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:
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
Go back to
Nickel Binding Sites List in 4ms0
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
|