0
C6N B:NAD503 4.0 12.4 1.0
O B:HOH707 4.0 4.9 0.5
CB B:ASP153 4.1 16.0 1.0
CG B:HIS62 4.2 16.4 1.0
ND1 B:HIS62 4.2 16.0 1.0
C4N B:NAD503 4.2 12.8 1.0
C2 B:9ON504 4.3 30.6 1.0
CA B:CYS38 4.6 15.8 1.0
NH2 B:ARG340 4.7 15.6 1.0
N B:SER40 4.8 16.0 1.0
CA B:SER40 4.9 16.4 1.0

Zinc binding site 5 out of 8 in 5o9d

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Zinc binding site 5 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, 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, F43H, H39Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:14.8
occ:1.00
 SG C:CYS95 2.3 15.8 1.0
SG C:CYS92 2.3 17.1 1.0
SG C:CYS106 2.3 17.5 1.0
SG C:CYS98 2.3 14.4 1.0
CB C:CYS106 3.3 17.8 1.0
CB C:CYS98 3.3 14.2 1.0
CB C:CYS95 3.4 16.7 1.0
N C:CYS92 3.5 16.8 1.0
CB C:CYS92 3.5 17.9 1.0
N C:CYS95 3.8 16.7 1.0
N C:GLY93 3.9 16.2 1.0
CA C:CYS92 3.9 17.4 1.0
CA C:CYS106 3.9 18.2 1.0
CA C:CYS95 4.2 16.7 1.0
N C:CYS98 4.2 13.4 1.0
O C:HOH646 4.3 34.8 1.0
C C:CYS92 4.3 17.1 1.0
CA C:CYS98 4.3 13.5 1.0
N C:ALA94 4.4 17.1 1.0
C C:GLY91 4.5 16.6 1.0
CB C:ARG108 4.5 31.3 1.0
CG C:ARG108 4.6 33.1 1.0
CA C:GLY91 4.7 16.2 1.0
C C:CYS106 4.8 20.7 1.0
N C:THR107 4.8 23.7 1.0
C C:CYS95 4.8 15.8 1.0
N C:ARG108 4.8 28.6 1.0
CA C:GLY93 4.9 16.2 1.0
O C:CYS95 4.9 15.0 1.0
C C:ALA94 5.0 17.4 1.0

Zinc binding site 6 out of 8 in 5o9d

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Zinc binding site 6 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, 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, F43H, H39Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:20.9
occ:1.00
 OD2 C:ASP153 1.9 22.4 1.0
O9 C:9ON504 2.0 28.4 1.0
NE2 C:HIS62 2.0 20.7 1.0
SG C:CYS38 2.3 20.1 1.0
C1 C:9ON504 3.0 32.8 1.0
CD2 C:HIS62 3.0 20.8 1.0
CE1 C:HIS62 3.0 21.0 1.0
CB C:CYS38 3.1 19.3 1.0
CG C:ASP153 3.1 20.5 1.0
O8 C:9ON504 3.3 30.8 1.0
C5N C:NAD503 3.4 14.5 1.0
CB C:SER40 3.8 20.4 1.0
OG C:SER40 3.8 20.5 1.0
OD1 C:ASP153 3.8 21.7 1.0
C6N C:NAD503 4.0 14.5 1.0
O C:HOH604 4.0 8.2 0.5
CB C:ASP153 4.1 19.3 1.0
ND1 C:HIS62 4.1 20.9 1.0
CG C:HIS62 4.1 20.5 1.0
C4N C:NAD503 4.2 14.5 1.0
C2 C:9ON504 4.3 36.9 1.0
CA C:CYS38 4.6 19.7 1.0
NH2 C:ARG340 4.7 18.6 1.0
N C:SER40 4.8 20.4 1.0
CA C:SER40 4.9 20.8 1.0

Zinc binding site 7 out of 8 in 5o9d

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Zinc binding site 7 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, 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, F43H, H39Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:15.0
occ:1.00
 SG D:CYS95 2.3 16.5 1.0
SG D:CYS92 2.3 17.2 1.0
SG D:CYS106 2.3 17.6 1.0
SG D:CYS98 2.3 15.2 1.0
CB D:CYS106 3.3 17.4 1.0
CB D:CYS98 3.3 15.3 1.0
CB D:CYS95 3.4 17.4 1.0
N D:CYS92 3.5 17.3 1.0
CB D:CYS92 3.5 18.2 1.0
N D:CYS95 3.8 17.8 1.0
N D:GLY93 3.9 17.3 1.0
CA D:CYS92 3.9 18.1 1.0
CA D:CYS106 4.0 17.6 1.0
CA D:CYS95 4.2 17.5 1.0
N D:CYS98 4.2 14.2 1.0
C D:CYS92 4.3 18.0 1.0
O D:HOH656 4.3 25.8 1.0
CA D:CYS98 4.4 14.5 1.0
N D:ALA94 4.4 18.1 1.0
C D:GLY91 4.5 17.5 1.0
CB D:ARG108 4.5 29.4 1.0
CG D:ARG108 4.6 30.9 1.0
CA D:GLY91 4.7 17.0 1.0
C D:CYS106 4.8 19.6 1.0
C D:CYS95 4.9 16.6 1.0
N D:ARG108 4.9 26.1 1.0
N D:THR107 4.9 21.7 1.0
CA D:GLY93 4.9 17.5 1.0
O D:CYS95 5.0 16.0 1.0
C D:ALA94 5.0 18.5 1.0

Zinc binding site 8 out of 8 in 5o9d

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Zinc binding site 8 out of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, 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, F43H, H39Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:26.5
occ:1.00
 OD2 D:ASP153 1.9 26.0 1.0
O8 D:9ON504 2.0 38.3 1.0
NE2 D:HIS62 2.1 28.9 1.0
SG D:CYS38 2.3 25.8 1.0
CD2 D:HIS62 3.0 28.7 1.0
C1 D:9ON504 3.1 43.8 1.0
CE1 D:HIS62 3.1 29.3 1.0
CG D:ASP153 3.1 23.8 1.0
CB D:CYS38 3.2 25.7 1.0
C5N D:NAD503 3.4 15.8 1.0
O9 D:9ON504 3.4 40.4 1.0
CB D:SER40 3.7 27.0 1.0
OG D:SER40 3.8 27.0 1.0
OD1 D:ASP153 3.8 24.5 1.0
C6N D:NAD503 4.0 15.8 1.0
O D:HOH603 4.0 24.9 1.0
CB D:ASP153 4.1 22.9 1.0
CG D:HIS62 4.2 28.9 1.0
ND1 D:HIS62 4.2 29.3 1.0
C4N D:NAD503 4.2 16.1 1.0
C2 D:9ON504 4.4 47.7 1.0
CA D:CYS38 4.6 26.2 1.0
NH2 D:ARG340 4.7 26.3 1.0
N D:SER40 4.8 27.2 1.0
CA D:SER40 4.9 27.5 1.0

Reference:

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
Page generated: Sun Oct 27 23:20:58 2024

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