Sodium in PDB 1zor: Isocitrate Dehydrogenase From the Hyperthermophile Thermotoga Maritima

All present enzymatic activity of Isocitrate Dehydrogenase From the Hyperthermophile Thermotoga Maritima:
1.1.1.42;

The structure of Isocitrate Dehydrogenase From the Hyperthermophile Thermotoga Maritima, PDB code: 1zor was solved by M.Karlstrom, I.H.Steen, N.-K.Birkeland, R.Ladenstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.56 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.470, 88.051, 180.926, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.3

The binding sites of Sodium atom in the Isocitrate Dehydrogenase From the Hyperthermophile Thermotoga Maritima (pdb code 1zor). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Isocitrate Dehydrogenase From the Hyperthermophile Thermotoga Maritima, PDB code: 1zor:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Isocitrate Dehydrogenase From the Hyperthermophile Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Isocitrate Dehydrogenase From the Hyperthermophile Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:41.0 occ:1.00 OD1 A:ASP270 2.2 47.7 1.0 OD1 A:ASP274 2.3 45.7 1.0 OD2 B:ASP247 2.4 49.1 1.0 O A:HOH1347 2.5 52.7 1.0 O A:HOH1160 2.5 38.5 1.0 O A:ASP270 2.6 43.4 1.0 CG A:ASP274 3.2 46.4 1.0 CG A:ASP270 3.3 45.7 1.0 C A:ASP270 3.4 43.5 1.0 CG B:ASP247 3.4 48.0 1.0 O A:HOH1155 3.6 49.3 1.0 CB B:ASP247 3.6 45.8 1.0 OD2 A:ASP274 3.8 51.3 1.0 CA A:ASP270 3.9 43.6 1.0 CB A:ASP270 4.1 43.8 1.0 OD2 A:ASP270 4.1 43.7 1.0 CB A:ASP274 4.3 45.4 1.0 OG A:SER273 4.3 46.6 1.0 N A:ILE271 4.5 43.5 1.0 OD1 B:ASP247 4.6 50.0 1.0 NZ B:LYS208 4.6 51.0 1.0 O A:HOH1229 4.6 38.9 1.0 N A:ASP274 4.8 44.7 1.0 CA A:ILE271 5.0 43.2 1.0

Sodium binding site 2 out of 2 in the Isocitrate Dehydrogenase From the Hyperthermophile Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Isocitrate Dehydrogenase From the Hyperthermophile Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1002 b:42.8 occ:1.00 OD1 B:ASP274 2.3 45.9 1.0 OD1 B:ASP270 2.4 44.9 1.0 O B:ASP270 2.4 43.8 1.0 O B:HOH1056 2.5 43.8 1.0 OD2 A:ASP247 2.5 49.4 1.0 O B:HOH1055 2.5 46.1 1.0 CG B:ASP274 3.2 45.8 1.0 C B:ASP270 3.3 43.7 1.0 CG B:ASP270 3.4 44.9 1.0 CG A:ASP247 3.4 45.6 1.0 CB A:ASP247 3.5 45.0 1.0 O B:HOH1076 3.6 52.6 1.0 O A:HOH1336 3.6 52.9 1.0 OD2 B:ASP274 3.8 47.4 1.0 CA B:ASP270 3.8 43.5 1.0 OG B:SER273 3.9 47.6 1.0 CB B:ASP274 4.1 45.2 1.0 CB B:ASP270 4.2 43.3 1.0 OD2 B:ASP270 4.2 45.1 1.0 O B:HOH1022 4.4 58.4 1.0 N B:ILE271 4.4 43.4 1.0 O A:HOH1324 4.5 49.7 1.0 OD1 A:ASP247 4.6 48.6 1.0 N B:ASP274 4.6 44.8 1.0 NZ A:LYS208 4.7 49.7 1.0 CA B:ILE271 4.9 43.4 1.0 CA A:ASP247 5.0 44.6 1.0 CA B:ASP274 5.0 44.8 1.0

M.Karlstrom, I.H.Steen, D.Madern, A.E.Fedoy, N.K.Birkeland, R.Ladenstein. The Crystal Structure of A Hyperthermostable Subfamily II Isocitrate Dehydrogenase From Thermotoga Maritima. Febs J. V. 273 2851 2006.
ISSN: ISSN 1742-464X
PubMed: 16759231
DOI: 10.1111/J.1742-4658.2006.05298.X