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Zinc in PDB 2pmp: Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From the Isoprenoid Biosynthetic Pathway of Arabidopsis Thaliana

Enzymatic activity of Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From the Isoprenoid Biosynthetic Pathway of Arabidopsis Thaliana

All present enzymatic activity of Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From the Isoprenoid Biosynthetic Pathway of Arabidopsis Thaliana:
4.6.1.12;

Protein crystallography data

The structure of Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From the Isoprenoid Biosynthetic Pathway of Arabidopsis Thaliana, PDB code: 2pmp was solved by B.M.Calisto, J.Perez-Gil, J.Querol-Audi, I.Fita, S.Imperial, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.60 / 2.30
Space group I 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 135.795, 135.795, 135.795, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From the Isoprenoid Biosynthetic Pathway of Arabidopsis Thaliana (pdb code 2pmp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From the Isoprenoid Biosynthetic Pathway of Arabidopsis Thaliana, PDB code: 2pmp:

Zinc binding site 1 out of 1 in 2pmp

Go back to Zinc Binding Sites List in 2pmp
Zinc binding site 1 out of 1 in the Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From the Isoprenoid Biosynthetic Pathway of Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From the Isoprenoid Biosynthetic Pathway of Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:53.0
occ:1.00
ND1 A:HIS45 2.0 39.3 1.0
OD2 A:ASP11 2.0 32.7 1.0
NE2 A:HIS13 2.3 38.7 1.0
O A:HOH704 2.6 43.4 1.0
CE1 A:HIS13 2.7 40.1 1.0
CG A:ASP11 2.9 30.8 1.0
CE1 A:HIS45 2.9 38.9 1.0
OD1 A:ASP11 3.1 32.1 1.0
CG A:HIS45 3.1 36.1 1.0
CD2 A:HIS13 3.5 37.8 1.0
CB A:HIS45 3.5 36.5 1.0
ND1 A:HIS13 3.9 40.0 1.0
NE2 A:HIS45 4.1 38.7 1.0
CD2 A:HIS45 4.2 38.5 1.0
CG A:HIS13 4.3 35.2 1.0
CB A:ASP11 4.3 30.4 1.0
OG A:SER38 4.6 55.0 1.0
CA A:VAL42 4.8 38.5 1.0
O A:ASP41 4.9 40.4 1.0
O A:LEU12 5.0 29.1 1.0

Reference:

B.M.Calisto, J.Perez-Gil, M.Bergua, J.Querol-Audi, I.Fita, S.Imperial. Biosynthesis of Isoprenoids in Plants: Structure of the 2C-Methyl-D-Erithrytol 2,4-Cyclodiphosphate Synthase From Arabidopsis Thaliana. Comparison with the Bacterial Enzymes. Protein Sci. V. 16 2082 2007.
ISSN: ISSN 0961-8368
PubMed: 17660251
DOI: 10.1110/PS.072972807
Page generated: Sat Sep 26 03:32:00 2020
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