Sodium in PDB 4ia6: Hydratase From Lactobacillus Acidophilus in A Ligand Bound Form (La Lah)

The structure of Hydratase From Lactobacillus Acidophilus in A Ligand Bound Form (La Lah), PDB code: 4ia6 was solved by S.Khoshnevis, P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.73 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	165.100, 77.740, 104.810, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19.2

The structure of Hydratase From Lactobacillus Acidophilus in A Ligand Bound Form (La Lah) also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Sodium atom in the Hydratase From Lactobacillus Acidophilus in A Ligand Bound Form (La Lah) (pdb code 4ia6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hydratase From Lactobacillus Acidophilus in A Ligand Bound Form (La Lah), PDB code: 4ia6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hydratase From Lactobacillus Acidophilus in A Ligand Bound Form (La Lah)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hydratase From Lactobacillus Acidophilus in A Ligand Bound Form (La Lah) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na609 b:22.0 occ:0.97 O A:HOH999 2.7 15.1 1.0 CG A:ASP209 2.9 14.4 1.0 OD1 A:ASP209 2.9 11.7 1.0 O A:HIS206 3.0 9.8 1.0 N A:ASP209 3.0 14.6 1.0 NE A:ARG545 3.2 14.6 1.0 CB A:ASP209 3.3 11.9 1.0 OD2 A:ASP209 3.3 16.2 1.0 C A:HIS206 3.5 10.8 1.0 CD A:ARG545 3.5 13.9 1.0 N A:ILE208 3.5 8.8 1.0 CA A:ASP209 3.7 13.8 1.0 CG A:ARG545 3.8 12.8 1.0 C A:HIS207 4.0 9.1 1.0 N A:HIS207 4.0 9.7 1.0 C A:ILE208 4.0 12.7 1.0 O A:ILE205 4.0 13.7 1.0 CA A:HIS207 4.1 12.3 1.0 O A:HOH913 4.1 26.4 1.0 CA A:ILE208 4.1 11.6 1.0 O A:HOH1120 4.1 27.5 1.0 OE1 A:GLN542 4.2 17.4 1.0 CA A:HIS206 4.3 8.5 1.0 CZ A:ARG545 4.4 15.5 1.0 CB A:ILE208 4.5 19.7 1.0 NH2 A:ARG545 4.7 14.1 1.0 O A:HIS207 4.8 13.0 1.0 CD2 A:TYR549 4.8 12.1 1.0 CB A:ARG545 4.9 9.7 1.0 C A:ASP209 4.9 17.8 1.0

Sodium binding site 2 out of 2 in the Hydratase From Lactobacillus Acidophilus in A Ligand Bound Form (La Lah)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hydratase From Lactobacillus Acidophilus in A Ligand Bound Form (La Lah) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na614 b:28.3 occ:1.00 OG B:SER106 2.7 11.8 1.0 O A:PHE11 2.9 12.7 1.0 OD1 B:ASP109 3.0 15.9 1.0 O B:HOH995 3.0 30.4 1.0 OD2 A:ASP13 3.1 25.4 0.5 O A:HOH970 3.3 37.9 1.0 CB B:SER106 3.6 11.5 1.0 CG B:ASP109 3.6 14.5 1.0 OD2 B:ASP109 3.7 17.0 1.0 CB B:ARG95 3.8 9.2 1.0 C A:PHE11 3.9 14.5 1.0 O B:ARG95 4.0 11.0 1.0 CA B:ARG95 4.0 8.3 1.0 CD2 B:LEU108 4.2 19.4 1.0 CB B:LEU108 4.2 7.4 1.0 CG A:ASP13 4.3 22.0 0.5 CG B:LEU108 4.4 12.2 1.0 N B:ASP109 4.4 8.8 1.0 CA A:ALA12 4.5 11.8 1.0 C B:ARG95 4.5 10.8 1.0 N A:ALA12 4.6 12.3 1.0 N A:ASP13 4.6 14.4 0.5 N A:ASP13 4.6 14.3 0.5 CB A:PHE11 4.7 10.8 1.0 CB B:ASP109 4.8 9.0 1.0 C A:ALA12 4.8 13.1 1.0 CA A:PHE11 4.9 12.7 1.0 CA B:SER106 4.9 13.3 1.0 OD1 A:ASP13 4.9 25.0 0.5 CA B:ASP109 5.0 11.3 1.0

A.Volkov, S.Khoshnevis, P.Neumann, C.Herrfurth, D.Wohlwend, R.Ficner, I.Feussner. Crystal Structure Analysis of A Fatty Acid Double-Bond Hydratase From Lactobacillus Acidophilus Acta Crystallogr.,Sect.D V. 69 648 2013.
ISSN: ISSN 0907-4449
PubMed: 23519674
DOI: 10.1107/S0907444913000991