Atomistry » Zinc » PDB 5o1j-5of9 » 5o8q
Atomistry »
  Zinc »
    PDB 5o1j-5of9 »
      5o8q »

Zinc in PDB 5o8q: Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A

Protein crystallography data

The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, PDB code: 5o8q 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) 29.64 / 2.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.689, 109.458, 256.653, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.6

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A (pdb code 5o8q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, PDB code: 5o8q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 1 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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

b:74.5
occ:1.00
 OD2 A:ASP153 1.9 40.3 1.0
CE1 A:HIS62 2.6 50.9 1.0
SG A:CYS38 2.7 56.6 1.0
OG A:SER40 2.8 62.3 1.0
NE2 A:HIS62 2.8 51.8 1.0
CG A:ASP153 3.1 37.5 1.0
C5N A:NAD503 3.2 26.3 1.0
CB A:CYS38 3.3 50.2 1.0
ND1 A:HIS62 3.9 48.8 1.0
C6N A:NAD503 3.9 26.6 1.0
CB A:ASP153 4.0 34.5 1.0
C4N A:NAD503 4.0 25.8 1.0
OD1 A:ASP153 4.0 38.8 1.0
CB A:SER40 4.1 60.4 1.0
CD2 A:HIS62 4.2 49.5 1.0
N A:SER40 4.6 58.5 1.0
NH2 A:ARG340 4.7 35.0 1.0
CG A:HIS62 4.7 47.1 1.0
CA A:CYS38 4.8 49.6 1.0
OE2 A:GLU63 4.9 45.2 1.0

Zinc binding site 2 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 2 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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

b:27.9
occ:1.00
 SG A:CYS106 2.3 32.9 1.0
SG A:CYS98 2.3 27.1 1.0
SG A:CYS92 2.3 32.7 1.0
SG A:CYS95 2.4 30.8 1.0
CB A:CYS106 3.3 33.6 1.0
CB A:CYS98 3.3 27.2 1.0
CB A:CYS95 3.4 32.8 1.0
N A:CYS92 3.4 31.2 1.0
CB A:CYS92 3.5 33.7 1.0
N A:CYS95 3.8 32.4 1.0
CA A:CYS106 3.9 34.5 1.0
CA A:CYS92 3.9 32.4 1.0
N A:GLY93 3.9 30.3 1.0
CA A:CYS95 4.2 32.7 1.0
N A:CYS98 4.3 26.4 1.0
C A:CYS92 4.3 31.9 1.0
CA A:CYS98 4.4 26.2 1.0
N A:ALA94 4.4 31.8 1.0
N A:THR107 4.4 44.3 1.0
C A:GLY91 4.5 30.4 1.0
C A:CYS106 4.5 39.3 1.0
CB A:ARG108 4.7 57.4 1.0
CA A:GLY91 4.7 29.4 1.0
N A:ARG108 4.7 53.3 1.0
C A:CYS95 4.9 31.4 1.0
CA A:GLY93 4.9 29.9 1.0
C A:ALA94 4.9 33.2 1.0
O A:CYS95 5.0 30.4 1.0

Zinc binding site 3 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 3 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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

b:84.0
occ:1.00
 OD2 B:ASP153 2.1 39.5 1.0
NE2 B:HIS62 2.4 47.2 1.0
SG B:CYS38 2.8 55.0 1.0
CB B:CYS38 3.0 48.7 1.0
CD2 B:HIS62 3.0 45.6 1.0
CG B:ASP153 3.2 35.9 1.0
CE1 B:HIS62 3.5 47.2 1.0
OG B:SER40 3.7 48.9 1.0
CB B:ASP153 3.9 33.1 1.0
C5N B:NAD503 3.9 24.1 1.0
CB B:SER40 4.1 50.0 1.0
OD1 B:ASP153 4.2 37.2 1.0
CG B:HIS62 4.3 43.9 1.0
ND1 B:HIS62 4.5 46.0 1.0
CA B:CYS38 4.5 47.2 1.0
OE2 B:GLU63 4.6 44.0 1.0
O B:HOH678 4.6 36.5 1.0
NH2 B:ARG340 4.6 35.2 1.0
N B:SER40 4.7 49.9 1.0
C6N B:NAD503 4.7 24.1 1.0
C4N B:NAD503 4.7 23.6 1.0
CG B:GLU63 4.8 40.3 1.0
C B:CYS38 5.0 47.7 1.0

Zinc binding site 4 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 4 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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

b:28.2
occ:1.00
 SG B:CYS98 2.3 26.9 1.0
SG B:CYS95 2.3 28.8 1.0
SG B:CYS106 2.4 31.9 1.0
SG B:CYS92 2.4 31.9 1.0
CB B:CYS98 3.2 26.6 1.0
CB B:CYS106 3.3 32.1 1.0
CB B:CYS95 3.4 31.0 1.0
N B:CYS92 3.5 31.0 1.0
CB B:CYS92 3.5 33.2 1.0
N B:CYS95 3.8 31.1 1.0
CA B:CYS106 3.9 32.8 1.0
N B:GLY93 3.9 30.0 1.0
CA B:CYS92 4.0 32.2 1.0
CA B:CYS95 4.1 31.2 1.0
N B:CYS98 4.2 25.8 1.0
CA B:CYS98 4.3 25.5 1.0
C B:CYS92 4.3 31.5 1.0
N B:ALA94 4.4 30.9 1.0
N B:THR107 4.4 42.5 1.0
C B:GLY91 4.6 30.4 1.0
C B:CYS106 4.6 37.5 1.0
CB B:ARG108 4.8 56.7 1.0
CA B:GLY91 4.8 29.1 1.0
N B:ARG108 4.8 51.6 1.0
C B:CYS95 4.8 29.9 1.0
CA B:GLY93 4.9 29.5 1.0
C B:ALA94 4.9 32.0 1.0
O B:CYS95 4.9 28.8 1.0

Zinc binding site 5 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 5 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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

b:86.6
occ:1.00
 OD2 C:ASP153 2.2 42.9 1.0
NE2 C:HIS62 2.7 59.7 1.0
SG C:CYS38 2.8 54.6 1.0
CB C:CYS38 3.3 52.2 1.0
C5N C:NAD503 3.3 26.7 1.0
CG C:ASP153 3.4 39.2 1.0
CD2 C:HIS62 3.4 58.0 1.0
CE1 C:HIS62 3.7 59.4 1.0
OG C:SER40 3.8 56.0 1.0
CB C:SER40 3.9 58.0 1.0
C6N C:NAD503 4.0 25.8 1.0
C4N C:NAD503 4.1 26.2 1.0
OD1 C:ASP153 4.2 40.8 1.0
O C:HOH630 4.3 33.7 1.0
CB C:ASP153 4.3 37.1 1.0
N C:SER40 4.5 59.5 1.0
CG C:HIS62 4.7 56.4 1.0
CA C:CYS38 4.8 53.0 1.0
ND1 C:HIS62 4.8 58.1 1.0
NH2 C:ARG340 4.8 39.4 1.0
CA C:SER40 4.8 60.4 1.0

Zinc binding site 6 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 6 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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

b:27.0
occ:1.00
 SG C:CYS98 2.3 27.1 1.0
SG C:CYS106 2.3 29.8 1.0
SG C:CYS95 2.3 27.8 1.0
SG C:CYS92 2.4 30.7 1.0
CB C:CYS106 3.3 28.6 1.0
CB C:CYS98 3.3 26.8 1.0
CB C:CYS95 3.4 30.1 1.0
N C:CYS92 3.5 31.5 1.0
CB C:CYS92 3.5 33.2 1.0
CA C:CYS106 3.8 28.2 1.0
N C:CYS95 3.8 31.4 1.0
N C:GLY93 3.9 31.2 1.0
CA C:CYS92 4.0 32.7 1.0
CA C:CYS95 4.2 30.4 1.0
N C:CYS98 4.2 24.6 1.0
CA C:CYS98 4.3 25.1 1.0
C C:CYS92 4.3 32.4 1.0
N C:THR107 4.4 32.8 1.0
N C:ALA94 4.4 31.8 1.0
C C:CYS106 4.5 30.8 1.0
C C:GLY91 4.5 31.3 1.0
CA C:GLY91 4.7 30.1 1.0
N C:ARG108 4.7 41.2 1.0
CB C:ARG108 4.8 45.6 1.0
C C:CYS95 4.9 29.0 1.0
CA C:GLY93 4.9 31.0 1.0
O C:CYS95 5.0 27.7 1.0
C C:ALA94 5.0 32.1 1.0

Zinc binding site 7 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 7 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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

b:75.8
occ:1.00
 OD2 D:ASP153 2.0 41.2 1.0
CE1 D:HIS62 2.5 47.4 1.0
O D:HOH697 2.5 42.7 1.0
SG D:CYS38 2.7 53.5 1.0
NE2 D:HIS62 2.7 48.0 1.0
CG D:ASP153 3.2 37.1 1.0
CB D:CYS38 3.3 46.6 1.0
C5N D:NAD503 3.3 25.0 1.0
ND1 D:HIS62 3.8 45.6 1.0
OG D:SER40 3.8 50.6 1.0
CB D:SER40 3.9 53.0 1.0
C6N D:NAD503 4.0 25.2 1.0
O D:HOH690 4.0 38.3 1.0
CB D:ASP153 4.1 34.1 1.0
OD1 D:ASP153 4.1 38.2 1.0
CD2 D:HIS62 4.1 45.8 1.0
C4N D:NAD503 4.1 24.9 1.0
N D:SER40 4.5 53.2 1.0
CG D:HIS62 4.6 43.4 1.0
O D:HOH695 4.6 38.8 1.0
CA D:CYS38 4.7 45.4 1.0
NH2 D:ARG340 4.8 32.7 1.0
CA D:SER40 4.9 54.6 1.0
OE2 D:GLU63 4.9 41.3 1.0

Zinc binding site 8 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 8 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


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

b:24.8
occ:1.00
 SG D:CYS92 2.3 27.6 1.0
SG D:CYS98 2.3 25.4 1.0
SG D:CYS106 2.3 29.1 1.0
SG D:CYS95 2.4 25.7 1.0
CB D:CYS98 3.3 24.2 1.0
CB D:CYS106 3.3 29.3 1.0
CB D:CYS95 3.4 27.4 1.0
N D:CYS92 3.5 27.0 1.0
CB D:CYS92 3.5 28.6 1.0
N D:CYS95 3.8 27.0 1.0
N D:GLY93 3.9 25.6 1.0
CA D:CYS92 3.9 27.8 1.0
CA D:CYS106 3.9 29.9 1.0
CA D:CYS95 4.2 27.3 1.0
C D:CYS92 4.3 26.9 1.0
N D:CYS98 4.3 23.3 1.0
N D:ALA94 4.3 26.4 1.0
CA D:CYS98 4.4 23.0 1.0
N D:THR107 4.4 37.2 1.0
C D:GLY91 4.5 26.9 1.0
C D:CYS106 4.6 33.5 1.0
CB D:ARG108 4.7 49.0 1.0
CA D:GLY91 4.7 26.2 1.0
N D:ARG108 4.8 45.5 1.0
CA D:GLY93 4.9 25.2 1.0
C D:CYS95 4.9 26.1 1.0
C D:ALA94 4.9 27.4 1.0
O D:CYS95 5.0 24.8 1.0

Zinc binding site 9 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 9 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:71.0
occ:1.00
 OD2 E:ASP153 2.2 38.7 1.0
CE1 E:HIS62 2.6 47.2 1.0
SG E:CYS38 2.7 54.2 1.0
NE2 E:HIS62 2.9 47.7 1.0
C5N E:NAD503 3.1 24.3 1.0
CB E:CYS38 3.3 49.6 1.0
CG E:ASP153 3.4 35.7 1.0
C6N E:NAD503 3.7 24.7 1.0
OG E:SER40 3.8 59.2 1.0
CB E:SER40 3.9 60.3 1.0
C4N E:NAD503 3.9 25.4 1.0
ND1 E:HIS62 3.9 45.2 1.0
O E:HOH653 4.0 38.1 1.0
OD1 E:ASP153 4.2 36.7 1.0
CD2 E:HIS62 4.2 45.5 1.0
CB E:ASP153 4.3 33.8 1.0
N E:SER40 4.4 60.4 1.0
CG E:HIS62 4.7 43.7 1.0
CA E:CYS38 4.7 49.5 1.0
O E:HOH636 4.7 41.0 1.0
CA E:SER40 4.8 61.8 1.0
NH2 E:ARG340 4.8 34.4 1.0
N1N E:NAD503 4.8 25.3 1.0
N E:HIS39 5.0 55.0 1.0

Zinc binding site 10 out of 16 in 5o8q

Go back to Zinc Binding Sites List in 5o8q
Zinc binding site 10 out of 16 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:22.6
occ:1.00
 SG E:CYS106 2.3 24.4 1.0
SG E:CYS98 2.3 23.3 1.0
SG E:CYS92 2.4 26.6 1.0
SG E:CYS95 2.4 23.4 1.0
CB E:CYS106 3.3 24.9 1.0
CB E:CYS98 3.3 23.2 1.0
CB E:CYS95 3.4 25.3 1.0
N E:CYS92 3.5 26.5 1.0
CB E:CYS92 3.5 28.0 1.0
N E:CYS95 3.8 26.1 1.0
CA E:CYS106 3.8 25.3 1.0
CA E:CYS92 3.9 27.2 1.0
N E:GLY93 3.9 25.3 1.0
CA E:CYS95 4.2 25.7 1.0
N E:CYS98 4.3 22.5 1.0
C E:CYS92 4.3 26.9 1.0
CA E:CYS98 4.4 22.5 1.0
N E:THR107 4.4 31.8 1.0
N E:ALA94 4.4 26.1 1.0
C E:GLY91 4.5 26.2 1.0
C E:CYS106 4.5 28.3 1.0
N E:ARG108 4.7 38.8 1.0
CB E:ARG108 4.7 43.2 1.0
CA E:GLY91 4.7 25.4 1.0
C E:CYS95 4.9 24.9 1.0
CA E:GLY93 4.9 25.2 1.0
C E:ALA94 4.9 27.0 1.0
O E:CYS95 5.0 24.0 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 23:20:01 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy