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Zinc in PDB 2xaa: Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol

Enzymatic activity of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol

All present enzymatic activity of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol:
1.1.1.1;

Protein crystallography data

The structure of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol, PDB code: 2xaa was solved by W.Kroutil, K.Gruber, G.Grogan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 109.15 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.674, 105.100, 109.176, 90.00, 91.27, 90.00
R / Rfree (%) 18.816 / 25.756

Zinc Binding Sites:

The binding sites of Zinc atom in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol (pdb code 2xaa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol, PDB code: 2xaa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2xaa

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Zinc binding site 1 out of 8 in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1346

b:51.0
occ:1.00
 OD2 A:ASP153 2.2 34.7 1.0
SG A:CYS38 2.5 37.8 0.5
NE2 A:HIS62 2.8 40.1 1.0
C5N A:NAD503 3.0 34.5 1.0
CB A:CYS38 3.1 41.0 0.5
CG A:ASP153 3.2 33.7 1.0
CB A:CYS38 3.2 40.6 0.5
SG A:CYS38 3.2 39.9 0.5
O A:HOH2028 3.3 37.1 1.0
OD1 A:ASP153 3.4 35.2 1.0
CD2 A:HIS62 3.5 40.6 1.0
OG A:SER40 3.6 45.2 1.0
CB A:SER40 3.7 44.8 1.0
C6N A:NAD503 3.8 33.4 1.0
C4N A:NAD503 3.8 34.5 1.0
CE1 A:HIS62 3.9 41.3 1.0
CB A:ASP153 4.5 31.9 1.0
CA A:CYS38 4.6 40.9 0.5
CA A:CYS38 4.7 40.6 0.5
CG A:HIS62 4.7 41.1 1.0
ND1 A:HIS62 4.8 41.3 1.0
N A:SER40 4.9 44.3 1.0
NH2 A:ARG340 4.9 39.0 1.0
N1N A:NAD503 4.9 34.0 1.0
CA A:SER40 5.0 44.6 1.0
C3N A:NAD503 5.0 34.4 1.0

Zinc binding site 2 out of 8 in 2xaa

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Zinc binding site 2 out of 8 in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1347

b:33.6
occ:1.00
 SG A:CYS98 2.2 30.1 1.0
SG A:CYS95 2.2 34.6 1.0
SG A:CYS92 2.3 31.6 1.0
SG A:CYS106 2.3 30.3 1.0
CB A:CYS98 3.2 30.0 1.0
CB A:CYS106 3.2 32.9 1.0
CB A:CYS92 3.4 31.0 1.0
N A:CYS92 3.4 31.5 1.0
CB A:CYS95 3.5 31.6 1.0
N A:CYS95 3.7 31.8 1.0
N A:GLY93 3.8 31.8 1.0
CA A:CYS106 3.8 33.4 1.0
CA A:CYS92 3.8 31.3 1.0
CA A:CYS95 4.2 31.5 1.0
N A:THR107 4.2 37.3 1.0
C A:CYS92 4.2 31.3 1.0
N A:ALA94 4.3 31.6 1.0
CA A:CYS98 4.3 29.8 1.0
N A:CYS98 4.4 29.7 1.0
C A:GLY91 4.4 31.7 1.0
C A:CYS106 4.4 35.4 1.0
N A:ARG108 4.6 41.9 1.0
CA A:GLY91 4.7 31.9 1.0
CB A:ARG108 4.8 43.8 1.0
CA A:GLY93 4.8 31.5 1.0
C A:ALA94 4.9 31.8 1.0

Zinc binding site 3 out of 8 in 2xaa

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Zinc binding site 3 out of 8 in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1346

b:42.4
occ:1.00
 OD2 B:ASP153 2.0 32.1 1.0
NE2 B:HIS62 2.2 37.8 1.0
SG B:CYS38 2.3 40.5 1.0
O5 B:BU11347 2.9 49.7 1.0
CE1 B:HIS62 3.1 38.0 1.0
CG B:ASP153 3.1 32.9 1.0
C5N B:NAD503 3.1 42.9 1.0
CD2 B:HIS62 3.1 37.7 1.0
CB B:CYS38 3.3 40.9 1.0
OD1 B:ASP153 3.5 34.6 1.0
CB B:SER40 3.6 44.5 1.0
C6N B:NAD503 3.7 41.4 1.0
C4N B:NAD503 3.9 43.5 1.0
OG B:SER40 3.9 44.2 1.0
ND1 B:HIS62 4.1 38.5 1.0
CG B:HIS62 4.2 39.8 1.0
C1 B:BU11347 4.3 53.4 1.0
CB B:ASP153 4.4 31.5 1.0
CA B:CYS38 4.7 41.1 1.0
CA B:SER40 4.8 44.1 1.0
N1N B:NAD503 4.9 41.0 1.0
N B:SER40 4.9 43.1 1.0
NH2 B:ARG340 5.0 36.1 1.0
C3N B:NAD503 5.0 43.0 1.0

Zinc binding site 4 out of 8 in 2xaa

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Zinc binding site 4 out of 8 in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1348

b:32.3
occ:1.00
 SG B:CYS106 2.2 29.6 1.0
SG B:CYS95 2.2 33.9 1.0
SG B:CYS92 2.2 30.5 1.0
SG B:CYS98 2.4 31.1 1.0
CB B:CYS106 3.1 33.4 1.0
CB B:CYS92 3.1 31.8 1.0
N B:CYS92 3.3 32.6 1.0
CB B:CYS98 3.4 30.4 1.0
CB B:CYS95 3.4 31.9 1.0
CA B:CYS92 3.6 31.9 1.0
CA B:CYS106 3.7 34.1 1.0
N B:CYS95 3.7 31.7 1.0
N B:GLY93 3.8 31.4 1.0
C B:CYS92 4.1 31.6 1.0
CA B:CYS95 4.1 31.5 1.0
N B:THR107 4.3 37.9 1.0
N B:ALA94 4.3 31.6 1.0
C B:CYS106 4.4 36.0 1.0
C B:GLY91 4.4 33.2 1.0
N B:CYS98 4.4 29.9 1.0
CA B:CYS98 4.5 30.0 1.0
N B:ARG108 4.6 41.8 1.0
CB B:ARG108 4.7 43.2 1.0
CA B:GLY91 4.7 33.3 1.0
CG B:ARG108 4.8 46.0 1.0
CA B:GLY93 4.8 31.3 1.0
C B:ALA94 4.9 31.9 1.0
C B:CYS95 5.0 31.1 1.0
N B:CYS106 5.0 32.9 1.0

Zinc binding site 5 out of 8 in 2xaa

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Zinc binding site 5 out of 8 in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1346

b:37.1
occ:1.00
 OD2 C:ASP153 1.7 32.3 1.0
NE2 C:HIS62 2.1 37.2 1.0
SG C:CYS38 2.3 35.7 1.0
O5 C:BU11348 2.8 38.9 1.0
CG C:ASP153 2.8 32.5 1.0
CD2 C:HIS62 3.1 38.1 1.0
CE1 C:HIS62 3.1 37.7 1.0
C5N C:NAD503 3.2 27.7 1.0
CB C:CYS38 3.3 38.2 1.0
OD1 C:ASP153 3.3 34.5 1.0
OG C:SER40 3.3 42.0 1.0
CB C:SER40 3.6 41.8 1.0
C6N C:NAD503 3.8 29.5 1.0
CB C:ASP153 4.1 31.4 1.0
C1 C:BU11348 4.1 40.9 1.0
C4N C:NAD503 4.1 28.1 1.0
ND1 C:HIS62 4.2 39.2 1.0
CG C:HIS62 4.2 39.3 1.0
CA C:CYS38 4.7 38.4 1.0
NH2 C:ARG340 4.8 37.6 1.0
N C:SER40 4.8 41.3 1.0
CA C:SER40 4.8 41.8 1.0
N1N C:NAD503 4.9 29.1 1.0
C2 C:BU11348 5.0 41.3 1.0

Zinc binding site 6 out of 8 in 2xaa

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Zinc binding site 6 out of 8 in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1347

b:31.2
occ:1.00
 SG C:CYS98 2.2 30.8 1.0
SG C:CYS95 2.2 34.3 1.0
SG C:CYS92 2.3 33.5 1.0
SG C:CYS106 2.4 35.1 1.0
CB C:CYS98 3.2 29.9 1.0
CB C:CYS106 3.3 34.4 1.0
CB C:CYS95 3.3 31.2 1.0
N C:CYS92 3.3 31.4 1.0
CB C:CYS92 3.3 31.3 1.0
CA C:CYS106 3.7 34.9 1.0
CA C:CYS92 3.8 31.5 1.0
N C:GLY93 3.8 31.5 1.0
N C:CYS95 3.9 31.2 1.0
CA C:CYS95 4.1 31.2 1.0
C C:CYS92 4.2 31.6 1.0
N C:THR107 4.2 37.4 1.0
CA C:CYS98 4.3 30.6 1.0
N C:CYS98 4.4 30.6 1.0
C C:CYS106 4.4 36.1 1.0
C C:GLY91 4.4 32.2 1.0
N C:ALA94 4.4 31.0 1.0
N C:ARG108 4.5 41.2 1.0
CB C:ARG108 4.7 43.1 1.0
CA C:GLY91 4.8 32.3 1.0
CA C:GLY93 4.8 31.0 1.0
C C:CYS95 4.8 31.0 1.0
O C:CYS95 4.9 31.0 1.0
CG C:ARG108 4.9 45.7 1.0
C C:GLY93 4.9 31.3 1.0
C C:ALA94 4.9 31.1 1.0
N C:CYS106 5.0 33.1 1.0

Zinc binding site 7 out of 8 in 2xaa

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Zinc binding site 7 out of 8 in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1346

b:35.6
occ:1.00
 OD2 D:ASP153 1.9 32.0 1.0
NE2 D:HIS62 2.1 38.8 1.0
SG D:CYS38 2.2 37.2 1.0
O6 D:BU11347 2.3 25.1 1.0
CE1 D:HIS62 3.0 38.8 1.0
CG D:ASP153 3.1 32.7 1.0
CD2 D:HIS62 3.1 39.4 1.0
CB D:CYS38 3.1 38.5 1.0
C5N D:NAD503 3.2 36.0 1.0
OG D:SER40 3.3 42.3 1.0
OD1 D:ASP153 3.7 32.9 1.0
C4 D:BU11347 3.7 31.3 1.0
CB D:SER40 3.7 42.0 1.0
C6N D:NAD503 3.9 36.3 1.0
C4N D:NAD503 4.0 36.7 1.0
ND1 D:HIS62 4.1 39.6 1.0
CG D:HIS62 4.2 39.6 1.0
CB D:ASP153 4.2 31.7 1.0
CA D:CYS38 4.6 39.0 1.0
NH2 D:ARG340 4.6 36.8 1.0
N D:SER40 4.8 41.5 1.0
C3 D:BU11347 4.8 33.7 1.0
CA D:SER40 4.9 42.0 1.0
N1N D:NAD503 5.0 35.5 1.0

Zinc binding site 8 out of 8 in 2xaa

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Zinc binding site 8 out of 8 in the Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Alcohol Dehydrogenase Adh-'A' From Rhodococcus Ruber Dsm 44541 at pH 8.5 in Complex with Nad and Butane-1,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1348

b:34.2
occ:1.00
 SG D:CYS98 2.2 30.9 1.0
SG D:CYS106 2.4 30.9 1.0
SG D:CYS92 2.4 33.5 1.0
SG D:CYS95 2.4 35.4 1.0
CB D:CYS95 3.2 32.2 1.0
CB D:CYS92 3.3 31.2 1.0
CB D:CYS98 3.3 30.7 1.0
N D:CYS92 3.4 32.3 1.0
CB D:CYS106 3.5 33.4 1.0
N D:CYS95 3.7 32.5 1.0
CA D:CYS92 3.8 32.1 1.0
N D:GLY93 3.9 32.0 1.0
CA D:CYS106 3.9 34.1 1.0
CA D:CYS95 4.0 32.6 1.0
C D:CYS92 4.1 32.2 1.0
N D:CYS98 4.2 31.1 1.0
CG D:ARG108 4.3 46.5 1.0
N D:ALA94 4.3 31.8 1.0
N D:THR107 4.3 37.9 1.0
CA D:CYS98 4.4 30.8 1.0
C D:GLY91 4.4 32.7 1.0
C D:CYS106 4.5 35.9 1.0
CB D:ARG108 4.5 43.4 1.0
C D:CYS95 4.7 32.2 1.0
N D:ARG108 4.7 41.8 1.0
C D:ALA94 4.8 32.2 1.0
CA D:GLY91 4.8 32.7 1.0
O D:CYS95 4.8 31.7 1.0
CA D:GLY93 4.9 31.6 1.0
C D:GLY93 4.9 31.5 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.) V. 46 6314 2010.
ISSN: ISSN 1359-7345
PubMed: 20676439
DOI: 10.1039/C0CC00929F
Page generated: Thu Oct 17 05:13:28 2024

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