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Zinc in PDB 6b98: PDE2 in Complex with Compound 1

Enzymatic activity of PDE2 in Complex with Compound 1

All present enzymatic activity of PDE2 in Complex with Compound 1:
3.1.4.17;

Protein crystallography data

The structure of PDE2 in Complex with Compound 1, PDB code: 6b98 was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.09 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.034, 94.186, 102.526, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24

Other elements in 6b98:

The structure of PDE2 in Complex with Compound 1 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the PDE2 in Complex with Compound 1 (pdb code 6b98). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the PDE2 in Complex with Compound 1, PDB code: 6b98:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6b98

Go back to Zinc Binding Sites List in 6b98
Zinc binding site 1 out of 2 in the PDE2 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:30.9
occ:1.00
NE2 A:HIS696 2.0 25.0 1.0
O A:HOH1121 2.1 28.9 1.0
OD2 A:ASP697 2.1 18.6 1.0
NE2 A:HIS660 2.1 23.0 1.0
OD1 A:ASP808 2.3 30.3 1.0
O A:HOH1183 2.8 39.4 1.0
CD2 A:HIS696 2.9 24.8 1.0
CD2 A:HIS660 3.1 23.3 1.0
CG A:ASP697 3.1 19.4 1.0
CE1 A:HIS660 3.1 22.1 1.0
CE1 A:HIS696 3.2 24.1 1.0
CG A:ASP808 3.2 30.8 1.0
OD2 A:ASP808 3.4 37.8 1.0
OD1 A:ASP697 3.7 21.2 1.0
MG A:MG1002 3.9 36.7 1.0
CG A:HIS696 4.0 23.2 1.0
CD2 A:HIS656 4.2 23.4 1.0
ND1 A:HIS696 4.2 24.3 1.0
CG A:HIS660 4.2 22.6 1.0
ND1 A:HIS660 4.2 23.7 1.0
CB A:ASP697 4.3 19.5 1.0
O A:HOH1155 4.3 44.3 1.0
O A:HOH1165 4.3 34.7 1.0
NE2 A:HIS656 4.6 23.1 1.0
CB A:ASP808 4.6 22.1 1.0
O A:HOH1110 4.7 28.5 1.0
CG2 A:VAL664 4.8 25.4 1.0
CA A:ASP808 5.0 21.3 1.0

Zinc binding site 2 out of 2 in 6b98

Go back to Zinc Binding Sites List in 6b98
Zinc binding site 2 out of 2 in the PDE2 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PDE2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:30.1
occ:1.00
NE2 B:HIS660 2.1 23.0 1.0
OD2 B:ASP697 2.1 24.0 1.0
NE2 B:HIS696 2.1 23.3 1.0
O B:HOH1143 2.1 37.5 1.0
OD1 B:ASP808 2.2 28.0 1.0
CD2 B:HIS696 2.9 23.2 1.0
CD2 B:HIS660 3.0 22.9 1.0
CE1 B:HIS660 3.1 22.4 1.0
CG B:ASP697 3.1 25.4 1.0
CG B:ASP808 3.2 30.1 1.0
CE1 B:HIS696 3.3 22.9 1.0
OD2 B:ASP808 3.4 35.5 1.0
OD1 B:ASP697 3.7 22.1 1.0
MG B:MG1002 3.9 31.5 1.0
CG B:HIS696 4.1 22.3 1.0
CG B:HIS660 4.2 21.5 1.0
CD2 B:HIS656 4.2 24.4 1.0
ND1 B:HIS660 4.2 23.0 1.0
O B:HOH1151 4.3 27.3 1.0
ND1 B:HIS696 4.3 23.7 1.0
CB B:ASP697 4.3 20.8 1.0
NE2 B:HIS656 4.5 24.4 1.0
CB B:ASP808 4.6 21.5 1.0
CG2 B:VAL664 4.8 21.5 1.0
O B:HOH1102 4.9 28.5 1.0
CA B:ASP808 4.9 20.7 1.0
O B:ASP808 5.0 22.0 1.0

Reference:

A.B.Forster, P.Abeywickrema, J.Bunda, C.D.Cox, T.D.Cabalu, M.Egbertson, J.Fay, K.Getty, D.Hall, M.Kornienko, J.Lu, G.Parthasarathy, J.Reid, S.Sharma, W.D.Shipe, S.M.Smith, S.Soisson, S.J.Stachel, H.P.Su, D.Wang, R.Berger. The Identification of A Novel Lead Class For Phosphodiesterase 2 Inhibition By Fragment-Based Drug Design. Bioorg. Med. Chem. Lett. V. 27 5167 2017.
ISSN: ESSN 1464-3405
PubMed: 29113762
DOI: 10.1016/J.BMCL.2017.10.054
Page generated: Wed Dec 16 11:31:38 2020

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