Sodium in PDB 4omg: Crystal Structure of A Diterpene Cyclase

The structure of Crystal Structure of A Diterpene Cyclase, PDB code: 4omg was solved by R.Janke, C.Goerner, M.Hirte, T.Brueck, B.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.83 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.060, 100.650, 108.730, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20

The binding sites of Sodium atom in the Crystal Structure of A Diterpene Cyclase (pdb code 4omg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Diterpene Cyclase, PDB code: 4omg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Diterpene Cyclase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Diterpene Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:20.1 occ:1.00 O A:HOH625 2.1 36.5 1.0 O A:HOH559 2.2 31.5 1.0 O A:GLN85 2.3 18.5 1.0 O A:TRP83 2.4 15.5 1.0 O A:HOH519 2.5 20.4 1.0 O A:THR42 2.8 23.9 1.0 C A:TRP83 3.3 13.4 1.0 C A:GLN85 3.6 16.1 1.0 CD A:PRO87 3.7 18.4 1.0 N A:THR42 3.8 17.4 1.0 C A:THR42 4.0 23.1 1.0 C A:SER84 4.0 15.6 1.0 N A:SER84 4.1 13.3 1.0 N A:GLN85 4.1 12.8 1.0 CA A:TRP83 4.1 13.4 1.0 CA A:SER84 4.2 10.2 1.0 O A:LEU82 4.4 16.5 1.0 CA A:PRO41 4.4 19.9 1.0 CB A:ASP280 4.4 13.0 1.0 CB A:PRO41 4.4 19.6 1.0 O A:SER84 4.5 20.0 1.0 N A:SER86 4.5 12.6 1.0 CA A:GLN85 4.5 12.7 1.0 CA A:SER86 4.5 14.1 1.0 O A:ASP280 4.5 13.3 1.0 OG1 A:THR42 4.5 25.8 1.0 O A:HOH577 4.5 35.1 1.0 CA A:THR42 4.6 20.4 1.0 CG A:ASP280 4.6 31.1 1.0 C A:PRO41 4.6 19.5 1.0 CG A:PRO87 4.7 23.4 1.0 OD2 A:ASP280 4.9 26.2 1.0 OD1 A:ASP280 4.9 38.1 1.0 N A:PRO87 4.9 15.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Diterpene Cyclase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Diterpene Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:20.9 occ:1.00 O B:HOH636 2.1 41.1 1.0 O B:HOH549 2.3 29.2 1.0 O B:TRP83 2.3 16.0 1.0 O B:GLN85 2.4 19.6 1.0 O B:HOH532 2.5 22.0 1.0 O B:THR42 2.6 22.9 1.0 C B:TRP83 3.3 11.4 1.0 C B:GLN85 3.6 15.3 1.0 N B:THR42 3.7 20.6 1.0 CD B:PRO87 3.8 21.6 1.0 C B:THR42 3.8 19.9 1.0 C B:SER84 4.1 14.7 1.0 N B:SER84 4.1 13.0 1.0 N B:GLN85 4.1 11.4 1.0 CA B:TRP83 4.1 15.6 1.0 CA B:SER84 4.2 14.9 1.0 O B:LEU82 4.3 19.7 1.0 OG1 B:THR42 4.4 25.2 1.0 CG B:ASP280 4.4 29.0 1.0 CB B:ASP280 4.4 19.0 1.0 CA B:PRO41 4.4 25.4 1.0 OD1 B:ASP280 4.4 30.5 1.0 CA B:THR42 4.4 18.1 1.0 CG B:PRO87 4.4 24.2 1.0 CB B:PRO41 4.5 24.7 1.0 CA B:SER86 4.5 14.2 1.0 N B:SER86 4.5 14.9 1.0 O B:SER84 4.6 19.3 1.0 CA B:GLN85 4.6 11.9 1.0 C B:PRO41 4.6 20.5 1.0 O B:ASP280 4.7 12.9 1.0 O B:HOH592 4.7 32.0 1.0 N B:LYS43 4.9 23.8 1.0 OD2 B:ASP280 4.9 28.1 1.0 N B:PRO87 4.9 16.4 1.0

R.Janke, C.Gorner, M.Hirte, T.Bruck, B.Loll. The First Structure of A Bacterial Diterpene Cyclase: COTB2. Acta Crystallogr.,Sect.D V. 70 1528 2014.
ISSN: ISSN 0907-4449
PubMed: 24914964
DOI: 10.1107/S1399004714005513