Sodium in PDB 4n7b: Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Reductase From Plasmodium Falciparum

The structure of Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Reductase From Plasmodium Falciparum, PDB code: 4n7b was solved by I.Rekittke, H.Jomaa, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.05 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.960, 115.960, 76.930, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 19.5

The structure of Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Reductase From Plasmodium Falciparum also contains other interesting chemical elements:

Iron

(Fe)

3 atoms

The binding sites of Sodium atom in the Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Reductase From Plasmodium Falciparum (pdb code 4n7b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Reductase From Plasmodium Falciparum, PDB code: 4n7b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Reductase From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Reductase From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:53.2 occ:1.00 HH A:TYR107 2.4 52.6 1.0 HE3 A:LYS103 2.9 44.2 1.0 OH A:TYR107 3.0 43.8 1.0 HE2 A:TYR107 3.2 41.3 1.0 HG A:SER192 3.4 66.3 1.0 HE2 A:LYS103 3.7 44.2 1.0 CE A:LYS103 3.7 36.9 1.0 OG A:SER192 3.8 55.2 1.0 CE2 A:TYR107 3.8 34.5 1.0 CZ A:TYR107 3.9 37.3 1.0 HG23 A:ILE190 4.0 47.8 1.0 HG3 A:LYS103 4.2 33.6 1.0 HZ1 A:LYS103 4.4 45.7 1.0 HG21 A:ILE190 4.5 47.8 1.0 CG2 A:ILE190 4.6 39.8 1.0 NZ A:LYS103 4.6 38.1 1.0 HG22 A:ILE190 4.7 47.8 1.0 CD A:LYS103 4.8 33.0 1.0 HD2 A:PRO191 4.8 56.2 1.0 H A:SER192 4.9 53.6 1.0 HD2 A:LYS103 4.9 39.6 1.0 CG A:LYS103 4.9 28.0 1.0 HZ2 A:LYS103 4.9 45.7 1.0 HB3 A:SER192 5.0 57.8 1.0

Sodium binding site 2 out of 2 in the Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Reductase From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Reductase From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:47.7 occ:1.00 H A:HIS138 2.5 57.8 1.0 HD2 A:PRO137 2.8 55.2 1.0 HB2 A:HIS138 2.8 77.0 1.0 HA A:ALA136 2.9 48.9 1.0 N A:HIS138 3.3 48.2 1.0 C A:ALA136 3.4 41.5 1.0 H A:CYS139 3.5 57.1 1.0 CA A:ALA136 3.5 40.8 1.0 HB1 A:ALA136 3.5 49.1 1.0 CD A:PRO137 3.6 46.0 1.0 N A:PRO137 3.6 47.4 1.0 CB A:HIS138 3.6 64.1 1.0 O A:ALA136 3.7 41.5 1.0 HG2 A:PRO137 3.9 56.5 1.0 CA A:HIS138 3.9 59.4 1.0 N A:CYS139 4.0 47.6 1.0 CB A:ALA136 4.0 41.0 1.0 HD2 A:HIS138 4.1 99.0 1.0 CG A:HIS138 4.1 75.4 1.0 SG A:CYS139 4.2 61.8 1.0 C A:HIS138 4.3 59.0 1.0 C A:PRO137 4.3 51.5 1.0 CG A:PRO137 4.3 47.1 1.0 CD2 A:HIS138 4.3 82.5 1.0 HD3 A:PRO137 4.3 55.2 1.0 HB3 A:HIS138 4.4 77.0 1.0 HB2 A:ALA136 4.5 49.1 1.0 HB3 A:CYS139 4.5 57.7 1.0 CA A:PRO137 4.5 48.6 1.0 HG A:CYS139 4.6 74.2 1.0 CB A:CYS139 4.8 48.1 1.0 N A:ALA136 4.8 39.5 1.0 HB3 A:ALA136 4.8 49.1 1.0 HA A:HIS138 4.8 71.3 1.0 CA A:CYS139 5.0 44.9 1.0

I.Rekittke, E.Olkhova, J.Wiesner, U.Demmer, E.Warkentin, H.Jomaa, U.Ermler. Structure of the (E)-4-Hydroxy-3-Methyl-But-2-Enyl-Diphosphate Reductase From Plasmodium Falciparum. Febs Lett. V. 587 3968 2013.
ISSN: ISSN 0014-5793
PubMed: 24188825
DOI: 10.1016/J.FEBSLET.2013.10.029