Sodium in PDB 6sbc: Structure of Type II Terpene Cyclase Mste From Scytonema in Complex with Farnesyl Dihydroxybenzoate

The structure of Structure of Type II Terpene Cyclase Mste From Scytonema in Complex with Farnesyl Dihydroxybenzoate, PDB code: 6sbc was solved by P.Moosmann, F.Ecker, S.Leopold-Messer, J.K.B.Cahn, M.Groll, J.Piel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.980, 77.420, 90.910, 90.00, 90.00, 90.00
R / Rfree (%)	11.5 / 15.3

The structure of Structure of Type II Terpene Cyclase Mste From Scytonema in Complex with Farnesyl Dihydroxybenzoate also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Structure of Type II Terpene Cyclase Mste From Scytonema in Complex with Farnesyl Dihydroxybenzoate (pdb code 6sbc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Type II Terpene Cyclase Mste From Scytonema in Complex with Farnesyl Dihydroxybenzoate, PDB code: 6sbc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Type II Terpene Cyclase Mste From Scytonema in Complex with Farnesyl Dihydroxybenzoate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Type II Terpene Cyclase Mste From Scytonema in Complex with Farnesyl Dihydroxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na906 b:27.9 occ:1.00 O A:HOH1289 2.7 35.9 1.0 O A:HOH1304 2.9 27.7 1.0 N A:ARG128 3.1 15.2 1.0 CB A:ARG128 3.6 15.2 1.0 CL A:CL905 3.6 30.6 1.0 N A:GLU127 3.6 14.1 1.0 CB A:SER126 3.8 14.5 1.0 CB A:GLU127 3.9 18.6 1.0 CA A:ARG128 3.9 14.7 1.0 C A:GLU127 4.0 15.5 1.0 CA A:GLU127 4.0 14.8 1.0 OG A:SER126 4.2 14.8 1.0 CD A:LYS88 4.3 18.8 1.0 C A:SER126 4.3 14.1 1.0 CA A:SER126 4.5 14.3 1.0 O A:HOH1299 4.7 49.6 1.0 CG A:GLU127 4.8 22.7 1.0

Sodium binding site 2 out of 2 in the Structure of Type II Terpene Cyclase Mste From Scytonema in Complex with Farnesyl Dihydroxybenzoate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Type II Terpene Cyclase Mste From Scytonema in Complex with Farnesyl Dihydroxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na907 b:45.8 occ:1.00 O A:ILE158 2.2 30.1 1.0 O A:ARG155 2.3 26.2 1.0 C A:ILE158 3.4 25.3 1.0 C A:ARG155 3.5 21.8 1.0 O A:ALA156 4.2 34.3 1.0 N A:LYS159 4.3 25.8 1.0 CA A:LYS159 4.4 30.5 1.0 CA A:ILE158 4.4 21.4 1.0 C A:ALA156 4.4 28.4 1.0 N A:ALA156 4.4 24.6 1.0 CA A:ARG155 4.4 23.7 1.0 N A:ILE158 4.4 20.6 1.0 CA A:ALA156 4.4 24.7 1.0 CG A:LYS159 4.4 40.9 1.0 CB A:ILE158 4.7 22.8 1.0 CB A:ARG155 4.8 27.2 1.0 C A:TYR157 5.0 21.2 1.0

P.Moosmann, F.Ecker, S.Leopold-Messer, J.K.B.Cahn, C.L.Dieterich, M.Groll, J.Piel. A Monodomain Class II Terpene Cyclase Assembles Complex Isoprenoid Scaffolds. Nat.Chem. V. 12 968 2020.
ISSN: ESSN 1755-4349
PubMed: 32778689
DOI: 10.1038/S41557-020-0515-3