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Zinc in PDB 3jv7: Structure of Adh-A From Rhodococcus Ruber

Enzymatic activity of Structure of Adh-A From Rhodococcus Ruber

All present enzymatic activity of Structure of Adh-A From Rhodococcus Ruber:
1.1.1.1;

Protein crystallography data

The structure of Structure of Adh-A From Rhodococcus Ruber, PDB code: 3jv7 was solved by M.Karabec, A.Lyskowski, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.45 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.822, 106.119, 109.097, 90.00, 91.26, 90.00
R / Rfree (%) 15.9 / 20.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Adh-A From Rhodococcus Ruber (pdb code 3jv7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Adh-A From Rhodococcus Ruber, PDB code: 3jv7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3jv7

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Zinc binding site 1 out of 8 in the Structure of Adh-A From Rhodococcus Ruber


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Adh-A From Rhodococcus Ruber within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:23.2
occ:1.00
 SG A:CYS95 2.3 21.5 1.0
SG A:CYS98 2.3 21.9 1.0
SG A:CYS106 2.4 23.0 1.0
SG A:CYS92 2.4 24.3 1.0
CB A:CYS95 3.3 17.3 1.0
CB A:CYS106 3.3 26.4 1.0
CB A:CYS98 3.3 21.2 1.0
N A:CYS92 3.4 21.7 1.0
CB A:CYS92 3.5 21.6 1.0
N A:CYS95 3.7 20.3 1.0
CA A:CYS106 3.8 22.8 1.0
N A:GLY93 3.8 20.1 1.0
CA A:CYS92 3.9 22.5 1.0
CA A:CYS95 4.1 23.4 1.0
N A:THR107 4.2 21.6 1.0
N A:CYS98 4.2 18.6 1.0
C A:CYS92 4.3 25.6 1.0
CA A:CYS98 4.4 22.1 1.0
N A:ALA94 4.4 24.2 1.0
C A:CYS106 4.4 23.3 1.0
C A:GLY91 4.4 24.6 1.0
N A:ARG108 4.5 30.5 1.0
CB A:ARG108 4.5 29.9 1.0
CG A:ARG108 4.7 40.5 1.0
CA A:GLY91 4.7 22.4 1.0
C A:CYS95 4.8 23.2 1.0
CA A:GLY93 4.9 22.3 1.0
C A:ALA94 4.9 30.9 1.0
O A:CYS95 4.9 20.1 1.0

Zinc binding site 2 out of 8 in 3jv7

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Zinc binding site 2 out of 8 in the Structure of Adh-A From Rhodococcus Ruber


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Adh-A From Rhodococcus Ruber within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:22.6
occ:1.00
 OD2 A:ASP153 1.9 19.6 1.0
OXT A:ACY504 2.0 22.3 1.0
NE2 A:HIS62 2.1 16.8 1.0
SG A:CYS38 2.3 21.5 1.0
C A:ACY504 2.9 24.6 1.0
CD2 A:HIS62 3.0 16.8 1.0
CG A:ASP153 3.0 24.4 1.0
CB A:CYS38 3.1 24.5 1.0
CE1 A:HIS62 3.1 20.2 1.0
CH3 A:ACY504 3.3 27.2 1.0
C5N A:NAD503 3.4 14.5 1.0
OD1 A:ASP153 3.5 22.0 1.0
OG A:SER40 3.9 16.9 1.0
CB A:SER40 3.9 16.3 1.0
C6N A:NAD503 4.0 16.4 1.0
O A:ACY504 4.0 29.1 1.0
CG A:HIS62 4.2 18.1 1.0
C4N A:NAD503 4.2 18.3 1.0
ND1 A:HIS62 4.2 19.4 1.0
CB A:ASP153 4.3 21.4 1.0
CA A:CYS38 4.6 24.6 1.0
NH2 A:ARG340 4.6 19.0 1.0
N A:SER40 4.8 17.0 1.0
CA A:SER40 5.0 19.3 1.0

Zinc binding site 3 out of 8 in 3jv7

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Zinc binding site 3 out of 8 in the Structure of Adh-A From Rhodococcus Ruber


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Adh-A From Rhodococcus Ruber within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:21.9
occ:1.00
 SG B:CYS95 2.3 19.6 1.0
SG B:CYS98 2.4 18.5 1.0
SG B:CYS106 2.4 23.4 1.0
SG B:CYS92 2.4 22.9 1.0
CB B:CYS98 3.2 15.0 1.0
CB B:CYS106 3.3 20.3 1.0
CB B:CYS95 3.4 23.5 1.0
N B:CYS92 3.5 22.1 1.0
CB B:CYS92 3.6 20.6 1.0
N B:CYS95 3.7 20.6 1.0
CA B:CYS106 3.8 16.1 1.0
N B:GLY93 3.8 23.0 1.0
CA B:CYS92 4.0 20.3 1.0
CA B:CYS95 4.1 20.1 1.0
N B:CYS98 4.2 17.6 1.0
N B:THR107 4.2 24.2 1.0
N B:ALA94 4.2 22.5 1.0
CA B:CYS98 4.3 18.8 1.0
C B:CYS92 4.3 25.5 1.0
C B:CYS106 4.4 22.1 1.0
C B:GLY91 4.5 21.2 1.0
N B:ARG108 4.5 29.1 1.0
CB B:ARG108 4.5 28.7 1.0
CG B:ARG108 4.6 40.2 1.0
CA B:GLY91 4.7 18.4 1.0
CA B:GLY93 4.7 18.6 1.0
C B:CYS95 4.8 25.8 1.0
O B:CYS95 4.8 21.9 1.0
C B:ALA94 4.9 27.6 1.0
C B:GLY93 4.9 22.8 1.0

Zinc binding site 4 out of 8 in 3jv7

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Zinc binding site 4 out of 8 in the Structure of Adh-A From Rhodococcus Ruber


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Adh-A From Rhodococcus Ruber within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:21.5
occ:1.00
 OXT B:ACY504 1.9 18.9 1.0
OD2 B:ASP153 1.9 18.3 1.0
NE2 B:HIS62 2.1 15.7 1.0
SG B:CYS38 2.3 21.4 1.0
C B:ACY504 2.8 29.4 1.0
CD2 B:HIS62 3.0 14.9 1.0
CG B:ASP153 3.0 20.3 1.0
CB B:CYS38 3.1 23.5 1.0
CE1 B:HIS62 3.1 18.7 1.0
CH3 B:ACY504 3.2 26.7 1.0
C5N B:NAD503 3.4 18.0 1.0
OD1 B:ASP153 3.5 21.0 1.0
CB B:SER40 3.9 19.6 1.0
OG B:SER40 3.9 23.7 1.0
O B:ACY504 4.0 27.2 1.0
C6N B:NAD503 4.0 17.2 1.0
C4N B:NAD503 4.1 22.1 1.0
CG B:HIS62 4.2 16.8 1.0
ND1 B:HIS62 4.2 14.4 1.0
CB B:ASP153 4.2 18.4 1.0
NH2 B:ARG340 4.5 18.0 1.0
CA B:CYS38 4.5 20.1 1.0
N B:SER40 4.8 19.6 1.0
CA B:SER40 5.0 22.7 1.0

Zinc binding site 5 out of 8 in 3jv7

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Zinc binding site 5 out of 8 in the Structure of Adh-A From Rhodococcus Ruber


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Adh-A From Rhodococcus Ruber within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:27.4
occ:1.00
 SG C:CYS92 2.3 26.5 1.0
SG C:CYS98 2.3 26.1 1.0
SG C:CYS95 2.3 23.6 1.0
SG C:CYS106 2.5 24.6 1.0
CB C:CYS98 3.2 23.7 1.0
CB C:CYS106 3.3 23.2 1.0
CB C:CYS95 3.4 21.3 1.0
CB C:CYS92 3.5 27.8 1.0
N C:CYS92 3.5 32.7 1.0
N C:GLY93 3.7 28.0 1.0
N C:CYS95 3.8 24.9 1.0
CA C:CYS106 3.8 24.7 1.0
CA C:CYS92 3.9 29.6 1.0
CA C:CYS95 4.1 23.7 1.0
C C:CYS92 4.2 31.2 1.0
N C:CYS98 4.2 17.3 1.0
N C:THR107 4.3 26.2 1.0
N C:ALA94 4.3 29.6 1.0
CA C:CYS98 4.3 20.6 1.0
C C:GLY91 4.4 31.7 1.0
C C:CYS106 4.4 32.2 1.0
CB C:ARG108 4.5 37.2 1.0
N C:ARG108 4.6 32.0 1.0
CA C:GLY91 4.7 30.0 1.0
CG C:ARG108 4.7 46.9 1.0
CA C:GLY93 4.7 29.2 1.0
C C:CYS95 4.8 17.5 1.0
C C:GLY93 4.9 30.8 1.0
C C:ALA94 4.9 31.2 1.0
O C:CYS95 5.0 24.7 1.0

Zinc binding site 6 out of 8 in 3jv7

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Zinc binding site 6 out of 8 in the Structure of Adh-A From Rhodococcus Ruber


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Adh-A From Rhodococcus Ruber within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:32.8
occ:1.00
 OXT C:ACY504 1.9 34.1 1.0
OD2 C:ASP153 2.0 29.1 1.0
NE2 C:HIS62 2.1 35.0 1.0
SG C:CYS38 2.3 28.9 1.0
CD2 C:HIS62 2.9 38.7 1.0
C C:ACY504 2.9 36.6 1.0
CB C:CYS38 3.1 24.5 1.0
CE1 C:HIS62 3.1 37.5 1.0
CG C:ASP153 3.1 32.3 1.0
C5N C:NAD503 3.4 30.9 1.0
CH3 C:ACY504 3.4 28.2 1.0
OD1 C:ASP153 3.7 29.5 1.0
CB C:SER40 3.9 33.0 1.0
OG C:SER40 3.9 28.9 1.0
O C:ACY504 4.0 36.2 1.0
C6N C:NAD503 4.0 29.5 1.0
CG C:HIS62 4.1 41.5 1.0
C4N C:NAD503 4.2 29.3 1.0
ND1 C:HIS62 4.2 36.2 1.0
CB C:ASP153 4.3 31.9 1.0
NH2 C:ARG340 4.5 32.1 1.0
CA C:CYS38 4.6 29.6 1.0
N C:SER40 4.9 28.4 1.0
CA C:SER40 5.0 31.1 1.0

Zinc binding site 7 out of 8 in 3jv7

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Zinc binding site 7 out of 8 in the Structure of Adh-A From Rhodococcus Ruber


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Adh-A From Rhodococcus Ruber within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:23.2
occ:1.00
 SG D:CYS95 2.3 23.4 1.0
SG D:CYS98 2.3 21.3 1.0
SG D:CYS106 2.3 20.2 1.0
SG D:CYS92 2.4 24.2 1.0
CB D:CYS106 3.3 16.9 1.0
CB D:CYS98 3.3 18.8 1.0
CB D:CYS95 3.4 18.2 1.0
N D:CYS92 3.5 26.6 1.0
CB D:CYS92 3.5 28.4 1.0
N D:CYS95 3.7 22.8 1.0
CA D:CYS106 3.8 19.8 1.0
N D:GLY93 3.9 27.1 1.0
CA D:CYS92 3.9 25.5 1.0
CA D:CYS95 4.1 21.5 1.0
N D:CYS98 4.2 17.6 1.0
N D:THR107 4.3 23.0 1.0
C D:CYS92 4.3 30.0 1.0
N D:ALA94 4.3 24.8 1.0
CA D:CYS98 4.3 18.8 1.0
C D:CYS106 4.4 30.1 1.0
CB D:ARG108 4.5 28.9 1.0
C D:GLY91 4.5 30.5 1.0
N D:ARG108 4.5 23.5 1.0
CG D:ARG108 4.6 39.1 1.0
CA D:GLY91 4.7 27.3 1.0
C D:CYS95 4.8 20.9 1.0
CA D:GLY93 4.9 21.5 1.0
C D:ALA94 4.9 29.1 1.0
C D:GLY93 4.9 23.6 1.0
O D:CYS95 5.0 21.8 1.0

Zinc binding site 8 out of 8 in 3jv7

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Zinc binding site 8 out of 8 in the Structure of Adh-A From Rhodococcus Ruber


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Adh-A From Rhodococcus Ruber within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:24.0
occ:1.00
 OD2 D:ASP153 1.9 30.1 1.0
OXT D:ACY504 2.0 25.1 1.0
NE2 D:HIS62 2.0 19.5 1.0
SG D:CYS38 2.3 24.6 1.0
CD2 D:HIS62 2.9 20.1 1.0
C D:ACY504 2.9 31.6 1.0
CG D:ASP153 3.0 22.6 1.0
CE1 D:HIS62 3.1 21.4 1.0
CB D:CYS38 3.1 24.8 1.0
CH3 D:ACY504 3.3 28.8 1.0
C5N D:NAD503 3.4 25.4 1.0
OD1 D:ASP153 3.5 19.2 1.0
OG D:SER40 3.9 21.8 1.0
CB D:SER40 3.9 22.7 1.0
C6N D:NAD503 4.0 24.6 1.0
O D:ACY504 4.1 28.6 1.0
CG D:HIS62 4.1 24.4 1.0
C4N D:NAD503 4.1 23.7 1.0
ND1 D:HIS62 4.1 21.2 1.0
CB D:ASP153 4.3 19.5 1.0
NH2 D:ARG340 4.6 19.2 1.0
CA D:CYS38 4.6 26.5 1.0
N D:SER40 4.9 23.0 1.0
CA D:SER40 5.0 26.3 1.0

Reference:

M.Karabec, A.Lyskowski, K.C.Tauber, G.Steinkellner, W.Kroutil, G.Grogan, K.Gruber. Structural Insights Into Substrate Specificity and Solvent Tolerance in Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541. Chem.Commun.(Camb.) 2010.
ISSN: ESSN 1364-548X
PubMed: 20676439
DOI: 10.1039/C0CC00929F
Page generated: Wed Dec 16 04:28:47 2020

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