Magnesium in PDB 4za0: Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate

All present enzymatic activity of Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate:
4.2.1.11;

The structure of Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate, PDB code: 4za0 was solved by P.G.Leonard, D.Maxwell, B.Czako, F.L.Muller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.02 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.790, 108.671, 112.210, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.4

The binding sites of Magnesium atom in the Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate (pdb code 4za0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate, PDB code: 4za0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:1.2 occ:1.00 O3 A:PAH503 1.8 15.8 1.0 OE2 A:GLU293 2.0 22.2 1.0 O A:HOH635 2.1 14.1 1.0 OD2 A:ASP318 2.1 13.7 1.0 OD2 A:ASP245 2.1 19.5 1.0 O2 A:PAH503 2.4 14.7 1.0 N3 A:PAH503 2.7 12.7 1.0 C2 A:PAH503 2.9 13.3 1.0 CG A:ASP245 3.0 15.3 1.0 OD1 A:ASP245 3.1 18.2 1.0 CD A:GLU293 3.2 15.4 1.0 CG A:ASP318 3.2 15.6 1.0 O A:HOH702 3.7 18.0 1.0 CB A:ASP318 3.8 13.1 1.0 NE2 A:GLN166 3.9 17.2 1.0 NZ A:LYS394 3.9 13.1 1.0 NZ A:LYS343 3.9 13.6 1.0 OE1 A:GLU293 4.0 15.7 1.0 O A:HOH633 4.0 13.1 1.0 MG A:MG502 4.0 8.0 1.0 CG A:GLU293 4.1 13.5 1.0 OD2 A:ASP294 4.2 14.1 1.0 OD1 A:ASP318 4.2 14.6 1.0 CD2 A:LEU341 4.3 12.8 1.0 C1 A:PAH503 4.4 14.5 1.0 CB A:ASP245 4.4 14.1 1.0 OE2 A:GLU167 4.6 22.1 1.0 CE A:LYS343 4.9 9.6 1.0 CB A:ALA247 5.0 14.8 1.0 CG A:ASP294 5.0 14.9 1.0 CE A:LYS394 5.0 17.6 1.0

Magnesium binding site 2 out of 4 in the Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:8.0 occ:1.00 O2P A:PAH503 2.0 12.1 1.0 O A:SER40 2.1 15.0 1.0 O A:HOH633 2.1 13.1 1.0 OG A:SER40 2.1 17.9 1.0 O A:HOH702 2.1 18.0 1.0 O2 A:PAH503 2.1 14.7 1.0 C2 A:PAH503 3.0 13.3 1.0 C A:SER40 3.0 16.2 1.0 CB A:SER40 3.1 15.9 1.0 P A:PAH503 3.1 15.3 1.0 C1 A:PAH503 3.4 14.5 1.0 CA A:SER40 3.5 17.2 1.0 O3P A:PAH503 3.9 15.2 1.0 OD2 A:ASP318 3.9 13.7 1.0 OD1 A:ASP319 3.9 15.7 1.0 NZ A:LYS343 3.9 13.6 1.0 MG A:MG501 4.0 1.2 1.0 OD2 A:ASP319 4.0 22.5 1.0 N A:SER40 4.0 15.0 1.0 N A:THR41 4.2 17.7 1.0 N3 A:PAH503 4.2 12.7 1.0 O A:HOH635 4.2 14.1 1.0 NH2 A:ARG372 4.3 11.7 1.0 O1P A:PAH503 4.3 12.3 1.0 NE2 A:GLN166 4.4 17.2 1.0 CG A:ASP319 4.4 21.0 1.0 OE1 A:GLN166 4.4 17.3 1.0 O3 A:PAH503 4.5 15.8 1.0 CA A:THR41 4.6 17.6 1.0 CD A:GLN166 4.9 17.5 1.0 CG A:ASP318 4.9 15.6 1.0

Magnesium binding site 3 out of 4 in the Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:1.7 occ:1.00 O3 B:PAH503 1.7 16.4 1.0 OE2 B:GLU293 2.0 15.4 1.0 O B:HOH608 2.1 12.8 1.0 OD2 B:ASP318 2.1 16.4 1.0 OD2 B:ASP245 2.1 16.3 1.0 O2 B:PAH503 2.5 12.6 1.0 N3 B:PAH503 2.6 11.8 1.0 C2 B:PAH503 2.9 11.0 1.0 CG B:ASP245 2.9 17.3 1.0 OD1 B:ASP245 3.1 9.9 1.0 CG B:ASP318 3.1 15.5 1.0 CD B:GLU293 3.2 12.5 1.0 O B:HOH695 3.7 13.2 1.0 CB B:ASP318 3.7 11.1 1.0 O B:HOH630 3.8 14.2 1.0 NZ B:LYS394 3.8 15.0 1.0 OD2 B:ASP294 3.9 17.6 1.0 OE1 B:GLN166 4.0 15.7 1.0 NZ B:LYS343 4.0 17.2 1.0 OE1 B:GLU293 4.0 16.5 1.0 MG B:MG502 4.0 8.9 1.0 CG B:GLU293 4.1 9.9 1.0 OD1 B:ASP318 4.2 12.7 1.0 CD2 B:LEU341 4.2 13.0 1.0 CB B:ASP245 4.4 11.5 1.0 C1 B:PAH503 4.4 12.0 1.0 OE2 B:GLU167 4.6 21.9 1.0 CG B:ASP294 4.8 16.1 1.0 CE B:LYS343 4.9 12.6 1.0 CB B:ALA247 4.9 12.5 1.0 CE B:LYS394 5.0 15.7 1.0

Magnesium binding site 4 out of 4 in the Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Enolase 2 in Complex with Phosphonoacetohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:8.9 occ:1.00 O2P B:PAH503 1.9 11.6 1.0 O B:SER40 2.0 16.6 1.0 O B:HOH630 2.1 14.2 1.0 O B:HOH695 2.1 13.2 1.0 O2 B:PAH503 2.1 12.6 1.0 OG B:SER40 2.1 12.5 1.0 C2 B:PAH503 2.9 11.0 1.0 C B:SER40 3.0 13.6 1.0 P B:PAH503 3.1 13.6 1.0 CB B:SER40 3.2 16.6 1.0 C1 B:PAH503 3.4 12.0 1.0 CA B:SER40 3.5 15.7 1.0 OD2 B:ASP318 3.8 16.4 1.0 O3P B:PAH503 3.9 15.4 1.0 NZ B:LYS343 3.9 17.2 1.0 OD1 B:ASP319 4.0 15.7 1.0 MG B:MG501 4.0 1.7 1.0 OD2 B:ASP319 4.1 17.1 1.0 N B:SER40 4.1 14.8 1.0 N B:THR41 4.1 11.8 1.0 N3 B:PAH503 4.1 11.8 1.0 O1P B:PAH503 4.3 12.9 1.0 NH2 B:ARG372 4.3 14.8 1.0 O B:HOH608 4.3 12.8 1.0 O3 B:PAH503 4.4 16.4 1.0 OE1 B:GLN166 4.4 15.7 1.0 CG B:ASP319 4.5 16.3 1.0 CA B:THR41 4.5 16.2 1.0 NE2 B:GLN166 4.5 9.3 1.0 CG B:ASP318 4.9 15.5 1.0 CD B:GLN166 4.9 16.2 1.0

P.G.Leonard, N.Satani, D.Maxwell, Y.H.Lin, N.Hammoudi, Z.Peng, F.Pisaneschi, T.M.Link, G.R.Lee, D.Sun, B.A.Prasad, M.E.Di Francesco, B.Czako, J.M.Asara, Y.A.Wang, W.Bornmann, R.A.Depinho, F.L.Muller. SF2312 Is A Natural Phosphonate Inhibitor of Enolase. Nat.Chem.Biol. V. 12 1053 2016.
ISSN: ESSN 1552-4469
PubMed: 27723749
DOI: 10.1038/NCHEMBIO.2195