Zinc in PDB 5sfc: Crystal Structure of Human Phosphodiesterase 10 in Complex with

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with:
3.1.4.17;

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with, PDB code: 5sfc was solved by C.Joseph, J.U.Peters, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.51 / 2.18
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	135.257, 135.257, 235.691, 90, 90, 120
R / Rfree (%)	18.3 / 23.1

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with (pdb code 5sfc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with, PDB code: 5sfc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Phosphodiesterase 10 in Complex with within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:34.3 occ:1.00 OD2 A:ASP564 2.1 33.4 1.0 NE2 A:HIS529 2.2 33.7 1.0 O A:HOH945 2.2 28.9 1.0 NE2 A:HIS563 2.2 26.2 1.0 OD1 A:ASP674 2.2 33.4 1.0 O A:HOH968 2.5 40.4 1.0 CD2 A:HIS563 3.0 27.7 1.0 CG A:ASP564 3.1 30.2 1.0 CE1 A:HIS529 3.1 30.3 1.0 CG A:ASP674 3.1 35.6 1.0 CD2 A:HIS529 3.2 33.2 1.0 CE1 A:HIS563 3.3 29.6 1.0 OD2 A:ASP674 3.3 42.2 1.0 OD1 A:ASP564 3.6 28.5 1.0 MG A:MG802 3.9 31.5 1.0 O A:HOH991 4.2 29.8 1.0 CG A:HIS563 4.2 28.6 1.0 CD2 A:HIS525 4.2 35.2 1.0 ND1 A:HIS529 4.2 28.8 1.0 CB A:ASP564 4.3 28.7 1.0 CG A:HIS529 4.3 31.4 1.0 ND1 A:HIS563 4.3 27.2 1.0 O A:HOH937 4.4 40.9 1.0 CB A:ASP674 4.5 35.1 1.0 NE2 A:HIS525 4.6 34.3 1.0 O A:HOH926 4.6 25.6 1.0 CG2 A:VAL533 4.7 25.8 1.0 O A:ASP674 4.8 32.1 1.0 CA A:ASP674 4.9 32.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Phosphodiesterase 10 in Complex with within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:34.1 occ:1.00 NE2 B:HIS563 2.1 27.3 1.0 OD1 B:ASP674 2.2 33.9 1.0 O B:HOH943 2.2 22.5 1.0 OD2 B:ASP564 2.2 29.6 1.0 NE2 B:HIS529 2.2 29.1 1.0 O B:HOH975 2.3 38.1 1.0 CD2 B:HIS563 3.0 28.9 1.0 CG B:ASP674 3.0 36.0 1.0 CD2 B:HIS529 3.1 28.4 1.0 CG B:ASP564 3.1 28.4 1.0 CE1 B:HIS563 3.1 28.1 1.0 OD2 B:ASP674 3.2 36.7 1.0 CE1 B:HIS529 3.2 29.4 1.0 OD1 B:ASP564 3.6 29.3 1.0 MG B:MG802 3.8 28.6 1.0 O B:HOH983 4.0 27.6 1.0 CG B:HIS563 4.2 26.6 1.0 CD2 B:HIS525 4.2 34.0 1.0 ND1 B:HIS563 4.2 27.1 1.0 O B:HOH969 4.3 46.3 1.0 CG B:HIS529 4.3 29.9 1.0 CB B:ASP564 4.3 27.6 1.0 ND1 B:HIS529 4.3 30.1 1.0 CB B:ASP674 4.4 35.0 1.0 O B:HOH920 4.5 29.7 1.0 NE2 B:HIS525 4.5 33.5 1.0 CG2 B:VAL533 4.8 31.1 1.0 CA B:ASP674 4.8 34.7 1.0 O B:ASP674 4.9 31.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Phosphodiesterase 10 in Complex with within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:38.5 occ:1.00 O C:HOH947 2.0 27.0 1.0 NE2 C:HIS563 2.1 30.6 1.0 OD2 C:ASP564 2.1 35.0 1.0 NE2 C:HIS529 2.2 32.6 1.0 OD1 C:ASP674 2.2 34.7 1.0 O C:HOH975 2.2 40.0 1.0 CD2 C:HIS563 3.0 29.4 1.0 CD2 C:HIS529 3.1 32.1 1.0 CG C:ASP674 3.1 32.3 1.0 CG C:ASP564 3.1 33.1 1.0 CE1 C:HIS563 3.1 29.1 1.0 CE1 C:HIS529 3.2 32.0 1.0 OD2 C:ASP674 3.4 34.2 1.0 OD1 C:ASP564 3.6 30.2 1.0 MG C:MG802 3.8 31.3 1.0 O C:HOH995 4.1 29.2 1.0 CD2 C:HIS525 4.2 41.5 1.0 CG C:HIS563 4.2 30.2 1.0 ND1 C:HIS563 4.2 28.0 1.0 CG C:HIS529 4.2 34.1 1.0 ND1 C:HIS529 4.3 32.8 1.0 CB C:ASP564 4.3 28.7 1.0 O C:HOH966 4.3 45.8 1.0 CB C:ASP674 4.5 35.6 1.0 O C:HOH936 4.5 37.5 1.0 NE2 C:HIS525 4.5 41.9 1.0 CG2 C:VAL533 4.7 28.7 1.0 CA C:ASP674 4.8 36.5 1.0 O C:ASP674 4.8 38.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Phosphodiesterase 10 in Complex with within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn801 b:47.8 occ:1.00 NE2 D:HIS563 2.0 37.8 1.0 OD2 D:ASP564 2.1 50.2 1.0 O D:HOH911 2.2 30.2 1.0 NE2 D:HIS529 2.2 47.9 1.0 OD1 D:ASP674 2.2 48.5 1.0 O D:HOH942 2.4 46.6 1.0 CD2 D:HIS563 3.0 36.3 1.0 CG D:ASP674 3.0 44.3 1.0 CE1 D:HIS563 3.1 38.6 1.0 CG D:ASP564 3.1 40.1 1.0 OD2 D:ASP674 3.1 44.9 1.0 CD2 D:HIS529 3.1 47.8 1.0 CE1 D:HIS529 3.2 48.5 1.0 OD1 D:ASP564 3.7 46.8 1.0 MG D:MG802 3.9 43.0 1.0 O D:HOH939 4.1 38.5 1.0 O D:HOH938 4.1 48.2 1.0 CG D:HIS563 4.1 36.7 1.0 ND1 D:HIS563 4.2 36.3 1.0 CB D:ASP564 4.2 40.0 1.0 CD2 D:HIS525 4.3 48.1 1.0 CG D:HIS529 4.3 46.7 1.0 ND1 D:HIS529 4.3 44.0 1.0 CB D:ASP674 4.4 46.1 1.0 O D:HOH928 4.4 41.0 1.0 CG2 D:VAL533 4.7 47.3 1.0 NE2 D:HIS525 4.8 45.4 1.0 O D:ASP674 4.9 45.3 1.0 CA D:ASP674 4.9 43.0 1.0

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X