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Zinc in PDB 1yqx: Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution

Enzymatic activity of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution

All present enzymatic activity of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution:
1.1.1.195;

Protein crystallography data

The structure of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution, PDB code: 1yqx was solved by E.K.Bomati, J.P.Noel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.33 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.362, 138.165, 67.629, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution (pdb code 1yqx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution, PDB code: 1yqx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1yqx

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Zinc binding site 1 out of 4 in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:26.8
occ:1.00
SG A:CYS50 2.4 23.9 1.0
SG A:CYS166 2.4 27.2 1.0
NE2 A:HIS72 2.4 30.9 1.0
O A:HOH2001 2.7 7.7 1.0
CE1 A:HIS72 2.9 32.5 1.0
C5N A:NAP500 3.3 24.8 1.0
CB A:CYS50 3.3 22.6 1.0
CD2 A:HIS72 3.4 28.4 1.0
CB A:CYS166 3.6 24.9 1.0
OG A:SER52 3.8 22.1 1.0
C6N A:NAP500 3.9 23.1 1.0
CB A:SER52 3.9 22.2 1.0
ND1 A:HIS72 4.0 31.1 1.0
C4N A:NAP500 4.1 22.5 1.0
CG A:HIS72 4.3 30.1 1.0
CA A:CYS50 4.8 21.3 1.0
OE1 A:GLU73 4.8 30.0 1.0
CA A:CYS166 4.9 23.1 1.0
N A:SER52 5.0 22.5 1.0

Zinc binding site 2 out of 4 in 1yqx

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Zinc binding site 2 out of 4 in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2000

b:43.4
occ:1.00
SG A:CYS103 2.4 46.8 1.0
SG A:CYS109 2.4 40.7 1.0
SG A:CYS117 2.5 34.8 1.0
SG A:CYS106 2.7 60.2 1.0
CB A:CYS117 3.2 36.1 1.0
CB A:CYS103 3.4 47.3 1.0
N A:HIS104 3.4 49.3 1.0
N A:CYS103 3.6 46.2 1.0
CB A:CYS106 3.7 56.6 1.0
CB A:CYS109 3.7 44.7 1.0
CA A:CYS103 3.8 47.2 1.0
N A:CYS106 3.9 55.0 1.0
C A:CYS103 4.0 48.1 1.0
N A:SER105 4.1 54.0 1.0
CA A:CYS117 4.2 36.6 1.0
N A:CYS109 4.3 45.8 1.0
CA A:HIS104 4.3 51.7 1.0
CA A:CYS106 4.4 55.5 1.0
CB A:ALA102 4.5 43.0 1.0
CA A:CYS109 4.6 45.6 1.0
C A:ALA102 4.7 45.6 1.0
C A:HIS104 4.7 53.0 1.0
CD A:PRO118 4.8 35.1 1.0
C A:SER105 4.9 55.6 1.0
C A:CYS106 5.0 54.8 1.0

Zinc binding site 3 out of 4 in 1yqx

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Zinc binding site 3 out of 4 in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3000

b:32.9
occ:1.00
SG B:CYS103 2.3 36.4 1.0
SG B:CYS109 2.4 38.8 1.0
SG B:CYS106 2.5 37.3 1.0
SG B:CYS117 2.5 24.3 1.0
CB B:CYS103 3.3 34.4 1.0
CB B:CYS117 3.3 25.8 1.0
CB B:CYS109 3.5 37.0 1.0
CB B:CYS106 3.5 35.7 1.0
N B:CYS103 3.8 33.5 1.0
N B:HIS104 3.8 35.2 1.0
CA B:CYS103 3.9 34.6 1.0
N B:CYS106 4.1 37.1 1.0
C B:CYS103 4.2 34.5 1.0
N B:SER105 4.2 35.9 1.0
N B:CYS109 4.2 35.5 1.0
CA B:CYS117 4.2 28.6 1.0
OG B:SER108 4.2 43.5 1.0
CA B:CYS106 4.4 37.0 1.0
CA B:CYS109 4.4 35.7 1.0
CD B:PRO118 4.5 33.2 1.0
C B:SER105 4.6 36.6 1.0
CA B:HIS104 4.7 36.4 1.0
C B:CYS106 4.9 37.4 1.0
CB B:ALA102 4.9 31.0 1.0
C B:ALA102 4.9 33.9 1.0
C B:HIS104 5.0 35.3 1.0
O B:CYS106 5.0 36.3 1.0

Zinc binding site 4 out of 4 in 1yqx

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Zinc binding site 4 out of 4 in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4000

b:29.6
occ:1.00
NE2 B:HIS72 2.2 28.2 1.0
SG B:CYS166 2.3 27.0 1.0
O B:HOH4001 2.4 19.3 1.0
SG B:CYS50 2.5 25.7 1.0
CE1 B:HIS72 2.8 29.4 1.0
CD2 B:HIS72 3.3 27.4 1.0
C5N B:NAP600 3.3 28.9 1.0
CB B:CYS50 3.3 25.6 1.0
CB B:CYS166 3.5 25.7 1.0
ND1 B:HIS72 3.9 28.6 1.0
C6N B:NAP600 4.0 26.7 1.0
CB B:SER52 4.0 24.9 1.0
OG B:SER52 4.1 25.6 1.0
C4N B:NAP600 4.1 29.0 1.0
CG B:HIS72 4.2 26.5 1.0
OE1 B:GLU73 4.7 27.0 1.0
CA B:CYS50 4.8 24.7 1.0
CA B:CYS166 4.9 25.8 1.0
SG B:CYS98 4.9 43.7 1.0

Reference:

E.K.Bomati, J.P.Noel. Structural and Kinetic Basis For Substrate Selectivity in Populus Tremuloides Sinapyl Alcohol Dehydrogenase. Plant Cell V. 17 1598 2005.
ISSN: ISSN 1040-4651
PubMed: 15829607
DOI: 10.1105/TPC.104.029983
Page generated: Wed Dec 16 03:14:54 2020

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