Sodium in PDB 2vv6: Bjfixlh in Ferric Form

All present enzymatic activity of Bjfixlh in Ferric Form:
2.7.13.3;

The structure of Bjfixlh in Ferric Form, PDB code: 2vv6 was solved by R.A.Ayers, K.Moffat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.72 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.803, 50.002, 58.999, 73.68, 70.36, 72.33
R / Rfree (%)	18.2 / 21.1

The structure of Bjfixlh in Ferric Form also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Bjfixlh in Ferric Form (pdb code 2vv6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Bjfixlh in Ferric Form, PDB code: 2vv6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Bjfixlh in Ferric Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bjfixlh in Ferric Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1260 b:18.1 occ:1.00 O C:LEU181 2.1 19.5 1.0 O C:ILE184 2.3 20.4 1.0 O C:HOH2034 2.8 20.9 1.0 C C:LEU181 3.3 18.8 1.0 C C:ILE184 3.5 19.6 1.0 O C:GLU182 3.6 21.1 1.0 C C:GLU182 3.9 19.8 1.0 CA C:GLU182 4.0 18.9 1.0 N C:GLU182 4.1 19.2 1.0 CA C:ILE184 4.2 19.6 1.0 N C:ILE184 4.2 20.1 1.0 CA C:LEU181 4.4 18.8 1.0 CB C:ILE184 4.4 20.3 1.0 N C:GLY185 4.5 19.7 1.0 N C:ALA183 4.6 20.3 1.0 C C:ALA183 4.7 19.9 1.0 CA C:GLY185 4.7 20.0 1.0 CG2 C:ILE184 4.8 20.5 1.0

Sodium binding site 2 out of 3 in the Bjfixlh in Ferric Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bjfixlh in Ferric Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1263 b:18.4 occ:1.00 CL C:CL1264 2.2 35.2 1.0 O C:ILE218 2.3 19.1 1.0 O C:GLY219 2.6 19.4 1.0 NA C:NA1265 3.0 35.6 1.0 O C:HOH2086 3.2 26.9 1.0 C C:GLY219 3.2 18.9 1.0 C C:ILE218 3.3 18.7 1.0 CA C:GLY219 3.6 18.4 1.0 N C:GLY219 3.8 18.7 1.0 N C:ARG220 4.2 19.6 1.0 CG2 C:ILE218 4.3 20.4 1.0 NE2 C:HIS235 4.4 21.1 1.0 CA C:ILE218 4.5 19.3 1.0 O C:HOH2087 4.5 24.1 1.0 CA C:ARG220 4.7 20.1 1.0

Sodium binding site 3 out of 3 in the Bjfixlh in Ferric Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bjfixlh in Ferric Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1265 b:35.6 occ:1.00 CL C:CL1262 2.8 22.2 1.0 NA C:NA1263 3.0 18.4 1.0 O C:ILE218 3.1 19.1 1.0 CL C:CL1261 3.1 17.1 1.0 CL C:CL1264 3.4 35.2 1.0 NE2 C:HIS235 3.5 21.1 1.0 CE1 C:HIS235 3.6 22.6 1.0 CA C:GLY219 4.0 18.4 1.0 C C:ILE218 4.1 18.7 1.0 CA D:GLY244 4.2 19.9 1.0 N D:GLY244 4.2 19.0 1.0 O C:HOH2083 4.3 31.2 1.0 O D:HOH2137 4.4 30.1 1.0 C C:GLY219 4.5 18.9 1.0 N C:GLY219 4.5 18.7 1.0 O C:GLY219 4.7 19.4 1.0 CD2 C:HIS235 4.7 21.9 1.0 ND1 C:HIS235 4.9 22.5 1.0

R.A.Ayers, K.Moffat. Changes in Quaternary Structure in the Signaling Mechanisms of Pas Domains. Biochemistry V. 47 12078 2008.
ISSN: ISSN 0006-2960
PubMed: 18942854
DOI: 10.1021/BI801254C