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Zinc in PDB 4c1i: Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System

Enzymatic activity of Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System

All present enzymatic activity of Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System:
3.1.4.17;

Protein crystallography data

The structure of Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System, PDB code: 4c1i was solved by M.Jorgensen, J.Kehler, M.Langgard, N.Svenstrup, L.Tagmose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.47 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.050, 81.810, 93.340, 110.16, 95.66, 93.21
R / Rfree (%) 22.489 / 28.66

Other elements in 4c1i:

The structure of Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System (pdb code 4c1i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System, PDB code: 4c1i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4c1i

Go back to Zinc Binding Sites List in 4c1i
Zinc binding site 1 out of 4 in the Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1907

b:18.0
occ:1.00
OD2 A:ASP697 2.0 17.0 1.0
OD1 A:ASP808 2.0 18.9 1.0
O A:HOH2031 2.1 16.5 1.0
NE2 A:HIS696 2.1 16.9 1.0
NE2 A:HIS660 2.2 16.4 1.0
O A:HOH2026 2.4 19.2 1.0
CG A:ASP808 3.0 19.2 1.0
CE1 A:HIS660 3.0 16.1 1.0
CE1 A:HIS696 3.1 16.9 1.0
CD2 A:HIS696 3.1 16.7 1.0
CG A:ASP697 3.1 16.5 1.0
CD2 A:HIS660 3.2 16.2 1.0
OD2 A:ASP808 3.3 19.5 1.0
OD1 A:ASP697 3.7 16.5 1.0
O A:HOH2025 4.0 16.2 1.0
MG A:MG1908 4.0 16.6 1.0
O A:HOH2024 4.1 14.2 1.0
ND1 A:HIS660 4.2 16.1 1.0
ND1 A:HIS696 4.2 17.1 1.0
CD2 A:HIS656 4.2 16.4 1.0
CG A:HIS696 4.2 16.7 1.0
CG A:HIS660 4.3 16.3 1.0
CB A:ASP697 4.4 16.6 1.0
NE2 A:HIS656 4.4 16.6 1.0
CB A:ASP808 4.4 19.1 1.0
O A:HOH2030 4.8 16.4 1.0
CA A:ASP808 4.8 19.0 1.0
O A:ASP808 4.9 18.2 1.0
CG2 A:VAL664 4.9 15.7 1.0

Zinc binding site 2 out of 4 in 4c1i

Go back to Zinc Binding Sites List in 4c1i
Zinc binding site 2 out of 4 in the Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1901

b:20.6
occ:1.00
OD2 B:ASP697 2.0 19.4 1.0
OD1 B:ASP808 2.0 19.4 1.0
O B:HOH2026 2.1 17.8 1.0
NE2 B:HIS696 2.1 18.1 1.0
NE2 B:HIS660 2.2 19.9 1.0
CG B:ASP808 3.0 19.2 1.0
CD2 B:HIS696 3.1 17.6 1.0
CE1 B:HIS660 3.1 19.9 1.0
CG B:ASP697 3.1 18.3 1.0
CE1 B:HIS696 3.2 17.7 1.0
CD2 B:HIS660 3.2 19.9 1.0
OD2 B:ASP808 3.4 19.6 1.0
OD1 B:ASP697 3.6 17.6 1.0
MG B:MG1902 3.8 16.5 1.0
O B:HOH2018 3.9 16.9 1.0
O B:HOH2021 3.9 16.7 1.0
CD2 B:HIS656 4.0 22.2 1.0
NE2 B:HIS656 4.1 22.4 1.0
CG B:HIS696 4.2 17.4 1.0
ND1 B:HIS696 4.2 17.5 1.0
ND1 B:HIS660 4.3 19.9 1.0
CG B:HIS660 4.3 19.6 1.0
CB B:ASP697 4.3 18.0 1.0
CB B:ASP808 4.4 18.9 1.0
O B:HOH2025 4.5 15.7 1.0
CA B:ASP808 4.9 18.6 1.0

Zinc binding site 3 out of 4 in 4c1i

Go back to Zinc Binding Sites List in 4c1i
Zinc binding site 3 out of 4 in the Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1901

b:21.6
occ:1.00
OD2 C:ASP697 2.0 19.1 1.0
OD1 C:ASP808 2.0 19.6 1.0
O C:HOH2026 2.1 21.2 1.0
NE2 C:HIS660 2.2 19.2 1.0
NE2 C:HIS696 2.2 18.5 1.0
CG C:ASP808 3.0 19.8 1.0
CD2 C:HIS696 3.1 18.0 1.0
CD2 C:HIS660 3.1 18.8 1.0
CG C:ASP697 3.1 18.5 1.0
CE1 C:HIS696 3.1 18.2 1.0
CE1 C:HIS660 3.2 18.6 1.0
OD2 C:ASP808 3.3 20.7 1.0
OD1 C:ASP697 3.5 18.5 1.0
MG C:MG1902 3.9 20.7 1.0
O C:HOH2020 4.0 21.4 1.0
CD2 C:HIS656 4.1 18.6 1.0
CG C:HIS696 4.2 17.9 1.0
ND1 C:HIS696 4.2 18.2 1.0
O C:HOH2019 4.2 7.0 1.0
ND1 C:HIS660 4.2 18.5 1.0
CG C:HIS660 4.2 18.5 1.0
CB C:ASP808 4.3 19.6 1.0
CB C:ASP697 4.3 18.2 1.0
NE2 C:HIS656 4.4 18.6 1.0
O C:HOH2048 4.5 18.0 1.0
O C:HOH2025 4.6 21.0 1.0
CA C:ASP808 4.8 19.5 1.0
O C:ASP808 4.9 17.6 1.0
CG2 C:VAL664 4.9 16.6 1.0

Zinc binding site 4 out of 4 in 4c1i

Go back to Zinc Binding Sites List in 4c1i
Zinc binding site 4 out of 4 in the Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1901

b:26.0
occ:1.00
OD2 D:ASP697 2.0 22.5 1.0
OD1 D:ASP808 2.0 23.7 1.0
O D:HOH2015 2.1 21.4 1.0
NE2 D:HIS696 2.1 23.9 1.0
NE2 D:HIS660 2.2 25.5 1.0
CG D:ASP697 3.0 22.1 1.0
CG D:ASP808 3.1 23.3 1.0
CD2 D:HIS696 3.1 23.8 1.0
CE1 D:HIS696 3.1 23.9 1.0
CD2 D:HIS660 3.1 26.0 1.0
CE1 D:HIS660 3.1 25.9 1.0
OD2 D:ASP808 3.5 23.1 1.0
OD1 D:ASP697 3.5 21.2 1.0
O D:HOH2010 3.8 24.9 1.0
MG D:MG1902 3.8 19.8 1.0
O D:HOH2011 3.9 20.2 1.0
ND1 D:HIS696 4.2 23.8 1.0
CG D:HIS696 4.2 23.5 1.0
CD2 D:HIS656 4.2 31.0 1.0
ND1 D:HIS660 4.3 26.3 1.0
CG D:HIS660 4.3 26.4 1.0
CB D:ASP697 4.3 22.5 1.0
CB D:ASP808 4.4 23.5 1.0
O D:HOH2014 4.4 18.8 1.0
NE2 D:HIS656 4.6 31.3 1.0
CA D:ASP808 4.9 23.6 1.0
CG2 D:VAL664 4.9 25.0 1.0
O D:ASP808 5.0 25.0 1.0

Reference:

M.Jorgensen, J.Kehler, M.Langgard, N.Svenstrup, L.Tagmose. Chapter 4: Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System To Be Published.
Page generated: Sat Oct 26 20:18:00 2024

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