Magnesium in PDB 6b63: Impase (AF2372) with 25 Mm Asp

All present enzymatic activity of Impase (AF2372) with 25 Mm Asp:
3.1.3.11; 3.1.3.25;

The structure of Impase (AF2372) with 25 Mm Asp, PDB code: 6b63 was solved by R.I.Goldstein, M.Roberts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.97 / 2.70
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	89.645, 89.645, 101.915, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 21.3

The binding sites of Magnesium atom in the Impase (AF2372) with 25 Mm Asp (pdb code 6b63). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Impase (AF2372) with 25 Mm Asp, PDB code: 6b63:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Impase (AF2372) with 25 Mm Asp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:21.3 occ:1.00 O A:HOH603 2.1 19.2 1.0 O A:HOH610 2.1 18.8 1.0 OE1 A:GLU67 2.1 31.4 1.0 O4 A:PO4502 2.5 29.3 1.0 CD A:GLU67 3.0 27.0 1.0 OE2 A:GLU67 3.3 20.0 1.0 O A:HOH629 3.3 29.2 1.0 OE2 A:GLU68 3.4 28.3 1.0 OD2 A:ASP46 3.4 17.6 1.0 O A:HOH601 3.5 16.4 1.0 OG1 A:THR87 3.7 19.9 1.0 OD1 A:ASP46 3.8 26.6 1.0 P A:PO4502 3.8 30.6 1.0 CG A:ASP46 3.9 24.5 1.0 O2 A:PO4502 4.0 16.9 1.0 MG A:MG504 4.3 38.5 1.0 O A:PRO41 4.3 30.3 1.0 CB A:THR87 4.3 17.4 1.0 OG1 A:THR40 4.3 17.2 1.0 CG A:GLU67 4.4 20.6 1.0 O A:HOH607 4.4 37.0 1.0 CD A:GLU68 4.4 27.4 1.0 OE1 A:GLU68 4.6 27.6 1.0 O3 A:PO4502 4.7 42.5 1.0 O A:LEU84 4.7 18.4 1.0 CG2 A:THR87 4.8 17.9 1.0 O1 A:PO4502 4.9 49.9 1.0

Magnesium binding site 2 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Impase (AF2372) with 25 Mm Asp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:38.5 occ:1.00 O2 A:PO4502 1.7 16.9 1.0 OD2 A:ASP82 2.0 16.5 1.0 OD1 A:ASP82 2.0 26.3 1.0 CG A:ASP82 2.3 18.6 1.0 OE2 A:GLU67 2.3 20.0 1.0 O A:LEU84 2.4 18.4 1.0 O A:HOH601 2.5 16.4 1.0 MG A:MG507 2.7 22.6 1.0 P A:PO4502 3.1 30.6 1.0 C A:LEU84 3.3 16.7 1.0 CA A:ASP85 3.4 16.0 1.0 CD A:GLU67 3.5 27.0 1.0 O4 A:PO4502 3.7 29.3 1.0 N A:ASP85 3.7 22.6 1.0 OD1 A:ASP85 3.7 22.5 1.0 O1 A:PO4502 3.7 49.9 1.0 CB A:ASP82 3.8 17.0 1.0 OD1 A:ASP200 3.9 31.5 1.0 CB A:ASP85 3.9 13.2 1.0 OE1 A:GLU67 4.1 31.4 1.0 O3 A:PO4502 4.1 42.5 1.0 MG A:MG503 4.3 21.3 1.0 NH2 A:ARG197 4.3 30.8 1.0 CG A:ASP85 4.3 20.6 1.0 N A:LEU84 4.5 14.1 1.0 CA A:LEU84 4.5 15.9 1.0 OG1 A:THR87 4.6 19.9 1.0 CA A:ASP82 4.6 15.9 1.0 CG A:GLU67 4.6 20.6 1.0 C A:ASP85 4.7 16.1 1.0 CB A:GLU67 4.7 14.6 1.0 N A:GLY86 4.8 12.0 1.0 C A:ASP82 4.9 16.9 1.0

Magnesium binding site 3 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Impase (AF2372) with 25 Mm Asp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:22.6 occ:1.00 OD1 A:ASP85 1.9 22.5 1.0 OD1 A:ASP200 2.0 31.5 1.0 O1 A:PO4502 2.2 49.9 1.0 O2 A:PO4502 2.3 16.9 1.0 OD2 A:ASP82 2.3 16.5 1.0 MG A:MG504 2.7 38.5 1.0 P A:PO4502 2.8 30.6 1.0 CG A:ASP200 3.0 23.5 1.0 CG A:ASP85 3.0 20.6 1.0 NH2 A:ARG197 3.4 30.8 1.0 CG A:ASP82 3.5 18.6 1.0 O3 A:PO4502 3.7 42.5 1.0 CB A:ASP85 3.7 13.2 1.0 OD2 A:ASP200 3.8 21.0 1.0 O13 B:CU7301 3.8 37.8 0.8 CA A:ASP85 3.9 16.0 1.0 O4 A:PO4502 4.0 29.3 1.0 CB A:ASP200 4.0 19.4 1.0 OD2 A:ASP85 4.0 12.7 1.0 OD1 A:ASP82 4.1 26.3 1.0 OE2 A:GLU67 4.3 20.0 1.0 O11 B:CU7301 4.3 42.1 0.8 CA A:ASP200 4.4 12.2 1.0 C12 B:CU7301 4.5 56.1 0.8 N A:GLY86 4.6 12.0 1.0 CZ A:ARG197 4.6 45.2 1.0 O A:LEU84 4.6 18.4 1.0 CB A:ASP82 4.6 17.0 1.0 O A:HOH607 4.8 37.0 1.0 C A:ASP85 4.8 16.1 1.0 N A:ASP85 5.0 22.6 1.0

Magnesium binding site 4 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Impase (AF2372) with 25 Mm Asp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:26.6 occ:1.00 O3 B:PO4302 1.9 22.1 1.0 O B:HOH415 2.0 20.7 1.0 OD1 B:ASP82 2.0 21.7 1.0 OE1 B:GLU67 2.1 22.4 1.0 O B:LEU84 2.1 29.5 1.0 C B:LEU84 2.9 16.4 1.0 CG B:ASP82 3.0 15.2 1.0 CD B:GLU67 3.2 25.0 1.0 OD2 B:ASP82 3.3 21.6 1.0 P B:PO4302 3.4 26.7 1.0 MG B:MG304 3.5 21.8 1.0 N B:LEU84 3.6 21.1 1.0 N B:ASP85 3.7 20.5 1.0 OG1 B:THR87 3.8 25.6 1.0 CA B:LEU84 3.8 18.5 1.0 MG B:MG307 3.8 19.7 1.0 OE2 B:GLU67 3.8 32.7 1.0 CA B:ASP85 3.9 20.9 1.0 O4 B:PO4302 4.0 24.9 1.0 OD1 B:ASP46 4.1 29.8 1.0 OE1 B:GLU68 4.1 28.4 1.0 O1 B:PO4302 4.1 31.6 1.0 O2 B:PO4302 4.2 17.2 1.0 CB B:GLU67 4.3 16.2 1.0 CD B:PRO83 4.3 12.7 1.0 CG B:GLU67 4.3 20.7 1.0 CB B:ASP82 4.3 12.5 1.0 CB B:LEU84 4.4 19.9 1.0 N B:PRO83 4.6 16.2 1.0 CG B:PRO83 4.6 18.2 1.0 CA B:ASP82 4.6 12.1 1.0 C B:ASP82 4.6 14.1 1.0 CB B:ASP85 4.8 16.4 1.0 CG B:ASP46 4.8 20.6 1.0 C B:PRO83 4.9 18.3 1.0

Magnesium binding site 5 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Impase (AF2372) with 25 Mm Asp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:21.8 occ:1.00 O4 B:PO4302 1.7 24.9 1.0 OD2 B:ASP82 2.0 21.6 1.0 OD1 B:ASP200 2.1 26.4 1.0 OD1 B:ASP85 2.2 25.8 1.0 P B:PO4302 2.7 26.7 1.0 O3 B:PO4302 2.8 22.1 1.0 CG B:ASP82 3.1 15.2 1.0 CG B:ASP85 3.2 18.7 1.0 CG B:ASP200 3.3 20.0 1.0 NH2 B:ARG197 3.5 21.8 1.0 OD1 B:ASP82 3.5 21.7 1.0 MG B:MG303 3.5 26.6 1.0 CB B:ASP85 3.5 16.4 1.0 CA B:ASP85 3.7 20.9 1.0 O2 B:PO4302 3.7 17.2 1.0 O1 B:PO4302 3.8 31.6 1.0 OE1 B:GLU67 3.8 22.4 1.0 O1 A:CU7508 4.0 32.7 0.8 OD2 B:ASP200 4.0 16.4 1.0 CB B:ASP200 4.3 22.1 1.0 OD2 B:ASP85 4.3 21.0 1.0 CB B:ASP82 4.3 12.5 1.0 O B:LEU84 4.4 29.5 1.0 CA B:ASP200 4.5 12.6 1.0 N B:ASP85 4.6 20.5 1.0 CD B:GLU67 4.6 25.0 1.0 N B:GLY86 4.7 13.8 1.0 CZ B:ARG197 4.7 39.0 1.0 C B:ASP85 4.7 17.0 1.0 C B:LEU84 4.8 16.4 1.0 O A:HOH602 4.9 27.2 1.0 O B:HOH422 4.9 30.5 1.0 CD2 B:TYR199 4.9 17.7 1.0 OE2 B:GLU67 5.0 32.7 1.0

Magnesium binding site 6 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Impase (AF2372) with 25 Mm Asp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg307 b:19.7 occ:1.00 OE2 B:GLU67 2.2 32.7 1.0 O1 B:PO4302 2.7 31.6 1.0 CD B:GLU67 3.0 25.0 1.0 O3 B:PO4302 3.1 22.1 1.0 OD2 B:ASP46 3.2 21.0 1.0 OE1 B:GLU67 3.3 22.4 1.0 O B:HOH423 3.3 29.6 1.0 O B:HOH403 3.3 52.0 1.0 OE1 B:GLU68 3.4 28.4 1.0 P B:PO4302 3.4 26.7 1.0 OG1 B:THR87 3.5 25.6 1.0 MG B:MG303 3.8 26.6 1.0 O B:HOH415 3.9 20.7 1.0 CG B:ASP46 3.9 20.6 1.0 OD1 B:ASP46 3.9 29.8 1.0 O2 B:PO4302 4.1 17.2 1.0 OG1 B:THR40 4.2 11.9 1.0 CB B:THR87 4.2 22.7 1.0 CG B:GLU67 4.3 20.7 1.0 O B:PRO41 4.4 21.8 1.0 CD B:GLU68 4.4 26.3 1.0 OE2 B:GLU68 4.6 22.7 1.0 CG2 B:THR87 4.7 18.6 1.0 O B:LEU84 4.7 29.5 1.0 O4 B:PO4302 4.8 24.9 1.0

R.I.Goldstein, M.Roberts. Osmolyte Binding Capacity of A Dual Action Impase/Fbpase (AF2372) To Be Published.