Zinc in PDB 1gx1: Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase

All present enzymatic activity of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase:
4.6.1.12;

The structure of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase, PDB code: 1gx1 was solved by L.E.Kemp, C.S.Bond, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	54.202, 114.848, 87.748, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.6

The structure of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Zinc atom in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (pdb code 1gx1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase, PDB code: 1gx1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1157 b:23.8 occ:1.00 O2B B:CDP1157 1.7 26.1 1.0 NE2 A:HIS10 1.9 21.3 1.0 OD2 A:ASP8 2.0 21.8 1.0 ND1 A:HIS42 2.0 25.3 1.0 CG A:ASP8 2.8 22.4 1.0 CE1 A:HIS10 2.9 25.7 1.0 CE1 A:HIS42 2.9 30.0 1.0 CD2 A:HIS10 2.9 22.2 1.0 CG A:HIS42 3.0 22.5 1.0 OD1 A:ASP8 3.1 22.1 1.0 PB B:CDP1157 3.2 31.7 1.0 CB A:HIS42 3.5 20.0 1.0 O1B B:CDP1157 3.6 27.8 1.0 ND1 A:HIS10 4.0 26.0 1.0 O3B B:CDP1157 4.0 31.0 1.0 NE2 A:HIS42 4.1 29.9 1.0 CG A:HIS10 4.1 22.3 1.0 O B:HOH2098 4.1 29.9 1.0 CD2 A:HIS42 4.1 23.5 1.0 CB A:ASP8 4.2 19.9 1.0 O B:HOH2087 4.3 25.9 1.0 O3A B:CDP1157 4.5 32.0 1.0 O A:VAL9 4.6 20.6 1.0 O A:HOH2026 4.7 42.5 1.0 CD1 A:ILE57 4.7 33.1 1.0 CA A:VAL39 4.9 22.8 1.0 CA A:HIS42 5.0 18.6 1.0

Zinc binding site 2 out of 3 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1159 b:24.2 occ:1.00 O2B B:CDP1160 1.7 29.6 1.0 ND1 B:HIS42 1.9 25.6 1.0 OD2 B:ASP8 2.0 25.0 1.0 NE2 B:HIS10 2.0 23.6 1.0 CG B:ASP8 2.8 22.3 1.0 CE1 B:HIS42 2.8 31.5 1.0 CE1 B:HIS10 3.0 26.5 1.0 CG B:HIS42 3.0 25.1 1.0 CD2 B:HIS10 3.0 22.6 1.0 OD1 B:ASP8 3.0 21.1 1.0 PB B:CDP1160 3.2 37.9 1.0 CB B:HIS42 3.4 21.0 1.0 O1B B:CDP1160 3.8 31.9 1.0 O3B B:CDP1160 4.0 36.3 1.0 NE2 B:HIS42 4.0 29.4 1.0 CD2 B:HIS42 4.1 26.2 1.0 ND1 B:HIS10 4.1 25.7 1.0 CG B:HIS10 4.1 21.9 1.0 O C:HOH2093 4.2 32.4 1.0 CB B:ASP8 4.2 19.4 1.0 O C:HOH2087 4.2 31.2 1.0 O3A B:CDP1160 4.6 33.3 1.0 O B:VAL9 4.7 17.7 1.0 CD1 B:ILE57 4.7 35.7 1.0 CA B:VAL39 4.9 24.8 1.0 CA B:HIS42 4.9 20.5 1.0 O B:HOH2035 5.0 35.9 1.0 O B:ASP38 5.0 23.3 1.0

Zinc binding site 3 out of 3 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1157 b:22.9 occ:1.00 O2B A:CDP1158 1.7 28.5 1.0 OD2 C:ASP8 1.9 21.4 1.0 NE2 C:HIS10 1.9 23.6 1.0 ND1 C:HIS42 2.0 26.1 1.0 CG C:ASP8 2.8 21.5 1.0 CD2 C:HIS10 2.9 22.4 1.0 CE1 C:HIS10 2.9 24.1 1.0 CE1 C:HIS42 3.0 30.1 1.0 OD1 C:ASP8 3.1 20.5 1.0 CG C:HIS42 3.1 23.7 1.0 PB A:CDP1158 3.2 32.9 1.0 CB C:HIS42 3.5 20.4 1.0 O1B A:CDP1158 3.7 27.8 1.0 O3B A:CDP1158 3.9 32.0 1.0 O A:HOH2088 4.0 27.5 1.0 ND1 C:HIS10 4.0 25.8 1.0 CG C:HIS10 4.1 21.9 1.0 NE2 C:HIS42 4.1 28.3 1.0 CD2 C:HIS42 4.2 24.2 1.0 CB C:ASP8 4.2 18.6 1.0 O A:HOH2077 4.2 27.0 1.0 O3A A:CDP1158 4.5 30.8 1.0 CD1 C:ILE57 4.8 32.9 1.0 O C:VAL9 4.8 20.5 1.0 O C:ASP38 4.9 21.9 1.0 CA C:VAL39 4.9 22.1 1.0 CA C:HIS42 5.0 20.3 1.0

L.E.Kemp, C.S.Bond, W.N.Hunter. Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase: An Essential Enzyme For Isoprenoid Biosynthesis and Target For Antimicrobial Drug Development Proc.Natl.Acad.Sci.Usa V. 99 6591 2002.
ISSN: ISSN 0027-8424
PubMed: 11997478
DOI: 10.1073/PNAS.102679799