Sodium in PDB 3eor: Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand:
4.6.1.12;

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand, PDB code: 3eor was solved by W.N.Hunter, N.L.Ramsden, A.Dawson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.98 / 2.90
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	145.681, 145.681, 145.681, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 20.9

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand (pdb code 3eor). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand, PDB code: 3eor:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:66.8 occ:1.00 OD1 A:ASP8 2.8 57.3 1.0 ZN A:ZN800 3.3 85.6 1.0 CG A:ASP8 3.5 51.2 1.0 OD2 A:ASP8 3.9 56.4 1.0 O A:VAL9 4.4 48.4 1.0 CB A:ASP8 4.7 47.6 1.0 N A:VAL9 4.7 45.4 1.0 NE2 A:HIS10 4.9 50.7 1.0 CA A:ASP8 4.9 47.1 1.0 CE1 A:HIS10 4.9 52.0 1.0 NA A:NA802 4.9 67.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:67.9 occ:1.00 OG A:SER35 3.0 68.4 1.0 ZN A:ZN800 3.7 85.6 1.0 CE1 A:HIS10 3.8 52.0 1.0 CE1 A:HIS42 3.9 59.6 1.0 NE2 A:HIS10 4.0 50.7 1.0 CB A:SER35 4.1 73.5 1.0 ND1 A:HIS42 4.3 56.6 1.0 N A:HIS34 4.6 75.8 1.0 NE2 A:HIS42 4.6 57.7 1.0 N A:SER35 4.8 77.7 1.0 CB A:ALA33 4.9 66.0 1.0 NA A:NA801 4.9 66.8 1.0 OD1 A:ASP63 4.9 50.0 0.0

N.L.Ramsden, L.Buetow, A.Dawson, L.A.Kemp, V.Ulaganathan, R.Brenk, G.Klebe, W.N.Hunter. A Structure-Based Approach to Ligand Discovery For 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase: A Target For Antimicrobial Therapy J.Med.Chem. V. 52 2531 2009.
ISSN: ISSN 0022-2623
PubMed: 19320487
DOI: 10.1021/JM801475N