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Nickel in PDB 4mrw: Crystal Structure of PDE10A2 with Fragment ZT0120 (7-Chloroquinolin-4- Ol)

Enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT0120 (7-Chloroquinolin-4- Ol)

All present enzymatic activity of Crystal Structure of PDE10A2 with Fragment ZT0120 (7-Chloroquinolin-4- Ol):
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A2 with Fragment ZT0120 (7-Chloroquinolin-4- Ol), PDB code: 4mrw 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) 43.83 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.830, 82.231, 155.382, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 27.9

Other elements in 4mrw:

The structure of Crystal Structure of PDE10A2 with Fragment ZT0120 (7-Chloroquinolin-4- Ol) 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 ZT0120 (7-Chloroquinolin-4- Ol) (pdb code 4mrw). 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 ZT0120 (7-Chloroquinolin-4- Ol), PDB code: 4mrw:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4mrw

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Nickel binding site 1 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0120 (7-Chloroquinolin-4- Ol)


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 ZT0120 (7-Chloroquinolin-4- Ol) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni901

b:18.1
occ:1.00
 O A:HOH1092 1.7 11.8 1.0
OD2 A:ASP674 2.1 9.7 1.0
OD2 A:ASP564 2.1 8.3 1.0
NE2 A:HIS563 2.2 11.6 1.0
NE2 A:HIS529 2.2 9.8 1.0
O A:HOH1010 2.6 20.6 1.0
CG A:ASP674 3.1 13.7 1.0
CD2 A:HIS563 3.1 11.9 1.0
CD2 A:HIS529 3.1 5.8 1.0
CG A:ASP564 3.1 9.6 1.0
CE1 A:HIS563 3.2 11.2 1.0
CE1 A:HIS529 3.2 5.6 1.0
OD1 A:ASP674 3.4 15.2 1.0
OD1 A:ASP564 3.6 9.2 1.0
NI A:NI902 3.8 29.7 1.0
CD2 A:HIS525 4.1 13.2 1.0
O A:HOH1083 4.1 20.9 1.0
O A:HOH1093 4.1 13.6 1.0
CG A:HIS563 4.2 13.2 1.0
ND1 A:HIS563 4.3 11.4 1.0
CG A:HIS529 4.3 9.2 1.0
ND1 A:HIS529 4.3 7.2 1.0
CB A:ASP564 4.3 10.3 1.0
CB A:ASP674 4.4 12.0 1.0
NE2 A:HIS525 4.6 13.8 1.0
CG2 A:VAL533 4.7 11.4 1.0
O A:HOH1091 4.8 8.3 1.0
CA A:ASP674 4.8 12.2 1.0
O A:ASP674 4.8 12.3 1.0

Nickel binding site 2 out of 4 in 4mrw

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Nickel binding site 2 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0120 (7-Chloroquinolin-4- Ol)


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 ZT0120 (7-Chloroquinolin-4- Ol) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni902

b:29.7
occ:1.00
 O A:HOH1093 2.2 13.6 1.0
OD1 A:ASP564 2.2 9.2 1.0
O A:HOH1090 2.3 13.4 1.0
O A:HOH1091 2.3 8.3 1.0
O A:HOH1092 2.3 11.8 1.0
O A:HOH1002 2.4 3.5 1.0
CG A:ASP564 3.2 9.6 1.0
OD2 A:ASP564 3.5 8.3 1.0
NI A:NI901 3.8 18.1 1.0
OE2 A:GLU592 4.0 14.9 1.0
O A:HOH1010 4.1 20.6 1.0
OG1 A:THR633 4.1 10.8 1.0
NE2 A:HIS595 4.2 14.0 1.0
CD2 A:HIS563 4.3 11.9 1.0
O A:HIS563 4.4 14.2 1.0
CD2 A:HIS595 4.4 13.5 1.0
OD1 A:ASP674 4.4 15.2 1.0
O A:HOH1070 4.5 19.5 1.0
O A:THR633 4.5 8.9 1.0
CD2 A:HIS567 4.5 13.1 1.0
CD2 A:HIS525 4.6 13.2 1.0
CB A:ASP564 4.6 10.3 1.0
NE2 A:HIS563 4.7 11.6 1.0
NE2 A:HIS525 4.8 13.8 1.0
CB A:THR633 4.8 10.6 1.0
CD A:GLU592 4.8 13.5 1.0
CG A:GLU592 4.8 10.4 1.0
NE2 A:HIS567 4.9 13.5 1.0
CA A:ASP564 5.0 11.4 1.0

Nickel binding site 3 out of 4 in 4mrw

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Nickel binding site 3 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0120 (7-Chloroquinolin-4- Ol)


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 ZT0120 (7-Chloroquinolin-4- Ol) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni901

b:31.3
occ:1.00
 O B:HOH1079 2.1 26.1 1.0
NE2 B:HIS563 2.1 15.7 1.0
O B:HOH1065 2.2 20.9 1.0
OD1 B:ASP674 2.3 15.7 1.0
OD2 B:ASP564 2.5 19.9 1.0
NE2 B:HIS529 2.5 15.4 1.0
CD2 B:HIS563 2.8 13.1 1.0
CD2 B:HIS529 3.1 15.9 1.0
CG B:ASP564 3.2 17.4 1.0
CG B:ASP674 3.2 16.7 1.0
CE1 B:HIS563 3.3 15.3 1.0
OD2 B:ASP674 3.4 21.2 1.0
OD1 B:ASP564 3.5 14.8 1.0
NI B:NI902 3.6 37.8 1.0
CE1 B:HIS529 3.6 16.2 1.0
CG B:HIS563 4.1 15.2 1.0
CB B:ASP564 4.3 16.6 1.0
ND1 B:HIS563 4.3 15.3 1.0
CG B:HIS529 4.4 17.6 1.0
O B:HOH1041 4.4 18.3 1.0
CD2 B:HIS525 4.5 26.8 1.0
CB B:ASP674 4.6 16.1 1.0
O B:HOH1003 4.6 16.6 1.0
ND1 B:HIS529 4.6 16.2 1.0
CG2 B:VAL533 4.8 12.2 1.0
CA B:ASP674 5.0 14.5 1.0

Nickel binding site 4 out of 4 in 4mrw

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Nickel binding site 4 out of 4 in the Crystal Structure of PDE10A2 with Fragment ZT0120 (7-Chloroquinolin-4- Ol)


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 ZT0120 (7-Chloroquinolin-4- Ol) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni902

b:37.8
occ:1.00
 O B:HOH1079 1.9 26.1 1.0
O B:HOH1066 2.3 21.1 1.0
OD1 B:ASP564 2.4 14.8 1.0
O B:HOH1003 2.4 16.6 1.0
O B:HOH1041 2.4 18.3 1.0
O B:HOH1125 2.5 30.9 1.0
CG B:ASP564 3.4 17.4 1.0
NI B:NI901 3.6 31.3 1.0
OD2 B:ASP564 3.6 19.9 1.0
O B:HOH1065 3.8 20.9 1.0
OE2 B:GLU592 4.2 22.0 1.0
CD2 B:HIS563 4.2 13.1 1.0
O B:HOH1046 4.3 22.9 1.0
NE2 B:HIS595 4.3 20.4 1.0
OG1 B:THR633 4.3 17.3 1.0
CD2 B:HIS567 4.3 23.9 1.0
CD2 B:HIS525 4.4 26.8 1.0
NE2 B:HIS567 4.4 23.8 1.0
OD2 B:ASP674 4.5 21.2 1.0
O B:THR633 4.5 16.0 1.0
CD2 B:HIS595 4.6 18.9 1.0
O B:HIS563 4.6 18.5 1.0
NE2 B:HIS563 4.7 15.7 1.0
CB B:THR633 4.7 15.9 1.0
CB B:ASP564 4.7 16.6 1.0
NE2 B:HIS525 4.8 26.1 1.0
O B:HOH1081 4.9 28.6 1.0
CA B:ASP564 5.0 17.2 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 18:30:08 2024

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