Nickel in PDB 4mrz: Crystal Structure of PDE10A2 with Fragment ZT0429 (4-Methyl-3- Nitropyridin-2-Amine)

All present enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT0429 (4-Methyl-3- Nitropyridin-2-Amine):
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A2 with Fragment ZT0429 (4-Methyl-3- Nitropyridin-2-Amine), PDB code: 4mrz 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)	43.41 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.140, 82.133, 154.745, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.6

The binding sites of Nickel atom in the Crystal Structure of PDE10A2 with Fragment ZT0429 (4-Methyl-3- Nitropyridin-2-Amine) (pdb code 4mrz). 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 ZT0429 (4-Methyl-3- Nitropyridin-2-Amine), PDB code: 4mrz:
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 ZT0429 (4-Methyl-3- Nitropyridin-2-Amine)


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 ZT0429 (4-Methyl-3- Nitropyridin-2-Amine) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:24.9 occ:1.00 OD2 A:ASP564 2.1 16.9 1.0 OD2 A:ASP674 2.1 19.6 1.0 NE2 A:HIS563 2.2 17.1 1.0 O A:HOH1001 2.2 26.5 1.0 NE2 A:HIS529 2.2 23.9 1.0 O A:HOH1037 2.5 30.9 1.0 CD2 A:HIS563 3.0 17.7 1.0 CG A:ASP674 3.0 25.1 1.0 CG A:ASP564 3.1 21.8 1.0 CD2 A:HIS529 3.1 18.3 1.0 CE1 A:HIS529 3.2 20.9 1.0 CE1 A:HIS563 3.2 18.0 1.0 OD1 A:ASP674 3.3 28.1 1.0 OD1 A:ASP564 3.7 20.0 1.0 NI A:NI902 3.7 33.7 1.0 CD2 A:HIS525 4.1 26.3 1.0 O A:HOH1121 4.2 27.9 1.0 CG A:HIS563 4.2 19.5 1.0 CB A:ASP564 4.3 20.4 1.0 ND1 A:HIS563 4.3 18.8 1.0 CG A:HIS529 4.3 18.6 1.0 ND1 A:HIS529 4.3 21.7 1.0 CB A:ASP674 4.4 23.0 1.0 NE2 A:HIS525 4.6 26.6 1.0 O A:HOH1101 4.7 21.3 1.0 CG2 A:VAL533 4.8 20.2 1.0 CA A:ASP674 4.8 22.0 1.0 O A:ASP674 5.0 22.9 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0429 (4-Methyl-3- Nitropyridin-2-Amine)


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 ZT0429 (4-Methyl-3- Nitropyridin-2-Amine) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni902 b:33.7 occ:1.00 O A:HOH1121 2.2 27.9 1.0 O A:HOH1001 2.2 26.5 1.0 O A:HOH1120 2.2 22.1 1.0 OD1 A:ASP564 2.2 20.0 1.0 O A:HOH1101 2.4 21.3 1.0 O A:HOH1011 2.4 24.6 1.0 CG A:ASP564 3.1 21.8 1.0 OD2 A:ASP564 3.4 16.9 1.0 NI A:NI901 3.7 24.9 1.0 O A:HOH1037 4.1 30.9 1.0 OE2 A:GLU592 4.1 25.2 1.0 NE2 A:HIS595 4.2 22.5 1.0 CD2 A:HIS563 4.2 17.7 1.0 OG1 A:THR633 4.3 22.9 1.0 O A:HOH1042 4.4 25.6 1.0 CD2 A:HIS525 4.4 26.3 1.0 CD2 A:HIS595 4.5 21.9 1.0 CD2 A:HIS567 4.5 23.8 1.0 OD1 A:ASP674 4.5 28.1 1.0 O A:HIS563 4.5 19.9 1.0 CB A:ASP564 4.5 20.4 1.0 O A:THR633 4.5 20.8 1.0 NE2 A:HIS563 4.6 17.1 1.0 NE2 A:HIS525 4.7 26.6 1.0 NE2 A:HIS567 4.8 22.7 1.0 CB A:THR633 4.8 21.4 1.0 CA A:ASP564 4.9 20.7 1.0 CG A:GLU592 4.9 23.3 1.0 CD A:GLU592 5.0 21.4 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0429 (4-Methyl-3- Nitropyridin-2-Amine)


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 ZT0429 (4-Methyl-3- Nitropyridin-2-Amine) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni901 b:33.8 occ:1.00 O B:HOH1001 2.0 32.1 1.0 OD1 B:ASP674 2.2 26.6 1.0 O B:HOH1091 2.2 31.1 1.0 NE2 B:HIS563 2.2 25.9 1.0 NE2 B:HIS529 2.3 27.6 1.0 OD2 B:ASP564 2.4 28.4 1.0 CD2 B:HIS563 3.0 25.6 1.0 CD2 B:HIS529 3.1 28.9 1.0 CG B:ASP674 3.1 27.8 1.0 CG B:ASP564 3.2 26.0 1.0 CE1 B:HIS563 3.3 26.5 1.0 CE1 B:HIS529 3.3 28.5 1.0 OD2 B:ASP674 3.4 30.0 1.0 NI B:NI902 3.6 39.0 1.0 OD1 B:ASP564 3.6 28.4 1.0 O B:HOH1092 4.2 34.7 1.0 CG B:HIS563 4.2 25.3 1.0 CG B:HIS529 4.3 27.8 1.0 ND1 B:HIS563 4.3 25.6 1.0 ND1 B:HIS529 4.4 28.4 1.0 CB B:ASP564 4.4 26.1 1.0 O B:HOH1093 4.4 27.9 1.0 CB B:ASP674 4.5 24.9 1.0 CG2 B:VAL533 4.7 23.4 1.0 CD2 B:HIS525 4.8 40.2 1.0 CA B:ASP674 4.9 23.8 1.0 O B:ASP674 5.0 25.3 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0429 (4-Methyl-3- Nitropyridin-2-Amine)


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 ZT0429 (4-Methyl-3- Nitropyridin-2-Amine) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni902 b:39.0 occ:1.00 O B:HOH1001 1.9 32.1 1.0 O B:HOH1092 2.2 34.7 1.0 O B:HOH1093 2.2 27.9 1.0 O B:HOH1039 2.3 30.6 1.0 OD1 B:ASP564 2.3 28.4 1.0 O B:HOH1026 2.4 31.9 1.0 CG B:ASP564 3.3 26.0 1.0 OD2 B:ASP564 3.5 28.4 1.0 NI B:NI901 3.6 33.8 1.0 O B:HOH1091 3.8 31.1 1.0 OE2 B:GLU592 4.2 32.8 1.0 NE2 B:HIS595 4.2 29.6 1.0 CD2 B:HIS563 4.3 25.6 1.0 CD2 B:HIS567 4.3 33.9 1.0 OG1 B:THR633 4.3 25.8 1.0 O B:HOH1086 4.3 36.7 1.0 CD2 B:HIS525 4.4 40.2 1.0 NE2 B:HIS567 4.4 32.0 1.0 OD2 B:ASP674 4.5 30.0 1.0 O B:THR633 4.5 26.1 1.0 CD2 B:HIS595 4.6 29.1 1.0 NE2 B:HIS563 4.6 25.9 1.0 O B:HIS563 4.6 24.6 1.0 CB B:ASP564 4.7 26.1 1.0 CB B:THR633 4.7 26.7 1.0 OD1 B:ASP674 5.0 26.6 1.0 O B:HOH1085 5.0 33.9 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