Sodium in PDB 2oge: X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form

The structure of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form, PDB code: 2oge was solved by H.M.Holden, E.S.Burgie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.50 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.798, 143.820, 81.132, 90.00, 106.95, 90.00
R / Rfree (%)	n/a / n/a

The structure of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Sodium atom in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form (pdb code 2oge). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form, PDB code: 2oge:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1299 b:14.5 occ:1.00 OD1 A:ASN65 2.5 14.2 1.0 O B:HOH1309 2.5 25.5 1.0 O A:HOH1338 2.5 23.9 1.0 O B:HOH1454 2.6 28.2 1.0 OD1 B:ASN65 2.7 12.7 1.0 O B:HOH1308 2.8 29.6 1.0 CG A:ASN65 3.6 20.6 1.0 CG B:ASN65 3.8 24.2 1.0 O A:HOH1339 3.9 17.2 1.0 O B:HOH1413 4.0 27.3 1.0 ND2 A:ASN65 4.2 12.6 1.0 OD1 B:ASP239 4.3 30.2 1.0 OD2 B:ASP239 4.3 23.7 1.0 O A:ASP200 4.3 17.4 1.0 OD2 A:ASP239 4.3 21.9 1.0 ND2 B:ASN65 4.4 9.6 1.0 OD1 A:ASP239 4.5 20.3 1.0 O A:ARG237 4.5 16.0 1.0 CG B:ASP239 4.6 37.3 1.0 O B:ARG237 4.6 16.3 1.0 O B:ASP200 4.6 25.0 1.0 CB A:ASP200 4.6 13.7 1.0 CG A:ASP239 4.7 39.3 1.0 CB A:ASN65 4.8 16.4 1.0 O A:HOH1340 4.8 13.6 1.0 C A:ASP200 4.9 14.2 1.0 N A:ASP200 4.9 18.6 1.0 O B:HOH1307 5.0 13.5 1.0 CB B:ASN65 5.0 11.6 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1304 b:12.2 occ:1.00 OD1 D:ASN65 2.5 12.1 1.0 O D:HOH1476 2.5 28.9 1.0 O C:HOH1528 2.5 28.7 1.0 O D:HOH1477 2.5 25.3 1.0 O C:HOH1361 2.5 16.3 1.0 OD1 C:ASN65 2.6 12.9 1.0 CG D:ASN65 3.6 15.6 1.0 O D:HOH1372 3.7 32.4 1.0 CG C:ASN65 3.7 28.7 1.0 O C:HOH1362 3.9 21.6 1.0 OD2 C:ASP239 4.1 31.6 1.0 OD2 D:ASP239 4.2 25.0 1.0 ND2 D:ASN65 4.2 12.8 1.0 OD1 C:ASP239 4.3 33.9 1.0 ND2 C:ASN65 4.4 11.3 1.0 O D:ASP200 4.4 20.5 1.0 OD1 D:ASP239 4.5 29.4 1.0 CG C:ASP239 4.5 35.8 1.0 O D:ARG237 4.6 19.4 1.0 O C:ASP200 4.6 16.2 1.0 O C:ARG237 4.6 18.7 1.0 CG D:ASP239 4.7 37.1 1.0 CB D:ASP200 4.7 8.2 1.0 CB D:ASN65 4.8 13.0 1.0 CB C:ASP200 4.9 7.5 1.0 O D:HOH1321 4.9 10.3 1.0 CB C:ASN65 4.9 8.2 1.0 O D:HOH1320 4.9 17.3 1.0

E.S.Burgie, J.B.Thoden, H.M.Holden. Molecular Architecture of Desv From Streptomyces Venezuelae: A Plp-Dependent Transaminase Involved in the Biosynthesis of the Unusual Sugar Desosamine. Protein Sci. V. 16 887 2007.
ISSN: ISSN 0961-8368
PubMed: 17456741
DOI: 10.1110/PS.062711007