Zinc in PDB 1yqd: Sinapyl Alcohol Dehydrogenase Complexed with Nadp+

All present enzymatic activity of Sinapyl Alcohol Dehydrogenase Complexed with Nadp+:
1.1.1.195;

The structure of Sinapyl Alcohol Dehydrogenase Complexed with Nadp+, PDB code: 1yqd 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)	38.32 / 1.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	76.477, 137.796, 69.523, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 21.3

The binding sites of Zinc atom in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+ (pdb code 1yqd). 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 Complexed with Nadp+, PDB code: 1yqd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+


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 Complexed with Nadp+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:13.3 occ:1.00 O A:HOH2046 2.1 12.6 1.0 NE2 A:HIS72 2.2 11.9 1.0 SG A:CYS166 2.3 14.0 1.0 SG A:CYS50 2.4 11.0 1.0 CE1 A:HIS72 3.0 13.3 1.0 CD2 A:HIS72 3.2 11.3 1.0 CB A:CYS50 3.2 10.5 1.0 C5N A:NAP500 3.3 15.1 1.0 CB A:CYS166 3.5 12.3 1.0 OG A:SER52 3.6 11.4 1.0 CB A:SER52 3.7 9.8 1.0 C6N A:NAP500 3.9 13.8 1.0 SG A:CYS98 4.0 15.5 1.0 O2 A:DTT700 4.1 20.2 1.0 ND1 A:HIS72 4.1 12.3 1.0 C4N A:NAP500 4.2 15.5 1.0 CG A:HIS72 4.2 10.3 1.0 O3 A:DTT700 4.4 18.5 1.0 OE1 A:GLU73 4.7 13.9 1.0 CA A:CYS50 4.7 10.5 1.0 NH2 A:ARG348 4.9 9.8 1.0 CA A:CYS166 4.9 10.5 1.0 N A:SER52 4.9 9.9 1.0 S1 A:DTT700 4.9 30.5 1.0 CA A:SER52 4.9 9.4 1.0

Zinc binding site 2 out of 4 in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+


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 Complexed with Nadp+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:17.2 occ:1.00 SG A:CYS117 2.4 14.9 1.0 SG A:CYS106 2.4 17.7 1.0 SG A:CYS103 2.4 17.4 1.0 SG A:CYS109 2.4 16.2 1.0 CB A:CYS117 3.2 13.7 1.0 CB A:CYS106 3.4 19.1 1.0 CB A:CYS103 3.5 17.5 1.0 CB A:CYS109 3.5 15.3 1.0 N A:CYS103 3.7 14.9 1.0 N A:HIS104 3.8 18.7 1.0 N A:CYS106 3.9 20.6 1.0 CA A:CYS103 4.0 16.8 1.0 N A:CYS109 4.1 15.6 1.0 CA A:CYS117 4.1 13.8 1.0 CA A:CYS106 4.2 19.7 1.0 C A:CYS103 4.3 18.6 1.0 N A:SER105 4.3 23.1 1.0 CA A:CYS109 4.4 15.1 1.0 CD A:PRO118 4.6 16.8 1.0 CB A:ALA102 4.7 13.1 1.0 CA A:HIS104 4.7 20.7 1.0 C A:CYS106 4.8 20.3 1.0 O A:CYS106 4.8 18.9 1.0 C A:ALA102 4.9 14.2 1.0 C A:SER105 4.9 24.4 1.0 C A:CYS117 5.0 15.2 1.0

Zinc binding site 3 out of 4 in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+


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 Complexed with Nadp+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3000 b:17.1 occ:1.00 SG B:CYS106 2.3 17.5 1.0 SG B:CYS103 2.4 16.9 1.0 SG B:CYS117 2.4 15.6 1.0 SG B:CYS109 2.4 15.8 1.0 CB B:CYS117 3.2 15.0 1.0 CB B:CYS106 3.4 19.1 1.0 CB B:CYS103 3.5 15.7 1.0 CB B:CYS109 3.5 15.4 1.0 N B:HIS104 3.7 17.1 1.0 N B:CYS103 3.7 13.9 1.0 N B:CYS106 3.9 20.6 1.0 CA B:CYS103 4.0 15.8 1.0 N B:CYS109 4.1 15.7 1.0 CA B:CYS117 4.2 14.8 1.0 CA B:CYS106 4.2 19.5 1.0 C B:CYS103 4.2 18.0 1.0 N B:SER105 4.3 20.2 1.0 CA B:CYS109 4.4 15.5 1.0 CA B:HIS104 4.6 19.8 1.0 CB B:ALA102 4.7 12.6 1.0 CD B:PRO118 4.7 17.4 1.0 C B:CYS106 4.8 19.9 1.0 C B:ALA102 4.8 13.8 1.0 O B:CYS106 4.9 18.8 1.0 C B:SER105 4.9 21.5 1.0

Zinc binding site 4 out of 4 in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+


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 Complexed with Nadp+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4000 b:14.9 occ:1.00 O B:HOH4083 2.1 12.9 1.0 NE2 B:HIS72 2.2 13.2 1.0 SG B:CYS166 2.3 12.8 1.0 SG B:CYS50 2.4 11.4 1.0 CE1 B:HIS72 2.9 13.6 1.0 CB B:CYS50 3.2 11.4 1.0 CD2 B:HIS72 3.3 12.7 1.0 C5N B:NAP600 3.3 15.0 1.0 CB B:CYS166 3.5 12.6 1.0 OG B:SER52 3.6 13.6 1.0 CB B:SER52 3.8 11.9 1.0 C6N B:NAP600 3.9 14.8 1.0 O2 B:DTT800 4.0 24.2 1.0 SG B:CYS98 4.0 14.4 1.0 ND1 B:HIS72 4.1 13.9 1.0 C4N B:NAP600 4.2 15.7 1.0 CG B:HIS72 4.2 12.1 1.0 O3 B:DTT800 4.4 22.3 1.0 CA B:CYS50 4.7 11.4 1.0 OE1 B:GLU73 4.7 13.8 1.0 S1 B:DTT800 4.9 31.6 1.0 CA B:CYS166 4.9 11.5 1.0 N B:SER52 4.9 10.7 1.0 NH2 B:ARG348 4.9 10.5 1.0 CA B:SER52 5.0 11.9 1.0

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