Sodium in PDB 3qvm: The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica

The structure of The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica, PDB code: 3qvm was solved by A.U.Singer, O.Kagan, Y.Kim, A.M.Edwards, A.Joachimiak, A.Savchenko, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.77 / 2.00
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	123.067, 123.067, 49.218, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.5

The structure of The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica (pdb code 3qvm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica, PDB code: 3qvm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica within 5.0Å range: probe atom residue distance (Å) B Occ A:Na285 b:24.0 occ:1.00 CG A:GLN275 3.6 19.2 1.0 CB A:LYS28 3.7 23.1 1.0 CG A:LYS28 3.9 21.8 1.0 CE1 A:PHE54 3.9 20.4 1.0 CA A:GLN275 4.0 19.2 1.0 CB A:GLN275 4.2 20.0 1.0 CD1 A:PHE54 4.4 20.2 1.0 CD A:GLN275 4.7 20.6 1.0 O A:GLN275 4.7 19.9 1.0 NE2 A:GLN275 4.7 22.9 1.0 O A:ILE274 4.7 18.0 1.0 CD A:LYS28 4.8 21.9 1.0 N A:GLN275 4.8 19.6 1.0 C A:GLN275 4.9 19.5 1.0 CZ A:PHE54 5.0 18.5 1.0

Sodium binding site 2 out of 2 in the The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica within 5.0Å range: probe atom residue distance (Å) B Occ B:Na284 b:16.9 occ:1.00 O B:VAL62 3.0 13.8 1.0 OH B:TYR83 3.0 15.0 1.0 OG B:SER64 3.0 13.7 1.0 CE1 B:TYR83 3.5 14.2 1.0 N B:SER64 3.6 13.8 1.0 C B:GLY63 3.7 15.1 1.0 CZ B:TYR83 3.8 15.0 1.0 CD2 B:PHE200 3.8 14.7 1.0 CA B:GLY63 3.9 14.6 1.0 C B:VAL62 3.9 15.5 1.0 CB B:SER64 4.0 13.6 1.0 CE1 B:PHE72 4.1 16.5 1.0 CA B:SER64 4.2 14.3 1.0 CE2 B:PHE200 4.2 15.1 1.0 O B:GLY63 4.3 14.9 1.0 CG B:PHE200 4.3 14.9 1.0 N B:GLY63 4.3 16.1 1.0 CB B:TYR61 4.4 12.8 1.0 O B:TYR61 4.4 13.8 1.0 CB B:VAL196 4.4 17.0 1.0 CB B:PHE200 4.6 13.9 1.0 CD1 B:PHE72 4.6 16.4 1.0 C B:TYR61 4.7 14.3 1.0 CG2 B:VAL196 4.7 19.6 1.0 CD1 B:TYR83 4.8 13.6 1.0 O B:HOH290 4.8 15.0 1.0 CZ B:PHE72 5.0 17.0 1.0

M.Kube, T.N.Chernikova, Y.Al-Ramahi, A.Beloqui, N.Lopez-Cortez, M.E.Guazzaroni, H.J.Heipieper, S.Klages, O.R.Kotsyurbenko, I.Langer, T.Y.Nechitaylo, H.Lunsdorf, M.Fernandez, S.Juarez, S.Ciordia, A.Singer, O.Kagan, O.Egorova, P.Alain Petit, P.Stogios, Y.Kim, A.Tchigvintsev, R.Flick, R.Denaro, M.Genovese, J.P.Albar, O.N.Reva, M.Martinez-Gomariz, H.Tran, M.Ferrer, A.Savchenko, A.F.Yakunin, M.M.Yakimov, O.V.Golyshina, R.Reinhardt, P.N.Golyshin. Genome Sequence and Functional Genomic Analysis of the Oil-Degrading Bacterium Oleispira Antarctica. Nat Commun V. 4 2156 2013.
ISSN: ESSN 2041-1723
PubMed: 23877221
DOI: 10.1038/NCOMMS3156