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

The structure of Crystal Structure of A Diterpene Cyclase, PDB code: 4omh 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)	47.28 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.480, 98.360, 107.830, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.6

The binding sites of Sodium atom in the Crystal Structure of A Diterpene Cyclase (pdb code 4omh). 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: 4omh:
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:28.9 occ:1.00 O A:HOH658 2.3 54.2 1.0 O A:HOH604 2.3 46.5 1.0 O A:TRP83 2.6 13.3 1.0 O A:GLN85 2.6 18.5 1.0 O A:HOH532 2.8 25.4 1.0 O A:THR42 3.1 26.1 1.0 CD A:PRO87 3.4 21.1 1.0 C A:TRP83 3.5 13.4 1.0 N A:THR42 3.5 22.3 1.0 C A:GLN85 3.8 17.4 1.0 CA A:PRO41 3.8 27.3 1.0 CB A:PRO41 4.0 28.3 1.0 CG A:PRO87 4.0 23.6 1.0 N A:SER84 4.1 13.4 1.0 C A:PRO41 4.1 22.9 1.0 C A:THR42 4.1 24.3 1.0 N A:GLN85 4.2 11.3 1.0 CG A:ASP280 4.2 25.5 1.0 CB A:ASP280 4.2 13.2 1.0 CA A:SER84 4.3 9.2 1.0 C A:SER84 4.3 12.6 1.0 OD1 A:ASP280 4.3 26.6 1.0 CA A:TRP83 4.4 15.6 1.0 CA A:THR42 4.5 26.7 1.0 O A:ASP280 4.5 14.0 1.0 OD2 A:ASP280 4.6 24.4 1.0 N A:SER86 4.7 14.8 1.0 CA A:SER86 4.7 12.5 1.0 CA A:GLN85 4.7 12.7 1.0 O A:HOH626 4.7 32.7 1.0 N A:PRO87 4.7 15.6 1.0 O A:LEU82 4.8 15.4 1.0 OG1 A:THR42 4.8 28.5 1.0 CA A:ASP280 4.9 14.2 1.0 C A:ASP280 5.0 11.5 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:29.9 occ:1.00 O B:HOH620 2.2 33.9 1.0 O B:HOH579 2.2 35.2 1.0 O B:HOH529 2.3 28.9 1.0 O B:GLN85 2.5 20.5 1.0 O B:TRP83 2.7 19.9 1.0 O B:THR42 3.2 36.8 1.0 C B:TRP83 3.6 17.7 1.0 CD B:PRO87 3.6 23.1 1.0 C B:GLN85 3.7 20.2 1.0 N B:THR42 3.8 32.0 1.0 CB B:ASP280 4.1 12.8 1.0 N B:GLN85 4.2 11.7 1.0 CB B:PRO41 4.2 34.1 1.0 C B:SER84 4.2 14.1 1.0 O B:HOH625 4.3 41.7 1.0 N B:SER84 4.3 15.5 1.0 CA B:PRO41 4.3 34.5 1.0 C B:THR42 4.3 35.4 1.0 CA B:SER84 4.3 11.0 1.0 O B:ASP280 4.3 16.2 1.0 CG B:PRO87 4.3 26.3 1.0 CG B:ASP280 4.3 27.3 1.0 CA B:TRP83 4.5 20.0 1.0 CA B:SER86 4.5 14.8 1.0 N B:SER86 4.6 15.4 1.0 C B:PRO41 4.6 34.2 1.0 CA B:GLN85 4.6 16.9 1.0 OG1 B:THR42 4.6 39.3 1.0 OD1 B:ASP280 4.7 30.4 1.0 OD2 B:ASP280 4.7 27.6 1.0 CA B:THR42 4.7 35.0 1.0 CA B:ASP280 4.8 13.8 1.0 O B:SER84 4.8 17.6 1.0 C B:ASP280 4.8 13.4 1.0 N B:PRO87 4.9 17.0 1.0 O B:LEU82 4.9 19.6 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