Manganese 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:

Zinc

(Zn)

3 atoms

The binding sites of Manganese 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 Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase, PDB code: 1gx1:
Jump to Manganese binding site number: 1; 2; 3;

Manganese 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 Manganese with other atoms in the Mn 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:Mn1159 b:33.8 occ:1.00 O1B A:CDP1158 2.1 27.8 1.0 O A:HOH2091 2.2 37.4 1.0 OE1 A:GLU135 2.2 31.7 1.0 O A:HOH2092 2.3 34.7 1.0 O A:HOH2090 2.3 27.8 1.0 O2A A:CDP1158 2.3 32.2 1.0 CD A:GLU135 3.2 31.7 1.0 PA A:CDP1158 3.3 28.0 1.0 PB A:CDP1158 3.4 32.9 1.0 OE2 A:GLU135 3.5 32.5 1.0 O3A A:CDP1158 3.5 30.8 1.0 NE2 C:HIS34 3.7 63.0 0.0 O1A A:CDP1158 4.0 27.9 1.0 O3B A:CDP1158 4.1 32.0 1.0 O A:HOH2077 4.2 27.0 1.0 CE1 C:HIS10 4.2 24.1 1.0 CD2 C:HIS34 4.2 60.4 0.0 CG A:GLU135 4.6 25.7 1.0 O5' A:CDP1158 4.6 27.5 1.0 O2B A:CDP1158 4.6 28.5 1.0 O A:HOH2075 4.7 42.9 1.0 OG1 A:THR133 4.8 23.1 1.0 CE1 C:HIS34 4.8 61.4 0.0 ND1 C:HIS10 4.8 25.8 1.0 C5' A:CDP1158 4.9 27.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn1158 b:31.7 occ:1.00 O2A B:CDP1157 2.1 33.6 1.0 O B:HOH2100 2.2 33.5 1.0 O B:HOH2102 2.2 32.3 1.0 O1B B:CDP1157 2.2 27.8 1.0 OE1 B:GLU135 2.3 28.5 1.0 O B:HOH2101 2.4 31.9 1.0 PA B:CDP1157 3.3 27.4 1.0 CD B:GLU135 3.3 30.9 1.0 PB B:CDP1157 3.4 31.7 1.0 O3A B:CDP1157 3.6 32.0 1.0 OE2 B:GLU135 3.6 34.1 1.0 O3B B:CDP1157 4.1 31.0 1.0 O1A B:CDP1157 4.1 29.0 1.0 CE1 A:HIS10 4.2 25.7 1.0 O B:HOH2087 4.2 25.9 1.0 O A:HOH2026 4.3 42.5 1.0 O5' B:CDP1157 4.6 26.4 1.0 CD2 A:HIS34 4.6 61.3 0.0 CG B:GLU135 4.7 26.2 1.0 O2B B:CDP1157 4.7 26.1 1.0 ND1 A:HIS10 4.9 26.0 1.0 OG1 B:THR133 4.9 22.6 1.0 C5' B:CDP1157 4.9 30.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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 B:Mn1161 b:37.4 occ:1.00 O1B B:CDP1160 2.1 31.9 1.0 O B:HOH2104 2.1 36.3 1.0 O2A B:CDP1160 2.3 34.6 1.0 OE1 C:GLU135 2.3 32.5 1.0 O B:HOH2105 2.4 31.6 1.0 PA B:CDP1160 3.3 29.1 1.0 CD C:GLU135 3.3 31.5 1.0 PB B:CDP1160 3.3 37.9 1.0 O3A B:CDP1160 3.5 33.3 1.0 OE2 C:GLU135 3.5 35.1 1.0 O C:HOH2093 4.0 32.4 1.0 O3B B:CDP1160 4.1 36.3 1.0 O1A B:CDP1160 4.1 28.2 1.0 CE1 B:HIS10 4.3 26.5 1.0 O2B B:CDP1160 4.5 29.6 1.0 CD2 B:HIS34 4.5 54.2 0.0 O5' B:CDP1160 4.6 29.8 1.0 CG C:GLU135 4.6 27.1 1.0 O C:HOH2091 4.7 43.2 1.0 OG1 C:THR133 4.8 20.5 1.0 C5' B:CDP1160 4.9 31.5 1.0 ND1 B:HIS10 4.9 25.7 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