Zinc in PDB 5tpr: Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound

All present enzymatic activity of Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound:
4.2.3.4;

The structure of Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound, PDB code: 5tpr was solved by K.M.Kean, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.63 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.500, 120.261, 133.260, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.3

The binding sites of Zinc atom in the Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound (pdb code 5tpr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound, PDB code: 5tpr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:20.0 occ:0.50 OE2 A:GLU198 2.0 20.0 1.0 NE2 A:HIS271 2.1 16.3 1.0 O A:HOH852 2.1 19.8 0.5 NE2 A:HIS287 2.1 16.2 1.0 O A:HOH608 2.3 22.8 0.5 CE1 A:HIS271 2.9 16.9 1.0 H5N A:NAD503 3.0 32.3 1.0 CD A:GLU198 3.0 20.2 1.0 HE1 A:HIS271 3.0 20.3 1.0 CE1 A:HIS287 3.0 16.8 1.0 HE1 A:HIS287 3.2 20.1 1.0 CD2 A:HIS271 3.2 16.1 1.0 HG21 A:VAL291 3.2 14.8 1.0 CD2 A:HIS287 3.2 16.7 1.0 HD2 A:HIS287 3.4 20.0 1.0 HD2 A:HIS271 3.4 19.4 1.0 OE1 A:GLU198 3.5 20.8 1.0 C5N A:NAD503 3.5 26.9 1.0 OD2 A:ASP150 3.6 35.4 1.0 HZ3 A:LYS201 4.0 24.4 1.0 O A:HOH983 4.0 25.4 0.5 CG2 A:VAL291 4.1 12.4 1.0 C6N A:NAD503 4.1 26.2 1.0 ND1 A:HIS271 4.1 16.1 1.0 H6N A:NAD503 4.1 31.5 1.0 O A:HOH830 4.1 36.8 1.0 HG22 A:VAL291 4.2 14.8 1.0 C4N A:NAD503 4.2 28.3 1.0 ND1 A:HIS287 4.2 16.3 1.0 H4N A:NAD503 4.2 34.0 1.0 CG A:HIS271 4.2 14.5 1.0 CG A:GLU198 4.3 16.9 1.0 HG3 A:GLU198 4.3 20.3 1.0 CG A:HIS287 4.3 15.5 1.0 HG23 A:VAL291 4.4 14.8 1.0 HG2 A:GLU198 4.5 20.3 1.0 HG11 A:VAL291 4.6 14.2 1.0 HZ2 A:LYS201 4.7 24.4 1.0 NZ A:LYS201 4.8 20.4 1.0 CG A:ASP150 4.9 31.3 1.0 HD1 A:HIS271 4.9 19.4 1.0 H2D A:NAD503 4.9 31.3 1.0 HD12 A:ILE146 4.9 19.9 1.0 HD1 A:HIS287 5.0 19.6 1.0 O A:HOH910 5.0 34.2 1.0

Zinc binding site 2 out of 2 in the Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:18.5 occ:0.50 OE2 B:GLU198 2.0 21.0 1.0 NE2 B:HIS287 2.1 15.2 1.0 NE2 B:HIS271 2.1 17.6 1.0 O B:HOH625 2.6 18.6 0.5 H5N B:NAD502 2.9 32.4 0.8 CD B:GLU198 3.0 20.1 1.0 CE1 B:HIS271 3.0 17.2 1.0 CE1 B:HIS287 3.0 15.3 1.0 O B:HOH1001 3.1 34.9 0.5 CD2 B:HIS287 3.1 15.0 1.0 CD2 B:HIS271 3.1 16.8 1.0 HE1 B:HIS271 3.2 20.7 1.0 HE1 B:HIS287 3.2 18.4 1.0 HG21 B:VAL291 3.2 15.6 1.0 HD2 B:HIS287 3.3 18.1 1.0 HD2 B:HIS271 3.3 20.2 1.0 C5N B:NAD502 3.4 27.0 0.8 OE1 B:GLU198 3.5 21.4 1.0 OD2 B:ASP150 3.6 38.6 1.0 HZ3 B:LYS201 4.0 29.5 1.0 C6N B:NAD502 4.1 26.5 0.8 C4N B:NAD502 4.1 26.9 0.8 CG2 B:VAL291 4.1 13.0 1.0 H4N B:NAD502 4.1 32.3 0.8 H6N B:NAD502 4.1 31.9 0.8 ND1 B:HIS287 4.2 15.3 1.0 ND1 B:HIS271 4.2 16.4 1.0 HG22 B:VAL291 4.2 15.6 1.0 HG3 B:GLU198 4.2 20.1 1.0 CG B:HIS287 4.2 14.5 1.0 CG B:HIS271 4.3 16.5 1.0 CG B:GLU198 4.3 16.8 1.0 HG23 B:VAL291 4.4 15.6 1.0 HG2 B:GLU198 4.6 20.1 1.0 HG11 B:VAL291 4.7 14.1 1.0 NZ B:LYS201 4.8 24.6 1.0 CG B:ASP150 4.8 34.1 1.0 HZ2 B:LYS201 4.8 29.5 1.0 O B:HOH927 4.9 33.1 1.0 O B:HOH1000 4.9 48.2 1.0 H2D B:NAD502 4.9 27.2 0.8 HD12 B:ILE146 4.9 23.5 1.0 HD1 B:HIS287 5.0 18.4 1.0 HD1 B:HIS271 5.0 19.7 1.0 HD3 B:LYS201 5.0 27.4 1.0

A.R.Osborn, K.M.Kean, K.M.Alseud, K.H.Almabruk, S.Asamizu, J.A.Lee, P.A.Karplus, T.Mahmud. Evolution and Distribution of C7-Cyclitol Synthases in Prokaryotes and Eukaryotes. Acs Chem. Biol. V. 12 979 2017.
ISSN: ESSN 1554-8937
PubMed: 28182402
DOI: 10.1021/ACSCHEMBIO.7B00066