Atomistry » Zinc » PDB 5o1j-5of9 » 5o9d
Atomistry »
  Zinc »
    PDB 5o1j-5of9 »
      5o9d »

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

Go back to Zinc Binding Sites List in 5o9d
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

Go back to Zinc Binding Sites List in 5o9d
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

Go back to Zinc Binding Sites List in 5o9d
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

Go back to Zinc Binding Sites List in 5o9d
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

Go back to Zinc Binding Sites List in 5o9d
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

Go back to Zinc Binding Sites List in 5o9d
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

Go back to Zinc Binding Sites List in 5o9d
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

Go back to Zinc Binding Sites List in 5o9d
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy