Chlorine in PDB 6ezf: PDE2 in Complex with Molecule 5

Enzymatic activity of PDE2 in Complex with Molecule 5

All present enzymatic activity of PDE2 in Complex with Molecule 5:
3.1.4.17;

Protein crystallography data

The structure of PDE2 in Complex with Molecule 5, PDB code: 6ezf was solved by G.Tresadern, L.Perez-Benito, H.Keraenen, H.Van Vlijmen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.37 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.239, 65.315, 104.391, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 19.8

Other elements in 6ezf:

The structure of PDE2 in Complex with Molecule 5 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the PDE2 in Complex with Molecule 5 (pdb code 6ezf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the PDE2 in Complex with Molecule 5, PDB code: 6ezf:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6ezf

Go back to Chlorine Binding Sites List in 6ezf
Chlorine binding site 1 out of 2 in the PDE2 in Complex with Molecule 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of PDE2 in Complex with Molecule 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:27.1
occ:1.00
CL1 A:C6Z1003 0.0 27.1 1.0
C2 A:C6Z1003 1.7 23.8 1.0
C8 A:C6Z1003 2.7 22.2 1.0
C3 A:C6Z1003 2.7 23.2 1.0
O A:ALA717 3.2 17.1 1.0
C A:ALA717 3.4 14.2 1.0
CD2 A:LEU770 3.4 22.5 0.0
CB A:ALA717 3.5 16.9 1.0
N A:LEU718 3.8 13.5 1.0
CE1 A:PHE707 3.9 26.0 1.0
CA A:LEU718 4.0 13.9 1.0
CD2 A:LEU718 4.0 16.8 1.0
C6 A:C6Z1003 4.0 23.3 1.0
C4 A:C6Z1003 4.0 23.5 1.0
CA A:ALA717 4.0 15.4 1.0
CG A:LEU718 4.4 16.1 1.0
CE A:MET847 4.4 30.8 0.5
CD1 A:LEU770 4.5 25.7 0.5
C5 A:C6Z1003 4.5 21.5 1.0
CD1 A:PHE707 4.6 25.7 1.0
O A:HOH1213 4.7 19.9 1.0
CZ A:PHE707 4.7 26.3 1.0
CB A:LEU718 4.8 13.8 1.0
CG A:LEU770 4.8 21.9 0.5
CE A:MET847 4.8 16.4 0.5
CE1 A:PHE862 4.9 16.6 1.0
O A:HOH1377 5.0 43.3 1.0
CD1 A:PHE862 5.0 15.7 1.0

Chlorine binding site 2 out of 2 in 6ezf

Go back to Chlorine Binding Sites List in 6ezf
Chlorine binding site 2 out of 2 in the PDE2 in Complex with Molecule 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of PDE2 in Complex with Molecule 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:26.6
occ:1.00
CL7 A:C6Z1003 0.0 26.6 1.0
C6 A:C6Z1003 1.7 23.3 1.0
C8 A:C6Z1003 2.7 22.2 1.0
C5 A:C6Z1003 2.8 21.5 1.0
C9 A:C6Z1003 3.2 22.7 1.0
O A:HOH1105 3.4 41.2 1.0
OH A:TYR827 3.5 25.1 1.0
C10 A:C6Z1003 3.8 23.6 1.0
N11 A:C6Z1003 3.8 26.5 1.0
C2 A:C6Z1003 4.0 23.8 1.0
CG2 A:VAL714 4.0 19.1 1.0
C4 A:C6Z1003 4.0 23.5 1.0
CB A:PHE862 4.1 14.2 1.0
CD1 A:PHE862 4.2 15.7 1.0
CE A:MET847 4.2 30.8 0.5
O A:LEU858 4.2 14.4 1.0
SD A:MET847 4.3 19.9 0.5
C3 A:C6Z1003 4.5 23.2 1.0
CG A:PHE862 4.5 15.4 1.0
CB A:LEU858 4.6 13.0 1.0
CB A:MET847 4.6 19.5 0.5
CB A:MET847 4.7 18.9 0.5
CD2 A:LEU858 4.7 18.6 1.0
CZ A:TYR827 4.7 18.7 1.0
C A:LEU858 4.8 14.9 1.0
N12 A:C6Z1003 4.8 25.8 1.0
CG A:MET847 4.8 23.1 0.5
C16 A:C6Z1003 4.9 24.7 1.0
CG A:MET847 4.9 20.3 0.5
CD2 A:LEU718 5.0 16.8 1.0
CE2 A:PHE830 5.0 18.6 1.0

Reference:

L.Perez-Benito, H.Keranen, H.Van Vlijmen, G.Tresadern. Predicting Binding Free Energies of PDE2 Inhibitors. the Difficulties of Protein Conformation. Sci Rep V. 8 4883 2018.
ISSN: ESSN 2045-2322
PubMed: 29559702
DOI: 10.1038/S41598-018-23039-5
Page generated: Sat Dec 12 12:56:47 2020

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