Nickel in PDB 4llp: Crystal Structure of PDE10A2 with Fragment ZT401

All present enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT401:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A2 with Fragment ZT401, PDB code: 4llp was solved by V.Sridhar, J.Badger, C.Logan, B.Chie-Leon, V.Nienaber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.01 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.383, 82.588, 154.746, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.6

The binding sites of Nickel atom in the Crystal Structure of PDE10A2 with Fragment ZT401 (pdb code 4llp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of PDE10A2 with Fragment ZT401, PDB code: 4llp:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT401


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of PDE10A2 with Fragment ZT401 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni803 b:22.4 occ:1.00 O A:HOH1007 2.0 24.3 1.0 OD2 A:ASP674 2.1 15.4 1.0 OD2 A:ASP564 2.1 17.0 1.0 NE2 A:HIS529 2.2 20.6 1.0 NE2 A:HIS563 2.2 17.2 1.0 O A:HOH904 2.5 28.6 1.0 CG A:ASP674 3.0 23.8 1.0 CD2 A:HIS563 3.1 16.9 1.0 CG A:ASP564 3.1 20.1 1.0 CD2 A:HIS529 3.2 16.4 1.0 CE1 A:HIS529 3.2 16.5 1.0 OD1 A:ASP674 3.3 25.8 1.0 CE1 A:HIS563 3.3 19.1 1.0 OD1 A:ASP564 3.6 19.8 1.0 NI A:NI804 3.8 33.1 1.0 CD2 A:HIS525 4.1 24.6 1.0 O A:HOH971 4.1 38.6 1.0 O A:HOH1009 4.2 28.1 1.0 CG A:HIS563 4.3 19.6 1.0 ND1 A:HIS529 4.3 19.8 1.0 CB A:ASP564 4.3 18.9 1.0 CG A:HIS529 4.3 18.6 1.0 ND1 A:HIS563 4.3 18.7 1.0 CB A:ASP674 4.4 17.8 1.0 NE2 A:HIS525 4.6 25.6 1.0 O A:HOH902 4.7 21.7 1.0 CG2 A:VAL533 4.8 15.3 1.0 CA A:ASP674 4.8 19.5 1.0 O A:ASP674 4.9 19.8 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT401


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of PDE10A2 with Fragment ZT401 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni804 b:33.1 occ:1.00 OD1 A:ASP564 2.2 19.8 1.0 O A:HOH1009 2.2 28.1 1.0 O A:HOH1010 2.2 19.2 1.0 O A:HOH1007 2.3 24.3 1.0 O A:HOH1008 2.3 22.4 1.0 O A:HOH902 2.3 21.7 1.0 CG A:ASP564 3.1 20.1 1.0 OD2 A:ASP564 3.5 17.0 1.0 NI A:NI803 3.8 22.4 1.0 NE2 A:HIS595 4.1 20.3 1.0 OE2 A:GLU592 4.2 24.9 1.0 OG1 A:THR633 4.2 23.0 1.0 O A:HOH904 4.3 28.6 1.0 CD2 A:HIS563 4.3 16.9 1.0 O A:HOH956 4.4 28.6 1.0 OD1 A:ASP674 4.4 25.8 1.0 CD2 A:HIS595 4.4 19.8 1.0 O A:HIS563 4.4 20.7 1.0 CD2 A:HIS567 4.5 23.9 1.0 O A:THR633 4.5 20.4 1.0 CB A:ASP564 4.5 18.9 1.0 CD2 A:HIS525 4.7 24.6 1.0 NE2 A:HIS563 4.7 17.2 1.0 NE2 A:HIS567 4.7 22.2 1.0 CB A:THR633 4.8 22.1 1.0 CG A:GLU592 4.8 20.6 1.0 NE2 A:HIS525 4.8 25.6 1.0 CA A:ASP564 4.9 19.1 1.0 CD A:GLU592 4.9 23.8 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT401


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of PDE10A2 with Fragment ZT401 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni901 b:59.4 occ:1.00 OD1 B:ASP674 2.3 35.5 1.0 NE2 B:HIS563 2.3 42.7 1.0 NE2 B:HIS529 2.3 38.7 1.0 OD2 B:ASP564 2.5 49.9 1.0 O B:HOH1050 2.6 47.5 1.0 CD2 B:HIS529 2.9 36.4 1.0 CD2 B:HIS563 3.0 42.8 1.0 O B:HOH1056 3.1 57.5 1.0 CG B:ASP674 3.2 32.4 1.0 CE1 B:HIS563 3.4 41.8 1.0 CE1 B:HIS529 3.5 38.7 1.0 OD2 B:ASP674 3.5 37.6 1.0 CG B:ASP564 3.6 50.1 1.0 NI B:NI902 3.7 0.9 1.0 OD1 B:ASP564 4.0 52.4 1.0 CG B:HIS529 4.2 35.3 1.0 CD2 B:HIS525 4.2 62.5 1.0 CG B:HIS563 4.3 41.4 1.0 ND1 B:HIS529 4.4 37.2 1.0 ND1 B:HIS563 4.4 41.6 1.0 NE2 B:HIS525 4.6 63.6 1.0 CB B:ASP674 4.6 26.2 1.0 CG2 B:VAL533 4.6 21.8 1.0 CB B:ASP564 4.7 48.9 1.0 CA B:ASP674 5.0 25.9 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT401


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of PDE10A2 with Fragment ZT401 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni902 b:0.9 occ:1.00 OD1 B:ASP564 2.2 52.4 1.0 O B:HOH1057 2.4 56.5 1.0 O B:HOH1055 2.5 54.7 1.0 CG B:ASP564 3.1 50.1 1.0 CD2 B:HIS525 3.3 62.5 1.0 O B:HOH1056 3.3 57.5 1.0 OD2 B:ASP564 3.3 49.9 1.0 NE2 B:HIS525 3.5 63.6 1.0 NI B:NI901 3.7 59.4 1.0 OE2 B:GLU592 3.8 84.0 1.0 NE2 B:HIS567 4.0 72.0 1.0 CD2 B:HIS567 4.0 71.1 1.0 CD2 B:HIS563 4.2 42.8 1.0 O B:HOH1050 4.4 47.5 1.0 O B:HIS563 4.4 43.5 1.0 OG1 B:THR633 4.4 53.3 1.0 NE2 B:HIS595 4.5 73.8 1.0 CB B:ASP564 4.5 48.9 1.0 CG B:HIS525 4.6 61.3 1.0 NE2 B:HIS563 4.6 42.7 1.0 O B:THR633 4.7 52.2 1.0 CB B:THR633 4.7 52.4 1.0 CE1 B:HIS525 4.8 63.2 1.0 OD2 B:ASP674 4.9 37.6 1.0 CA B:ASP564 4.9 49.1 1.0 CD B:GLU592 4.9 84.6 1.0 CD2 B:HIS595 5.0 73.7 1.0

M.I.Recht, V.Sridhar, J.Badger, P.Y.Bounaud, C.Logan, B.Chie-Leon, V.Nienaber, F.E.Torres. Identification and Optimization of PDE10A Inhibitors Using Fragment-Based Screening By Nanocalorimetry and X-Ray Crystallography. J Biomol Screen V. 19 497 2014.
ISSN: ISSN 1087-0571
PubMed: 24375910
DOI: 10.1177/1087057113516493