Sodium in PDB 2v9v: Crystal Structure of Moorella Thermoacetica Selb(377-511)

The structure of Crystal Structure of Moorella Thermoacetica Selb(377-511), PDB code: 2v9v was solved by O.Ganichkin, M.C.Wahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.349, 46.087, 58.683, 90.00, 120.45, 90.00
R / Rfree (%)	12 / 14.1

The structure of Crystal Structure of Moorella Thermoacetica Selb(377-511) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Moorella Thermoacetica Selb(377-511) (pdb code 2v9v). 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 Moorella Thermoacetica Selb(377-511), PDB code: 2v9v:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Moorella Thermoacetica Selb(377-511)


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 Moorella Thermoacetica Selb(377-511) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1516 b:7.9 occ:1.00 O A:ASN430 2.3 7.1 1.0 O A:HOH2037 2.5 10.9 1.0 OD1 A:ASP431 2.7 9.9 1.0 C A:ASN430 3.3 6.3 1.0 HB3 A:ASN430 3.3 7.3 1.0 O A:HOH2016 3.4 6.7 0.5 HA A:ASP431 3.5 6.2 1.0 CG A:ASP431 3.8 9.4 1.0 HB2 A:ASN430 3.9 7.3 1.0 CB A:ASN430 3.9 7.8 1.0 N A:ASP431 4.0 6.4 1.0 CA A:ASP431 4.1 6.2 1.0 CA A:ASN430 4.2 6.7 1.0 O A:HOH2005 4.5 8.0 1.0 OD2 A:ASP431 4.5 13.8 1.0 CB A:ASP431 4.6 7.1 1.0 O A:HOH2027 4.6 12.5 1.0 H A:ASP431 4.8 6.3 1.0 O A:HOH2007 4.8 2.5 0.5 HA A:ASN430 4.8 7.0 1.0 HB3 A:ASP431 5.0 6.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Moorella Thermoacetica Selb(377-511)


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 Moorella Thermoacetica Selb(377-511) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1517 b:8.1 occ:1.00 O A:LEU425 2.2 9.5 1.0 O A:HOH2058 2.3 12.5 1.0 O A:HOH2038 2.3 10.4 1.0 O A:HOH2052 2.5 13.3 1.0 H A:LEU425 3.3 6.4 1.0 C A:LEU425 3.4 7.6 1.0 HG21 A:THR424 3.6 10.3 1.0 HB2 A:LEU425 3.8 7.4 1.0 N A:LEU425 3.9 6.3 1.0 HA A:LEU426 4.0 6.8 1.0 CA A:LEU425 4.2 6.8 1.0 OE1 A:GLU488 4.3 6.2 0.5 O A:HOH2003 4.4 22.8 1.0 CG2 A:THR424 4.4 11.5 1.0 N A:LEU426 4.5 6.9 1.0 CB A:LEU425 4.5 7.7 1.0 OE2 A:GLU488 4.6 7.5 0.5 HG23 A:THR424 4.6 10.3 1.0 CA A:LEU426 4.7 6.7 1.0 HG22 A:THR424 4.8 10.3 1.0 HB2 A:LEU426 4.8 7.2 1.0 HD11 A:LEU426 4.8 10.9 1.0 HD13 A:LEU426 4.9 10.9 1.0 HA A:THR424 4.9 6.5 1.0 CD A:GLU488 4.9 5.3 0.5 O A:HOH2006 4.9 7.4 1.0 HB3 A:LEU425 4.9 7.4 1.0

O.Ganichkin, M.C.Wahl. Conformational Switches in Winged-Helix Domains 1 and 2 of Bacterial Translation Elongation Factor Selb. Acta Crystallogr.,Sect.D V. 63 1075 2007.
ISSN: ISSN 0907-4449
PubMed: 17881825
DOI: 10.1107/S0907444907042229