Magnesium in PDB 4zkf: Crystal Structure of Human Phosphodiesterase 12

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 12:
3.1.13.4;

The structure of Crystal Structure of Human Phosphodiesterase 12, PDB code: 4zkf was solved by S.Y.Kim, T.Kohno, T.Mori, K.Kitano, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.76 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.817, 99.840, 104.690, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 12 (pdb code 4zkf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 12, PDB code: 4zkf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Phosphodiesterase 12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphodiesterase 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:15.6 occ:1.00 OE2 A:GLU351 2.0 11.5 1.0 O A:HOH881 2.0 14.5 1.0 O A:HOH892 2.2 11.4 1.0 O A:HOH865 2.2 17.5 1.0 O A:HOH1145 2.2 18.5 1.0 O A:HOH823 2.3 19.4 1.0 CD A:GLU351 2.9 13.8 1.0 OE1 A:GLU351 3.2 12.1 1.0 ND2 A:ASN301 4.0 9.2 1.0 OD2 A:ASP598 4.2 21.3 1.0 MG A:MG702 4.2 32.6 1.0 O A:HOH1146 4.3 29.8 1.0 CG A:GLU351 4.3 12.9 1.0 NE2 A:HIS599 4.3 13.7 1.0 OD1 A:ASN301 4.3 10.1 1.0 O A:HOH1203 4.3 41.6 1.0 O A:HOH968 4.3 24.8 1.0 OD1 A:ASP598 4.4 13.1 1.0 CG A:ASN301 4.6 9.8 1.0 CD1 A:LEU303 4.6 14.0 1.0 CD2 A:HIS599 4.8 11.8 1.0 CG A:ASP598 4.8 17.5 1.0 CE1 A:HIS456 4.9 14.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Phosphodiesterase 12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Phosphodiesterase 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:32.6 occ:1.00 OD2 A:ASP496 2.6 15.6 1.0 O A:HOH865 2.6 17.5 1.0 OD1 A:ASN498 2.8 21.2 1.0 NE2 A:HIS456 2.9 14.1 1.0 ND2 A:ASN498 3.1 20.6 1.0 CG A:ASN498 3.2 19.7 1.0 CG A:ASP496 3.3 14.3 1.0 OD1 A:ASP496 3.6 12.9 1.0 CE1 A:HIS456 3.8 14.7 1.0 O A:HOH1145 3.8 18.5 1.0 CD2 A:HIS456 3.9 15.6 1.0 O A:HOH1146 3.9 29.8 1.0 ND2 A:ASN301 4.0 9.2 1.0 NE2 A:HIS599 4.2 13.7 1.0 MG A:MG701 4.2 15.6 1.0 CE1 A:HIS599 4.3 12.8 1.0 OE2 A:GLU351 4.4 11.5 1.0 CB A:ASP496 4.6 11.3 1.0 CB A:ASN498 4.7 15.7 1.0 CD1 A:LEU560 4.9 16.5 1.0 CB A:TRP459 4.9 26.4 1.0 ND1 A:HIS456 5.0 14.1 1.0

S.Y.Kim, T.Kohno, T.Mori, K.Kitano, T.Hakoshima. Crystal Structure of Human Phosphodiesterase To Be Published.