Calcium in PDB 8a4d: 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor:
2.2.1.7;

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor, PDB code: 8a4d was solved by R.Hamid, A.Hirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.54 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.618, 137.618, 231.681, 90, 90, 90
R / Rfree (%)	17.6 / 24.1

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor also contains other interesting chemical elements:

Sodium	(Na)	5 atoms
Magnesium	(Mg)	11 atoms

The binding sites of Calcium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor (pdb code 8a4d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor, PDB code: 8a4d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:72.8 occ:1.00 O B:HOH1084 2.6 39.3 1.0 HH12 B:ARG358 3.5 49.2 1.0 HH22 B:ARG358 3.6 50.4 1.0 HE22 B:GLN327 3.8 43.4 1.0 NH1 B:ARG358 4.1 41.1 1.0 NH2 B:ARG358 4.2 42.0 1.0 O B:HOH904 4.4 36.6 1.0 CZ B:ARG358 4.5 44.4 1.0 O A:HOH1121 4.5 33.8 1.0 NE2 B:GLN327 4.5 36.2 1.0 HH11 B:ARG358 4.6 49.2 1.0 HH21 B:ARG358 4.7 50.4 1.0 HE21 B:GLN327 5.0 43.4 1.0

Calcium binding site 2 out of 2 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca706 b:47.0 occ:1.00 OD2 F:ASP455 2.6 20.9 1.0 O F:HOH865 2.7 18.5 1.0 OE2 F:GLU456 2.8 19.3 1.0 HG2 F:GLU456 2.9 17.4 1.0 O F:HOH1038 2.9 27.3 1.0 HB3 F:ASP455 3.0 26.7 1.0 HZ2 F:LYS459 3.1 33.4 1.0 HH22 F:ARG500 3.3 29.8 1.0 CG F:ASP455 3.5 26.7 1.0 CD F:GLU456 3.6 19.2 1.0 CG F:GLU456 3.7 14.5 1.0 CB F:ASP455 3.7 22.3 1.0 HD2 F:LYS459 3.9 35.9 1.0 NH2 F:ARG500 3.9 24.8 1.0 NZ F:LYS459 4.0 27.9 1.0 HH21 F:ARG533 4.0 20.8 1.0 HH12 F:ARG500 4.0 29.8 1.0 H F:GLU456 4.2 24.0 1.0 HG3 F:GLU456 4.2 17.4 1.0 N F:GLU456 4.3 20.0 1.0 HZ3 F:LYS459 4.3 33.4 1.0 HB2 F:ASP455 4.3 26.7 1.0 HA F:GLU456 4.3 24.7 1.0 HZ1 F:LYS459 4.3 33.4 1.0 HH21 F:ARG500 4.3 29.8 1.0 OD1 F:ASP453 4.4 14.5 1.0 O F:HOH860 4.5 27.5 1.0 C F:ASP455 4.5 25.3 1.0 HD3 F:LYS459 4.5 35.9 1.0 CD F:LYS459 4.5 29.9 1.0 NH1 F:ARG500 4.6 24.9 1.0 OD2 F:ASP453 4.6 22.0 1.0 CZ F:ARG500 4.7 22.0 1.0 CA F:GLU456 4.7 20.7 1.0 CE F:LYS459 4.7 24.5 1.0 OD1 F:ASP455 4.7 23.7 1.0 HE3 F:LYS459 4.7 29.3 1.0 NH2 F:ARG533 4.7 17.4 1.0 CB F:GLU456 4.8 20.9 1.0 CA F:ASP455 4.8 20.4 1.0 OE1 F:GLU456 4.8 21.4 1.0 HH22 F:ARG533 4.8 20.8 1.0 O F:HOH1136 4.9 30.6 1.0 CG F:ASP453 5.0 20.1 1.0

R.Hamid, R.Hamid, A.Hirsch. N/A N/A.