Zinc in PDB 5vkt: Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench

All present enzymatic activity of Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench:
1.1.1.195;

The structure of Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench, PDB code: 5vkt was solved by A.M.Walker, S.Y.Jun, C.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.68 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.597, 74.280, 97.288, 90.00, 96.74, 90.00
R / Rfree (%)	16.3 / 18.7

The binding sites of Zinc atom in the Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench (pdb code 5vkt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench, PDB code: 5vkt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:12.1 occ:1.00 NE2 A:HIS69 2.0 9.8 1.0 O1 A:FMT404 2.1 11.4 1.0 SG A:CYS165 2.3 13.1 1.0 SG A:CYS47 2.4 9.4 1.0 H5N A:NAP405 2.8 10.3 1.0 C A:FMT404 3.0 17.7 1.0 CD2 A:HIS69 3.0 8.4 1.0 CE1 A:HIS69 3.1 11.8 1.0 HD2 A:HIS69 3.1 10.1 1.0 HB A:THR49 3.2 11.8 1.0 HB2 A:CYS47 3.2 11.4 1.0 CB A:CYS47 3.2 9.5 1.0 HB3 A:CYS47 3.2 11.4 1.0 HE1 A:HIS69 3.3 14.1 1.0 HB3 A:CYS165 3.4 19.5 1.0 C5N A:NAP405 3.4 8.6 1.0 CB A:CYS165 3.4 16.3 1.0 HG1 A:THR49 3.5 14.6 1.0 HB2 A:CYS165 3.6 19.5 1.0 OG1 A:THR49 3.9 12.1 1.0 CB A:THR49 4.0 9.8 1.0 H6N A:NAP405 4.0 9.4 1.0 C6N A:NAP405 4.0 7.8 1.0 C4N A:NAP405 4.1 10.9 1.0 H4N A:NAP405 4.1 13.1 1.0 HD1 A:TYR95 4.1 14.1 1.0 CG A:HIS69 4.1 10.4 1.0 O2 A:FMT404 4.2 17.0 1.0 ND1 A:HIS69 4.2 11.4 1.0 HG21 A:THR49 4.3 14.8 1.0 H A:THR49 4.3 10.2 1.0 HG3 A:GLU70 4.4 14.9 1.0 OE2 A:GLU70 4.5 17.7 1.0 HH21 A:ARG347 4.5 14.4 1.0 HB2 A:TYR95 4.6 13.0 1.0 CD1 A:TYR95 4.6 11.8 1.0 HH22 A:ARG347 4.7 14.4 1.0 CG2 A:THR49 4.7 12.3 1.0 CA A:CYS47 4.7 10.3 1.0 CA A:CYS165 4.8 12.4 1.0 HD11 A:LEU194 4.8 10.7 1.0 NH2 A:ARG347 4.9 12.0 1.0 HD1 A:HIS69 4.9 13.7 1.0 HG2 A:GLU70 5.0 14.9 1.0 CG A:GLU70 5.0 12.4 1.0

Zinc binding site 2 out of 4 in the Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:24.5 occ:1.00 SG A:CYS100 1.9 18.7 1.0 SG A:CYS103 2.3 24.9 1.0 SG A:CYS106 2.3 23.6 1.0 SG A:CYS114 2.4 21.7 1.0 HB2 A:CYS114 2.7 23.3 1.0 H A:CYS100 3.0 23.5 1.0 HB2 A:CYS106 3.1 27.7 1.0 CB A:CYS114 3.1 19.4 1.0 H A:CYS103 3.1 32.4 1.0 H A:ARG101 3.3 25.9 1.0 CB A:CYS106 3.3 23.1 1.0 CB A:CYS100 3.4 28.9 1.0 HB3 A:CYS103 3.4 42.9 1.0 HD2 A:PRO115 3.4 35.8 1.0 CB A:CYS103 3.5 35.7 1.0 HB3 A:CYS100 3.6 34.7 1.0 HA A:CYS114 3.6 20.0 1.0 H A:CYS106 3.6 26.1 1.0 N A:CYS100 3.7 19.6 1.0 HB2 A:SER99 3.8 20.6 1.0 H A:THR102 3.8 35.0 1.0 HB3 A:CYS114 3.9 23.3 1.0 N A:CYS103 3.9 27.0 1.0 N A:ARG101 3.9 21.6 1.0 CA A:CYS114 3.9 16.7 1.0 CA A:CYS100 3.9 26.4 1.0 HB3 A:CYS106 4.0 27.7 1.0 HB2 A:CYS100 4.1 34.7 1.0 N A:CYS106 4.2 21.8 1.0 CA A:CYS103 4.3 30.8 1.0 HB2 A:CYS103 4.3 42.9 1.0 C A:CYS100 4.3 20.6 1.0 O A:HOH519 4.3 31.2 1.0 CA A:CYS106 4.3 33.4 1.0 CD A:PRO115 4.3 29.9 1.0 HB2 A:SER105 4.4 37.1 1.0 H A:ASP116 4.4 25.8 1.0 N A:THR102 4.4 29.1 1.0 CB A:SER99 4.6 17.2 1.0 HA A:CYS106 4.6 40.0 1.0 HB2 A:ASP116 4.7 28.6 1.0 HG A:SER99 4.7 23.0 1.0 C A:CYS114 4.7 25.0 1.0 OG A:SER99 4.8 19.1 1.0 HD3 A:PRO115 4.8 35.8 1.0 HA A:GLU111 4.8 24.6 1.0 N A:PRO115 4.8 22.6 1.0 C A:SER99 4.8 22.3 1.0 CA A:ARG101 4.9 25.7 1.0 HA A:CYS100 4.9 31.7 1.0 C A:CYS103 4.9 33.4 1.0 HA A:ARG101 4.9 30.8 1.0 C A:THR102 4.9 38.6 1.0 HG2 A:PRO115 5.0 40.2 1.0 C A:ARG101 5.0 35.7 1.0 O A:CYS103 5.0 31.1 1.0

Zinc binding site 3 out of 4 in the Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:22.6 occ:1.00 SG B:CYS114 2.3 17.9 1.0 SG B:CYS103 2.3 24.4 1.0 SG B:CYS100 2.3 25.1 1.0 SG B:CYS106 2.4 19.9 1.0 HB2 B:CYS114 2.8 23.9 1.0 H B:CYS103 3.0 35.8 1.0 H B:CYS100 3.1 26.3 1.0 CB B:CYS114 3.1 19.9 1.0 HB2 B:CYS106 3.2 19.3 1.0 HB3 B:CYS103 3.2 39.6 1.0 H B:ARG101 3.3 27.1 1.0 CB B:CYS103 3.4 33.0 1.0 HB3 B:CYS100 3.4 30.7 1.0 CB B:CYS106 3.4 16.1 1.0 CB B:CYS100 3.4 25.6 1.0 HA B:CYS114 3.5 28.3 1.0 H B:CYS106 3.6 24.2 1.0 HB2 B:SER99 3.7 19.8 1.0 N B:CYS100 3.7 21.9 1.0 N B:CYS103 3.8 29.8 1.0 HD2 B:PRO115 3.8 26.2 1.0 N B:ARG101 3.8 22.6 1.0 H B:THR102 3.9 35.6 1.0 HB3 B:CYS114 3.9 23.9 1.0 CA B:CYS114 3.9 23.6 1.0 CA B:CYS100 4.0 27.4 1.0 HB3 B:CYS106 4.1 19.3 1.0 O B:HOH658 4.1 40.2 1.0 HB2 B:CYS103 4.1 39.6 1.0 CA B:CYS103 4.2 29.5 1.0 HB2 B:CYS100 4.3 30.7 1.0 C B:CYS100 4.3 28.3 1.0 N B:CYS106 4.3 20.2 1.0 H B:ASP116 4.4 21.8 1.0 CA B:CYS106 4.4 22.9 1.0 N B:THR102 4.4 29.6 1.0 HD3 B:PRO115 4.5 26.2 1.0 CD B:PRO115 4.5 21.8 1.0 CB B:SER99 4.5 16.5 1.0 HG B:SER99 4.6 29.8 1.0 HB2 B:SER105 4.6 26.7 1.0 OG B:SER99 4.7 24.8 1.0 HB2 B:ASP116 4.7 20.3 1.0 HA B:CYS106 4.7 27.5 1.0 C B:CYS114 4.8 20.1 1.0 CA B:ARG101 4.8 28.7 1.0 HA B:ARG101 4.8 34.5 1.0 C B:SER99 4.8 21.0 1.0 C B:CYS103 4.8 29.5 1.0 HA B:GLU111 4.9 22.9 1.0 HA B:CYS100 4.9 33.0 1.0 N B:PRO115 4.9 19.1 1.0 C B:ARG101 4.9 33.1 1.0 HA B:CYS103 5.0 35.4 1.0 C B:THR102 5.0 30.5 1.0

Zinc binding site 4 out of 4 in the Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cinnamyl Alcohol Dehydrogenases (SBCAD4) From Sorghum Bicolor (L.) Moench within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:20.8 occ:0.88 O B:HOH501 1.9 15.0 1.0 OE1 B:GLU70 2.0 23.6 1.0 NE2 B:HIS69 2.1 21.9 1.0 SG B:CYS47 2.3 21.0 1.0 SG B:CYS165 2.4 21.5 1.0 HB3 B:CYS47 2.8 27.8 1.0 CE1 B:HIS69 2.9 23.0 1.0 CD2 B:HIS69 3.0 15.5 1.0 CD B:GLU70 3.1 20.1 1.0 HE1 B:HIS69 3.1 27.6 1.0 CB B:CYS47 3.1 23.1 1.0 HB3 B:CYS165 3.1 20.7 1.0 HB2 B:CYS165 3.1 20.7 1.0 CB B:CYS165 3.2 17.2 1.0 HD2 B:HIS69 3.3 18.6 1.0 HG3 B:GLU70 3.3 19.9 1.0 CG B:GLU70 3.6 16.6 1.0 HG2 B:GLU70 3.6 19.9 1.0 HB2 B:CYS47 3.6 27.8 1.0 HH12 B:ARG347 3.8 40.5 1.0 HB B:THR49 3.9 25.6 1.0 ND1 B:HIS69 4.0 21.1 1.0 CG B:HIS69 4.1 17.3 1.0 O B:HOH502 4.1 25.9 1.0 O B:HOH686 4.1 28.8 1.0 OE2 B:GLU70 4.2 16.7 1.0 O B:HOH547 4.3 40.9 1.0 CA B:CYS47 4.4 24.9 1.0 O B:HOH523 4.4 11.9 1.0 NH1 B:ARG347 4.5 33.7 1.0 H B:CYS47 4.5 16.3 1.0 HG1 B:THR49 4.6 29.7 1.0 N B:CYS47 4.6 13.6 1.0 H B:THR49 4.7 20.6 1.0 CA B:CYS165 4.7 14.9 1.0 O B:HOH730 4.7 39.8 1.0 O B:HOH873 4.8 40.7 1.0 HD1 B:HIS69 4.8 25.4 1.0 HH11 B:ARG347 4.8 40.5 1.0 O B:HOH847 4.8 36.1 1.0 CB B:THR49 4.8 21.3 1.0 OG1 B:THR49 4.8 24.8 1.0 H B:ALA166 4.9 18.8 1.0 HH22 B:ARG347 4.9 57.9 1.0 OD2 B:ASP50 4.9 18.1 1.0 HA B:CYS165 5.0 17.9 1.0

S.Y.Jun, A.M.Walker, H.Kim, J.Ralph, W.Vermerris, S.E.Sattler, C.Kang. The Enzyme Activity and Substrate Specificity of Two Major Cinnamyl Alcohol Dehydrogenases in Sorghum (Sorghum Bicolor), SBCAD2 and SBCAD4. Plant Physiol. V. 174 2128 2017.
ISSN: ESSN 1532-2548
PubMed: 28606901
DOI: 10.1104/PP.17.00576