Magnesium in PDB 2akm: Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex

All present enzymatic activity of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex:
4.2.1.11;

The structure of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex, PDB code: 2akm was solved by J.Qin, G.Chai, J.M.Brewer, L.L.Lovelace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.92
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.739, 119.692, 68.299, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.9

The binding sites of Magnesium atom in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex (pdb code 2akm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex, PDB code: 2akm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg440 b:39.6 occ:1.00 OD1 A:ASP317 1.8 27.5 1.0 OE1 A:GLU292 2.0 32.7 1.0 O A:HOH463 2.3 46.8 1.0 OD1 A:ASP244 2.3 37.4 1.0 O A:HOH461 2.4 47.9 1.0 O A:HOH462 2.7 39.6 1.0 CG A:ASP317 2.9 28.4 1.0 CD A:GLU292 3.1 28.1 1.0 CG A:ASP244 3.3 39.1 1.0 CB A:ASP317 3.6 28.8 1.0 OD2 A:ASP244 3.6 41.9 1.0 OE2 A:GLU292 3.7 27.6 1.0 OD2 A:ASP317 3.8 20.2 1.0 NZ A:LYS342 3.8 19.4 1.0 NZ A:LYS393 3.9 18.7 1.0 CD2 A:LEU340 3.9 16.8 1.0 MG A:MG441 3.9 38.2 1.0 NE2 A:GLN165 4.0 45.2 1.0 CG A:GLU292 4.1 29.4 1.0 OD2 A:ASP293 4.4 34.0 1.0 OE2 A:GLU166 4.4 31.6 1.0 O A:HOH464 4.4 36.2 1.0 CB A:ASP244 4.5 39.0 1.0 O A:HOH465 4.5 36.1 1.0 CE A:LYS342 4.7 19.3 1.0 O4 A:PO4442 4.9 35.7 1.0 O1 A:PO4442 5.0 34.6 1.0

Magnesium binding site 2 out of 3 in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg441 b:38.2 occ:1.00 O1 A:PO4442 2.1 34.6 1.0 O A:SER39 2.1 45.4 1.0 O A:HOH461 2.2 47.9 1.0 OG A:SER39 2.3 39.3 1.0 O A:HOH465 2.3 36.1 1.0 O A:HOH464 2.4 36.2 1.0 CB A:SER39 3.0 42.9 1.0 C A:SER39 3.1 44.7 1.0 P A:PO4442 3.3 32.8 1.0 CA A:SER39 3.6 43.3 1.0 NZ A:LYS342 3.6 19.4 1.0 O4 A:PO4442 3.6 35.7 1.0 OD1 A:ASP317 3.8 27.5 1.0 O3 A:PO4442 3.9 32.5 1.0 O A:HOH463 3.9 46.8 1.0 MG A:MG440 3.9 39.6 1.0 N A:SER39 4.1 42.2 1.0 O A:HOH462 4.3 39.6 1.0 N A:THR40 4.3 45.8 1.0 OE1 A:GLN165 4.3 44.3 1.0 OD1 A:ASP318 4.3 38.7 1.0 O2 A:PO4442 4.4 35.7 1.0 OD2 A:ASP318 4.5 40.8 1.0 NE2 A:GLN165 4.5 45.2 1.0 NH2 A:ARG371 4.6 17.9 1.0 CG A:ASP317 4.7 28.4 1.0 CA A:THR40 4.8 45.4 1.0 CG A:ASP318 4.8 41.0 1.0 CD A:GLN165 4.9 43.8 1.0

Magnesium binding site 3 out of 3 in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg440 b:29.4 occ:1.00 OE1 B:GLU292 2.0 19.1 1.0 O B:HOH444 2.1 33.2 1.0 O B:HOH445 2.2 35.1 1.0 OD1 B:ASP317 2.2 26.3 1.0 O B:HOH446 2.4 24.4 1.0 OD1 B:ASP244 2.8 40.8 1.0 CG B:ASP317 3.2 32.4 1.0 CD B:GLU292 3.2 26.1 1.0 OD2 B:ASP244 3.5 31.5 1.0 CG B:ASP244 3.5 30.5 1.0 CB B:ASP317 3.6 29.2 1.0 O1 B:PO4442 3.8 48.9 1.0 CG B:GLU292 4.0 23.8 1.0 OD2 B:ASP293 4.0 29.4 1.0 OE2 B:GLU292 4.2 27.6 1.0 NE2 B:GLN165 4.2 22.3 1.0 NZ B:LYS393 4.2 25.5 1.0 OD2 B:ASP317 4.4 34.8 1.0 NZ B:LYS342 4.4 26.6 1.0 CD2 B:LEU340 4.4 23.9 1.0 OE2 B:GLU166 4.8 31.5 1.0 CG B:ASP293 4.8 30.6 1.0 OD1 B:ASP318 4.8 32.5 1.0 OG B:SER39 5.0 60.5 1.0 CB B:ASP244 5.0 30.1 1.0

J.Qin, G.Chai, J.M.Brewer, L.L.Lovelace, L.Lebioda. Fluoride Inhibition of Enolase: Crystal Structure and Thermodynamics Biochemistry V. 45 793 2006.
ISSN: ISSN 0006-2960
PubMed: 16411755
DOI: 10.1021/BI051558S