Atomistry » Sodium » PDB 3e40-3ept » 3eor
Atomistry »
  Sodium »
    PDB 3e40-3ept »
      3eor »

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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 3eor:

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

Sodium Binding Sites:

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 3eor

Go back to Sodium Binding Sites List in 3eor
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 3eor

Go back to Sodium Binding Sites List in 3eor
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

Reference:

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
Page generated: Thu Oct 29 04:29:55 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy