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Nickel in PDB 4ms0: Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine)

Enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine)

All present enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine):
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine), PDB code: 4ms0 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) 31.46 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.304, 82.380, 155.611, 90.00, 90.00, 90.00
R / Rfree (%) 25.2 / 29.6

Other elements in 4ms0:

The structure of Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine) (pdb code 4ms0). 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 ZT0443 (6-Chloropyrimidine- 2,4-Diamine), PDB code: 4ms0:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4ms0

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Nickel binding site 1 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine)


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 ZT0443 (6-Chloropyrimidine- 2,4-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni901

b:27.9
occ:1.00
 O A:HOH1086 1.5 26.7 1.0
NE2 A:HIS563 2.0 24.0 1.0
OD2 A:ASP674 2.1 14.6 1.0
OD2 A:ASP564 2.1 16.9 1.0
NE2 A:HIS529 2.2 27.7 1.0
CG A:ASP674 3.0 28.7 1.0
CD2 A:HIS563 3.0 22.6 1.0
CE1 A:HIS563 3.0 22.2 1.0
CG A:ASP564 3.1 23.1 1.0
CD2 A:HIS529 3.2 23.2 1.0
CE1 A:HIS529 3.2 25.7 1.0
OD1 A:ASP674 3.3 33.1 1.0
O A:HOH1050 3.4 36.6 1.0
OD1 A:ASP564 3.6 21.2 1.0
NI A:NI902 3.8 44.5 1.0
CD2 A:HIS525 4.1 30.7 1.0
ND1 A:HIS563 4.1 26.0 1.0
CG A:HIS563 4.1 25.9 1.0
ND1 A:HIS529 4.3 25.2 1.0
CB A:ASP674 4.3 22.2 1.0
CG A:HIS529 4.3 26.1 1.0
CB A:ASP564 4.4 21.8 1.0
O A:HOH1090 4.4 32.2 1.0
NE2 A:HIS525 4.6 27.9 1.0
CA A:ASP674 4.6 23.5 1.0
CG2 A:VAL533 4.7 25.7 1.0
O A:ASP674 4.8 24.1 1.0
O A:HOH1003 4.9 24.6 1.0

Nickel binding site 2 out of 4 in 4ms0

Go back to Nickel Binding Sites List in 4ms0
Nickel binding site 2 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine)


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 ZT0443 (6-Chloropyrimidine- 2,4-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni902

b:44.5
occ:1.00
 OD1 A:ASP564 2.1 21.2 1.0
O A:HOH1069 2.3 25.5 1.0
O A:HOH1006 2.4 19.7 1.0
O A:HOH1003 2.4 24.6 1.0
O A:HOH1086 2.4 26.7 1.0
O A:HOH1090 2.5 32.2 1.0
CG A:ASP564 3.1 23.1 1.0
OD2 A:ASP564 3.5 16.9 1.0
NI A:NI901 3.8 27.9 1.0
OE2 A:GLU592 4.0 26.9 1.0
OG1 A:THR633 4.1 22.9 1.0
NE2 A:HIS595 4.2 30.6 1.0
CD2 A:HIS563 4.2 22.6 1.0
O A:HOH1050 4.4 36.6 1.0
CD2 A:HIS595 4.4 26.8 1.0
OD1 A:ASP674 4.4 33.1 1.0
O A:HOH1078 4.4 37.9 1.0
O A:THR633 4.5 21.0 1.0
O A:HIS563 4.5 28.0 1.0
CB A:ASP564 4.5 21.8 1.0
NE2 A:HIS563 4.5 24.0 1.0
CD2 A:HIS567 4.5 28.9 1.0
CD2 A:HIS525 4.6 30.7 1.0
CG A:GLU592 4.8 24.3 1.0
NE2 A:HIS525 4.8 27.9 1.0
CB A:THR633 4.8 24.4 1.0
CA A:ASP564 4.8 25.2 1.0
CD A:GLU592 4.9 24.2 1.0
NE2 A:HIS567 4.9 28.8 1.0
O A:HOH1054 5.0 31.7 1.0

Nickel binding site 3 out of 4 in 4ms0

Go back to Nickel Binding Sites List in 4ms0
Nickel binding site 3 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine)


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 ZT0443 (6-Chloropyrimidine- 2,4-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni901

b:41.9
occ:1.00
 O B:HOH1058 2.0 41.9 1.0
O B:HOH1057 2.1 39.7 1.0
NE2 B:HIS563 2.2 31.2 1.0
OD1 B:ASP674 2.3 31.1 1.0
NE2 B:HIS529 2.3 29.8 1.0
OD2 B:ASP564 2.4 34.8 1.0
CD2 B:HIS563 3.0 31.6 1.0
CD2 B:HIS529 3.1 26.7 1.0
CG B:ASP564 3.2 33.6 1.0
CG B:ASP674 3.2 29.7 1.0
CE1 B:HIS563 3.3 31.7 1.0
CE1 B:HIS529 3.4 28.9 1.0
OD2 B:ASP674 3.4 35.8 1.0
OD1 B:ASP564 3.5 34.3 1.0
NI B:NI902 3.6 52.3 1.0
O B:HOH1012 4.2 36.6 1.0
CG B:HIS563 4.2 28.7 1.0
CD2 B:HIS525 4.2 42.7 1.0
ND1 B:HIS563 4.3 28.9 1.0
CB B:ASP564 4.3 33.7 1.0
CG B:HIS529 4.3 29.4 1.0
ND1 B:HIS529 4.4 27.1 1.0
O B:HOH1004 4.5 30.6 1.0
CB B:ASP674 4.6 27.9 1.0
CG2 B:VAL533 4.9 25.9 1.0
NE2 B:HIS525 5.0 41.8 1.0

Nickel binding site 4 out of 4 in 4ms0

Go back to Nickel Binding Sites List in 4ms0
Nickel binding site 4 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0443 (6-Chloropyrimidine- 2,4-Diamine)


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 ZT0443 (6-Chloropyrimidine- 2,4-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni902

b:52.3
occ:1.00
 O B:HOH1058 2.0 41.9 1.0
OD1 B:ASP564 2.2 34.3 1.0
O B:HOH1047 2.3 32.7 1.0
O B:HOH1004 2.3 30.6 1.0
O B:HOH1012 2.3 36.6 1.0
O B:HOH1059 2.5 41.7 1.0
CG B:ASP564 3.2 33.6 1.0
OD2 B:ASP564 3.5 34.8 1.0
NI B:NI901 3.6 41.9 1.0
O B:HOH1057 3.8 39.7 1.0
OE2 B:GLU592 4.1 34.9 1.0
CD2 B:HIS563 4.2 31.6 1.0
CD2 B:HIS567 4.2 40.0 1.0
NE2 B:HIS567 4.2 40.8 1.0
NE2 B:HIS595 4.2 34.8 1.0
CD2 B:HIS525 4.3 42.7 1.0
OG1 B:THR633 4.3 31.2 1.0
CD2 B:HIS595 4.5 36.1 1.0
O B:THR633 4.5 31.6 1.0
NE2 B:HIS563 4.5 31.2 1.0
OD2 B:ASP674 4.6 35.8 1.0
O B:HIS563 4.6 32.4 1.0
CB B:ASP564 4.6 33.7 1.0
NE2 B:HIS525 4.7 41.8 1.0
CB B:THR633 4.7 30.0 1.0
CA B:ASP564 4.9 34.0 1.0

Reference:

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
Page generated: Wed Oct 9 18:30:29 2024

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