Nickel in PDB 4msn: Crystal Structure of PDE10A2 with Fragment ZT0451 (8-Nitroquinoline)

All present enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT0451 (8-Nitroquinoline):
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A2 with Fragment ZT0451 (8-Nitroquinoline), PDB code: 4msn 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)	39.73 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.859, 82.158, 156.130, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28.7

The binding sites of Nickel atom in the Crystal Structure of PDE10A2 with Fragment ZT0451 (8-Nitroquinoline) (pdb code 4msn). 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 ZT0451 (8-Nitroquinoline), PDB code: 4msn:
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 ZT0451 (8-Nitroquinoline)


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 ZT0451 (8-Nitroquinoline) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:24.4 occ:1.00 NE2 A:HIS563 2.2 17.7 1.0 OD2 A:ASP674 2.2 15.9 1.0 OD2 A:ASP564 2.3 7.4 1.0 NE2 A:HIS529 2.3 14.9 1.0 O A:HOH1008 2.6 13.3 1.0 CG A:ASP674 3.0 15.7 1.0 CD2 A:HIS563 3.1 16.4 1.0 OD1 A:ASP674 3.2 15.3 1.0 CE1 A:HIS529 3.2 17.1 1.0 CE1 A:HIS563 3.2 16.8 1.0 CG A:ASP564 3.3 12.3 1.0 CD2 A:HIS529 3.3 15.1 1.0 OD1 A:ASP564 3.7 13.3 1.0 NI A:NI902 3.7 48.9 1.0 O A:HOH1026 4.0 16.5 1.0 CD2 A:HIS525 4.2 19.5 1.0 CG A:HIS563 4.2 16.6 1.0 ND1 A:HIS563 4.3 16.0 1.0 ND1 A:HIS529 4.3 16.4 1.0 CB A:ASP674 4.4 16.5 1.0 CG A:HIS529 4.4 15.6 1.0 CB A:ASP564 4.5 14.5 1.0 NE2 A:HIS525 4.7 19.5 1.0 O A:HOH1006 4.7 2.0 1.0 O A:ASP674 4.8 16.7 1.0 CA A:ASP674 4.9 16.4 1.0 CG2 A:VAL533 4.9 15.7 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0451 (8-Nitroquinoline)


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 ZT0451 (8-Nitroquinoline) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni902 b:48.9 occ:1.00 OD1 A:ASP564 2.2 13.3 1.0 O A:HOH1026 2.3 16.5 1.0 O A:HOH1025 2.3 27.2 1.0 O A:HOH1006 2.4 2.0 1.0 CG A:ASP564 3.2 12.3 1.0 OD2 A:ASP564 3.5 7.4 1.0 NI A:NI901 3.7 24.4 1.0 OE2 A:GLU592 4.0 15.7 1.0 NE2 A:HIS595 4.0 23.2 1.0 CD2 A:HIS563 4.1 16.4 1.0 OG1 A:THR633 4.2 15.8 1.0 CD2 A:HIS595 4.3 23.4 1.0 O A:HIS563 4.4 15.2 1.0 NE2 A:HIS563 4.4 17.7 1.0 CB A:ASP564 4.5 14.5 1.0 OD1 A:ASP674 4.6 15.3 1.0 O A:HOH1008 4.6 13.3 1.0 CD2 A:HIS525 4.6 19.5 1.0 CD2 A:HIS567 4.7 21.4 1.0 CB A:THR633 4.8 17.1 1.0 CA A:ASP564 4.8 15.4 1.0 CD A:GLU592 4.9 17.3 1.0 O A:THR633 4.9 17.7 1.0 NE2 A:HIS525 4.9 19.5 1.0 CG A:GLU592 5.0 19.0 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0451 (8-Nitroquinoline)


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 ZT0451 (8-Nitroquinoline) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni901 b:31.5 occ:1.00 OD2 B:ASP564 2.1 26.5 1.0 NE2 B:HIS563 2.1 26.2 1.0 OD1 B:ASP674 2.2 19.6 1.0 O B:HOH1005 2.3 14.8 1.0 NE2 B:HIS529 2.6 22.8 1.0 CD2 B:HIS563 2.9 25.1 1.0 CG B:ASP564 3.1 26.4 1.0 CG B:ASP674 3.1 19.5 1.0 CE1 B:HIS563 3.2 25.9 1.0 OD2 B:ASP674 3.4 20.6 1.0 NI B:NI902 3.5 63.2 1.0 OD1 B:ASP564 3.5 23.9 1.0 CE1 B:HIS529 3.5 23.1 1.0 CD2 B:HIS529 3.5 23.3 1.0 O B:HOH1020 4.0 23.4 1.0 CG B:HIS563 4.1 25.5 1.0 ND1 B:HIS563 4.2 25.4 1.0 CB B:ASP564 4.4 27.7 1.0 CB B:ASP674 4.5 19.1 1.0 ND1 B:HIS529 4.6 23.1 1.0 CG B:HIS529 4.7 22.8 1.0 CA B:ASP674 4.9 18.6 1.0 CG2 B:VAL533 4.9 17.6 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0451 (8-Nitroquinoline)


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 ZT0451 (8-Nitroquinoline) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni902 b:63.2 occ:1.00 OD1 B:ASP564 2.3 23.9 1.0 O B:HOH1020 2.4 23.4 1.0 O B:HOH1019 2.5 23.0 1.0 CG B:ASP564 3.3 26.4 1.0 NI B:NI901 3.5 31.5 1.0 OD2 B:ASP564 3.5 26.5 1.0 OE2 B:GLU592 3.8 41.5 1.0 NE2 B:HIS595 4.1 30.6 1.0 O B:HOH1005 4.3 14.8 1.0 OG1 B:THR633 4.3 21.1 1.0 CD2 B:HIS563 4.3 25.1 1.0 CD2 B:HIS567 4.4 41.1 1.0 CD2 B:HIS595 4.4 32.5 1.0 NE2 B:HIS567 4.5 40.9 1.0 NE2 B:HIS563 4.6 26.2 1.0 O B:HIS563 4.6 27.4 1.0 OD2 B:ASP674 4.6 20.6 1.0 O B:THR633 4.6 22.6 1.0 CB B:ASP564 4.6 27.7 1.0 CB B:THR633 4.7 22.0 1.0 CD2 B:HIS525 4.8 38.0 1.0 CD B:GLU592 4.9 42.2 1.0 CA B:ASP564 4.9 28.1 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