Magnesium in PDB 5f9k: Dictyostelium Discoideum Dutpase at 2.2 Angstrom

All present enzymatic activity of Dictyostelium Discoideum Dutpase at 2.2 Angstrom:
3.6.1.23;

The structure of Dictyostelium Discoideum Dutpase at 2.2 Angstrom, PDB code: 5f9k was solved by N.Inoguchi, C.P.Chia, K.Heck, H.Moriyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.63 / 2.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.633, 72.458, 75.158, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.1

The binding sites of Magnesium atom in the Dictyostelium Discoideum Dutpase at 2.2 Angstrom (pdb code 5f9k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Dictyostelium Discoideum Dutpase at 2.2 Angstrom, PDB code: 5f9k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Dictyostelium Discoideum Dutpase at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dictyostelium Discoideum Dutpase at 2.2 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:56.1 occ:1.00 OD2 B:ASP81 2.7 47.0 1.0 O3G C:DUP203 3.2 77.7 1.0 NE2 C:GLN110 3.3 37.9 1.0 O B:VAL79 3.3 39.7 1.0 CG B:ASP81 3.5 44.3 1.0 CG1 B:VAL79 3.7 38.9 1.0 CB B:VAL79 3.7 38.8 1.0 OD1 B:ASP81 3.7 42.8 1.0 O C:HOH314 3.8 42.5 1.0 O2G C:DUP203 3.9 66.2 1.0 OE1 C:GLN110 4.0 39.4 1.0 PG C:DUP203 4.0 78.5 1.0 CD C:GLN110 4.1 40.3 1.0 OG C:SER65 4.1 56.2 1.0 C B:VAL79 4.2 42.3 1.0 C3' C:DUP203 4.2 54.4 1.0 O3' C:DUP203 4.4 53.4 1.0 O1G C:DUP203 4.4 58.4 1.0 C5' C:DUP203 4.5 60.9 1.0 CA B:VAL79 4.6 37.1 1.0 CG2 B:VAL79 4.7 35.2 1.0 O C:HOH320 4.7 46.3 1.0 CB B:ASP81 4.9 44.6 1.0 N B:ASP81 4.9 42.3 1.0

Magnesium binding site 2 out of 5 in the Dictyostelium Discoideum Dutpase at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dictyostelium Discoideum Dutpase at 2.2 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:62.5 occ:1.00 O2B B:DUP201 2.1 83.2 1.0 N B:SER65 2.8 52.7 1.0 PB B:DUP201 3.2 92.1 1.0 O1B B:DUP201 3.2 74.5 1.0 CA B:ARG64 3.5 50.0 1.0 NE2 B:GLN110 3.5 39.3 1.0 OG B:SER65 3.5 58.1 1.0 C B:ARG64 3.6 51.0 1.0 CB B:SER65 3.6 57.7 1.0 CA B:SER65 3.8 55.9 1.0 CB B:ARG64 3.9 52.9 1.0 O3B B:DUP201 4.1 95.1 1.0 O2A B:DUP201 4.1 89.2 1.0 CD B:GLN110 4.4 39.5 1.0 O B:HOH322 4.4 37.2 1.0 O B:PRO63 4.5 42.4 1.0 N3A B:DUP201 4.5 92.3 1.0 O1G B:DUP201 4.5 99.9 1.0 N B:GLY66 4.6 61.9 1.0 CG B:ARG64 4.6 47.3 1.0 N B:ARG64 4.7 44.2 1.0 OE1 B:GLN110 4.8 44.4 1.0 C B:SER65 4.8 57.7 1.0 O B:ARG64 4.8 48.1 1.0 PG B:DUP201 4.9 0.6 1.0 PA B:DUP201 5.0 0.9 1.0

Magnesium binding site 3 out of 5 in the Dictyostelium Discoideum Dutpase at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dictyostelium Discoideum Dutpase at 2.2 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:46.7 occ:1.00 O B:HOH323 2.5 36.7 1.0 O B:ILE61 2.9 41.4 1.0 O B:HOH315 3.0 39.5 1.0 NH1 B:ARG60 3.1 31.2 1.0 CG B:ARG60 3.4 35.2 1.0 MG C:MG201 3.7 48.0 1.0 CD B:ARG60 3.8 34.0 1.0 O B:HOH337 3.9 40.3 1.0 O B:ALA77 3.9 37.5 1.0 C B:ILE61 4.0 40.3 1.0 O B:HOH339 4.0 40.7 1.0 CZ B:ARG60 4.2 37.4 1.0 NH2 C:ARG60 4.2 50.7 1.0 CA B:GLY78 4.3 38.2 1.0 NE B:ARG60 4.4 36.7 1.0 N B:ILE61 4.5 37.1 1.0 O B:GLY78 4.6 37.4 1.0 CA B:ALA62 4.6 41.2 1.0 C B:GLY78 4.7 41.9 1.0 N B:ALA62 4.7 40.5 1.0 CA B:ILE61 4.8 36.0 1.0 C B:ALA77 4.9 42.2 1.0 O B:CYS75 4.9 43.7 1.0 CB B:ARG60 4.9 33.2 1.0 O A:HOH344 4.9 32.6 1.0

Magnesium binding site 4 out of 5 in the Dictyostelium Discoideum Dutpase at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dictyostelium Discoideum Dutpase at 2.2 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg205 b:51.7 occ:1.00 O B:HOH302 2.3 50.7 1.0 O C:HOH329 3.1 47.5 1.0 O C:HOH337 3.3 42.6 1.0 O B:HOH339 3.5 40.7 1.0 O B:HOH337 3.5 40.3 1.0 MG C:MG201 3.6 48.0 1.0 O A:HOH317 3.8 41.4 1.0 OD2 B:ASP74 3.8 49.4 1.0 O A:HOH303 3.9 37.1 1.0 O B:HOH315 4.2 39.5 1.0 O A:HOH316 4.2 37.8 1.0 OD2 C:ASP74 4.3 50.3 1.0 OD2 A:ASP74 4.3 50.2 1.0 O C:HOH332 4.5 35.2 1.0 O B:CYS75 4.7 43.7 1.0 CG B:ASP74 4.7 47.8 1.0 O A:CYS75 4.8 43.4 1.0 OD1 B:ASP74 4.9 47.6 1.0 O C:CYS75 4.9 39.0 1.0 OD1 C:ASP74 4.9 45.6 1.0

Magnesium binding site 5 out of 5 in the Dictyostelium Discoideum Dutpase at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dictyostelium Discoideum Dutpase at 2.2 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:48.0 occ:1.00 NH2 C:ARG60 2.5 50.7 1.0 O C:HOH337 2.7 42.6 1.0 O B:HOH315 2.8 39.5 1.0 O B:HOH323 3.3 36.7 1.0 MG B:MG205 3.6 51.7 1.0 MG B:MG204 3.7 46.7 1.0 CD C:PRO63 3.7 41.4 1.0 CZ C:ARG60 3.8 47.2 1.0 O C:HOH342 3.8 38.5 1.0 CG C:PRO63 4.2 42.5 1.0 O B:HOH337 4.3 40.3 1.0 NE C:ARG60 4.4 49.7 1.0 O B:ALA77 4.4 37.5 1.0 O A:HOH344 4.6 32.6 1.0 O C:HOH332 4.7 35.2 1.0 NH1 C:ARG60 4.7 40.0 1.0 O A:HOH303 4.8 37.1 1.0 O B:HOH339 4.9 40.7 1.0 OD1 C:ASP74 4.9 45.6 1.0

C.P.Chia, K.Varon, B.Bartholomai, N.Inoguchi, H.Moriyama. Mitochondrial Location of Dictyostelium Discoideum Dutpase Mediated By Its N-Terminus.(to Be Published) To Be Published.