Sodium in PDB 2oga: X-Ray Crystal Structure of S. Venezuelae Desv in Complex with Ketimine Intermediate

The structure of X-Ray Crystal Structure of S. Venezuelae Desv in Complex with Ketimine Intermediate, PDB code: 2oga 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)	36.00 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.730, 143.390, 92.560, 90.00, 108.49, 90.00
R / Rfree (%)	n/a / n/a

The structure of X-Ray Crystal Structure of S. Venezuelae Desv in Complex with Ketimine Intermediate also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the X-Ray Crystal Structure of S. Venezuelae Desv in Complex with Ketimine Intermediate (pdb code 2oga). 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 Crystal Structure of S. Venezuelae Desv in Complex with Ketimine Intermediate, PDB code: 2oga:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of S. Venezuelae Desv in Complex with Ketimine Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of S. Venezuelae Desv in Complex with Ketimine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1022 b:1.0 occ:1.00 OD1 B:ASN65 2.4 11.1 1.0 O A:HOH1040 2.5 10.8 1.0 O B:HOH1024 2.5 14.1 1.0 OD1 A:ASN65 2.5 12.6 1.0 O A:HOH1043 2.5 12.9 1.0 O A:HOH1041 2.5 13.9 1.0 CG A:ASN65 3.5 9.9 1.0 CG B:ASN65 3.5 30.0 1.0 ND2 A:ASN65 4.0 6.8 1.0 O B:HOH1067 4.1 7.9 1.0 OD2 A:ASP239 4.1 9.4 1.0 ND2 B:ASN65 4.2 18.6 1.0 O B:ASP200 4.2 20.4 1.0 OD2 B:ASP239 4.2 16.1 1.0 O A:HOH1042 4.2 13.3 1.0 O A:ASP200 4.2 8.9 1.0 OD1 A:ASP239 4.4 14.9 1.0 OD1 B:ASP239 4.4 13.9 1.0 O A:ARG237 4.5 8.3 1.0 CG A:ASP239 4.6 26.6 1.0 CB A:ASN65 4.6 10.8 1.0 CG B:ASP239 4.6 18.9 1.0 O B:ARG237 4.6 12.7 1.0 CB A:ASP200 4.7 3.9 1.0 CB B:ASN65 4.7 10.6 1.0 CB B:ASP200 4.8 6.2 1.0 O B:HOH1023 4.9 4.8 1.0 C A:ASP200 4.9 7.2 1.0 C B:ASP200 4.9 22.8 1.0 O A:HOH1100 5.0 9.0 1.0

Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of S. Venezuelae Desv in Complex with Ketimine Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of S. Venezuelae Desv in Complex with Ketimine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1025 b:2.7 occ:1.00 OD1 C:ASN65 2.4 11.6 1.0 OD1 D:ASN65 2.4 9.7 1.0 O C:HOH1042 2.5 14.1 1.0 O D:HOH1028 2.5 14.5 1.0 O D:HOH1026 2.5 25.9 1.0 O D:HOH1027 2.5 19.5 1.0 CG C:ASN65 3.5 27.8 1.0 CG D:ASN65 3.5 15.8 1.0 OD2 C:ASP239 4.0 14.0 1.0 ND2 C:ASN65 4.1 13.0 1.0 ND2 D:ASN65 4.1 10.2 1.0 O C:HOH1043 4.2 7.9 1.0 OD1 D:ASP239 4.2 22.7 1.0 O C:ASP200 4.2 22.0 1.0 O D:ASP200 4.3 9.9 1.0 OD1 C:ASP239 4.4 21.2 1.0 O D:HOH1029 4.4 19.6 1.0 OD2 D:ASP239 4.5 14.4 1.0 CG C:ASP239 4.6 26.9 1.0 O C:ARG237 4.6 9.8 1.0 O D:ARG237 4.6 10.1 1.0 CB D:ASP200 4.6 11.4 1.0 CB C:ASN65 4.6 11.4 1.0 CG D:ASP239 4.6 23.8 1.0 CB D:ASN65 4.6 17.5 1.0 CB C:ASP200 4.7 10.1 1.0 O C:HOH1044 4.8 14.9 1.0 O C:HOH1072 4.8 14.0 1.0 C D:ASP200 4.9 18.8 1.0 N D:ASP200 4.9 12.9 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