Nickel in PDB 4msa: Crystal Structure of PDE10A2 with Fragment ZT0449 (5-Nitro-1H- Benzimidazole)

All present enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT0449 (5-Nitro-1H- Benzimidazole):
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A2 with Fragment ZT0449 (5-Nitro-1H- Benzimidazole), PDB code: 4msa was solved by V.Sridar, 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)	43.46 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.202, 82.168, 155.075, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22

The binding sites of Nickel atom in the Crystal Structure of PDE10A2 with Fragment ZT0449 (5-Nitro-1H- Benzimidazole) (pdb code 4msa). 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 ZT0449 (5-Nitro-1H- Benzimidazole), PDB code: 4msa:
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 ZT0449 (5-Nitro-1H- Benzimidazole)


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 ZT0449 (5-Nitro-1H- Benzimidazole) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:19.6 occ:1.00 OD2 A:ASP564 2.1 14.6 1.0 OD2 A:ASP674 2.1 16.9 1.0 O A:HOH1153 2.1 20.2 1.0 NE2 A:HIS529 2.2 17.8 1.0 NE2 A:HIS563 2.2 13.3 1.0 O A:HOH1070 2.3 22.6 1.0 CG A:ASP674 3.1 18.8 1.0 CD2 A:HIS563 3.1 14.9 1.0 CG A:ASP564 3.1 16.6 1.0 CE1 A:HIS529 3.1 16.4 1.0 CD2 A:HIS529 3.1 15.1 1.0 CE1 A:HIS563 3.3 16.6 1.0 OD1 A:ASP674 3.4 23.1 1.0 OD1 A:ASP564 3.6 15.0 1.0 NI A:NI902 3.7 26.9 1.0 O A:HOH1099 4.1 25.2 1.0 O A:HOH1150 4.1 19.4 1.0 CD2 A:HIS525 4.1 19.2 1.0 ND1 A:HIS529 4.3 15.5 1.0 CB A:ASP564 4.3 14.4 1.0 CG A:HIS563 4.3 15.9 1.0 CG A:HIS529 4.3 13.9 1.0 ND1 A:HIS563 4.3 13.8 1.0 CB A:ASP674 4.4 15.1 1.0 O A:HOH1154 4.5 31.4 1.0 NE2 A:HIS525 4.6 20.0 1.0 O A:HOH1151 4.8 15.6 1.0 CA A:ASP674 4.8 14.6 1.0 CG2 A:VAL533 4.8 14.5 1.0 O A:ASP674 4.9 16.2 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0449 (5-Nitro-1H- Benzimidazole)


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 ZT0449 (5-Nitro-1H- Benzimidazole) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni902 b:26.9 occ:1.00 O A:HOH1150 2.1 19.4 1.0 O A:HOH1149 2.2 15.3 1.0 OD1 A:ASP564 2.2 15.0 1.0 O A:HOH1153 2.2 20.2 1.0 O A:HOH1152 2.3 18.8 1.0 O A:HOH1151 2.4 15.6 1.0 CG A:ASP564 3.2 16.6 1.0 OD2 A:ASP564 3.5 14.6 1.0 NI A:NI901 3.7 19.6 1.0 O A:HOH1154 4.0 31.4 1.0 O A:HOH1070 4.0 22.6 1.0 OE2 A:GLU592 4.0 18.9 1.0 NE2 A:HIS595 4.2 16.9 1.0 OG1 A:THR633 4.3 16.9 1.0 CD2 A:HIS563 4.3 14.9 1.0 O A:HOH1039 4.4 21.1 1.0 CD2 A:HIS595 4.4 16.0 1.0 CD2 A:HIS567 4.5 17.9 1.0 O A:HIS563 4.5 14.4 1.0 CD2 A:HIS525 4.5 19.2 1.0 OD1 A:ASP674 4.5 23.1 1.0 CB A:ASP564 4.5 14.4 1.0 O A:THR633 4.6 15.9 1.0 NE2 A:HIS563 4.7 13.3 1.0 NE2 A:HIS525 4.7 20.0 1.0 NE2 A:HIS567 4.8 16.3 1.0 CB A:THR633 4.8 14.0 1.0 CG A:GLU592 4.9 16.9 1.0 CA A:ASP564 4.9 15.6 1.0 CD A:GLU592 4.9 18.2 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0449 (5-Nitro-1H- Benzimidazole)


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 ZT0449 (5-Nitro-1H- Benzimidazole) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni901 b:28.6 occ:1.00 O B:HOH1123 1.9 26.2 1.0 NE2 B:HIS563 2.1 19.2 1.0 OD1 B:ASP674 2.2 19.9 1.0 O B:HOH1042 2.2 26.7 1.0 NE2 B:HIS529 2.3 20.8 1.0 OD2 B:ASP564 2.4 21.5 1.0 CD2 B:HIS563 3.0 19.9 1.0 CG B:ASP674 3.1 21.4 1.0 CD2 B:HIS529 3.1 22.9 1.0 CE1 B:HIS563 3.2 20.9 1.0 CG B:ASP564 3.2 19.1 1.0 OD2 B:ASP674 3.4 23.5 1.0 CE1 B:HIS529 3.4 22.8 1.0 OD1 B:ASP564 3.5 20.0 1.0 NI B:NI902 3.6 34.4 1.0 O B:HOH1122 4.2 29.6 1.0 CG B:HIS563 4.2 19.4 1.0 ND1 B:HIS563 4.3 19.8 1.0 CG B:HIS529 4.3 19.7 1.0 CB B:ASP564 4.4 20.1 1.0 ND1 B:HIS529 4.5 20.6 1.0 CB B:ASP674 4.5 18.6 1.0 O B:HOH1053 4.5 24.7 1.0 CD2 B:HIS525 4.8 35.0 1.0 CG2 B:VAL533 4.8 17.6 1.0 OH B:TYR524 4.8 42.9 1.0 CA B:ASP674 4.9 17.4 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0449 (5-Nitro-1H- Benzimidazole)


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 ZT0449 (5-Nitro-1H- Benzimidazole) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni902 b:34.4 occ:1.00 O B:HOH1123 2.0 26.2 1.0 O B:HOH1122 2.2 29.6 1.0 O B:HOH1094 2.3 24.9 1.0 O B:HOH1011 2.3 21.5 1.0 OD1 B:ASP564 2.3 20.0 1.0 O B:HOH1053 2.3 24.7 1.0 CG B:ASP564 3.3 19.1 1.0 NI B:NI901 3.6 28.6 1.0 OD2 B:ASP564 3.6 21.5 1.0 O B:HOH1042 3.8 26.7 1.0 OE2 B:GLU592 4.1 27.0 1.0 NE2 B:HIS595 4.1 21.4 1.0 CD2 B:HIS563 4.3 19.9 1.0 OG1 B:THR633 4.3 19.4 1.0 CD2 B:HIS567 4.3 24.9 1.0 NE2 B:HIS567 4.3 25.1 1.0 O B:HOH1071 4.4 29.8 1.0 CD2 B:HIS525 4.4 35.0 1.0 OD2 B:ASP674 4.5 23.5 1.0 O B:THR633 4.5 20.4 1.0 CD2 B:HIS595 4.5 23.5 1.0 NE2 B:HIS563 4.6 19.2 1.0 O B:HIS563 4.6 19.5 1.0 CB B:ASP564 4.7 20.1 1.0 CB B:THR633 4.7 21.0 1.0 O B:HOH1074 4.9 29.8 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