Magnesium in PDB 4zcw: Structure of Human Enolase 2 in Complex with SF2312

All present enzymatic activity of Structure of Human Enolase 2 in Complex with SF2312:
4.2.1.11;

The structure of Structure of Human Enolase 2 in Complex with SF2312, PDB code: 4zcw 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)	51.69 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.300, 109.460, 117.270, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 20.2

The binding sites of Magnesium atom in the Structure of Human Enolase 2 in Complex with SF2312 (pdb code 4zcw). 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 SF2312, PDB code: 4zcw:
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 SF2312


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 SF2312 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:5.6 occ:1.00 OE2 A:GLU293 1.9 17.1 1.0 OD2 A:ASP318 2.1 15.3 1.0 OAF A:4NG501 2.1 17.7 1.0 OD2 A:ASP245 2.1 17.8 1.0 O A:HOH619 2.2 12.9 1.0 OAG A:4NG501 2.4 19.5 1.0 NAB A:4NG501 2.8 18.2 1.0 CAA A:4NG501 2.9 16.7 1.0 CG A:ASP245 3.0 17.5 1.0 CD A:GLU293 3.1 13.1 1.0 CG A:ASP318 3.1 16.7 1.0 OD1 A:ASP245 3.3 15.6 1.0 CB A:ASP318 3.7 12.1 1.0 NZ A:LYS394 3.7 18.4 1.0 O A:HOH681 3.8 21.1 1.0 O A:HOH642 3.8 18.3 1.0 NZ A:LYS343 3.9 18.1 1.0 OE1 A:GLU293 3.9 15.9 1.0 OE1 A:GLN166 4.1 20.5 1.0 MG A:MG503 4.1 19.0 1.0 CG A:GLU293 4.1 12.5 1.0 OD2 A:ASP294 4.1 18.0 1.0 CD2 A:LEU341 4.1 13.2 1.0 OD1 A:ASP318 4.2 16.9 1.0 CAC A:4NG501 4.2 22.4 1.0 CAE A:4NG501 4.3 17.0 1.0 CB A:ASP245 4.4 13.4 1.0 OAH A:4NG501 4.7 18.8 1.0 CE A:LYS394 4.8 16.6 1.0 OE2 A:GLU167 4.8 23.6 1.0 CAD A:4NG501 4.9 19.0 1.0 CE A:LYS343 4.9 15.6 1.0

Magnesium binding site 2 out of 4 in the Structure of Human Enolase 2 in Complex with SF2312


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 SF2312 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:19.0 occ:1.00 OAK A:4NG501 1.9 19.8 1.0 O A:SER40 2.0 27.3 1.0 OAG A:4NG501 2.0 19.5 1.0 O A:HOH681 2.0 21.1 1.0 OG A:SER40 2.2 23.6 1.0 O A:HOH642 2.2 18.3 1.0 CAA A:4NG501 2.8 16.7 1.0 C A:SER40 2.9 28.9 1.0 PAI A:4NG501 3.0 23.0 1.0 CAE A:4NG501 3.1 17.0 1.0 CB A:SER40 3.1 31.6 1.0 CA A:SER40 3.4 28.2 1.0 N A:SER40 3.9 28.3 1.0 OAJ A:4NG501 3.9 26.6 1.0 OD2 A:ASP318 3.9 15.3 1.0 NAB A:4NG501 4.0 18.2 1.0 N A:THR41 4.1 32.5 1.0 OD1 A:ASP319 4.1 22.8 1.0 MG A:MG502 4.1 5.6 1.0 NZ A:LYS343 4.2 18.1 1.0 OAL A:4NG501 4.2 23.4 1.0 OD2 A:ASP319 4.3 24.7 1.0 OE1 A:GLN166 4.4 20.5 1.0 O A:HOH619 4.4 12.9 1.0 CA A:THR41 4.5 26.7 1.0 NE2 A:GLN166 4.5 12.4 1.0 CAD A:4NG501 4.6 19.0 1.0 NH2 A:ARG372 4.6 17.8 1.0 CG A:ASP319 4.6 23.4 1.0 OAF A:4NG501 4.7 17.7 1.0 CD A:GLN166 4.9 21.7 1.0 CAC A:4NG501 5.0 22.4 1.0 CG A:ASP318 5.0 16.7 1.0

Magnesium binding site 3 out of 4 in the Structure of Human Enolase 2 in Complex with SF2312


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 SF2312 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:15.1 occ:1.00 OAL B:4NG501 1.9 21.0 1.0 OAG B:4NG501 2.0 19.6 1.0 O B:HOH703 2.0 14.5 1.0 O B:SER40 2.1 18.9 1.0 OG B:SER40 2.1 18.6 1.0 O B:HOH676 2.1 16.9 1.0 CAA B:4NG501 2.8 13.5 1.0 C B:SER40 3.0 20.7 1.0 CB B:SER40 3.1 24.7 1.0 PAI B:4NG501 3.1 18.5 1.0 CAE B:4NG501 3.2 15.3 1.0 CA B:SER40 3.5 21.4 1.0 OAJ B:4NG501 3.9 21.8 1.0 N B:SER40 3.9 22.8 1.0 OD2 B:ASP318 3.9 15.1 1.0 NAB B:4NG501 3.9 18.8 1.0 OD1 B:ASP319 4.0 20.7 1.0 OD2 B:ASP319 4.1 23.3 1.0 N B:THR41 4.2 17.6 1.0 NZ B:LYS343 4.2 14.0 1.0 MG B:MG503 4.2 7.9 1.0 NH2 B:ARG372 4.2 16.3 1.0 OAK B:4NG501 4.3 25.2 1.0 O B:HOH639 4.3 13.1 1.0 OE1 B:GLN166 4.4 20.0 1.0 NE2 B:GLN166 4.4 14.5 1.0 CG B:ASP319 4.5 24.8 1.0 OAF B:4NG501 4.5 17.8 1.0 CA B:THR41 4.6 22.3 1.0 CAD B:4NG501 4.7 18.3 1.0 CD B:GLN166 4.9 19.2 1.0 CAC B:4NG501 4.9 22.8 1.0 CG B:ASP318 5.0 17.8 1.0

Magnesium binding site 4 out of 4 in the Structure of Human Enolase 2 in Complex with SF2312


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 SF2312 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:7.9 occ:1.00 OE2 B:GLU293 2.0 21.2 1.0 OAF B:4NG501 2.0 17.8 1.0 OD2 B:ASP318 2.1 15.1 1.0 OD2 B:ASP245 2.1 19.9 1.0 O B:HOH639 2.2 13.1 1.0 OAG B:4NG501 2.6 19.6 1.0 NAB B:4NG501 2.9 18.8 1.0 CG B:ASP245 3.0 19.9 1.0 CG B:ASP318 3.1 17.8 1.0 CAA B:4NG501 3.1 13.5 1.0 CD B:GLU293 3.1 19.8 1.0 OD1 B:ASP245 3.3 16.4 1.0 CB B:ASP318 3.7 11.6 1.0 NZ B:LYS394 3.7 16.4 1.0 NZ B:LYS343 3.8 14.0 1.0 OE1 B:GLU293 3.9 20.2 1.0 O B:HOH676 3.9 16.9 1.0 O B:HOH703 4.0 14.5 1.0 CD2 B:LEU341 4.1 13.6 1.0 CG B:GLU293 4.1 17.0 1.0 OE1 B:GLN166 4.1 20.0 1.0 OD1 B:ASP318 4.1 13.7 1.0 MG B:MG502 4.2 15.1 1.0 OD2 B:ASP294 4.2 21.4 1.0 CAC B:4NG501 4.3 22.8 1.0 CB B:ASP245 4.4 15.6 1.0 CAE B:4NG501 4.5 15.3 1.0 OAH B:4NG501 4.7 22.6 1.0 CE B:LYS394 4.7 19.0 1.0 OE2 B:GLU167 4.8 23.3 1.0 CE B:LYS343 4.9 13.3 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