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Zinc in PDB 6b97: Crystal Structure of PDE2 in Complex with Complex 9

Enzymatic activity of Crystal Structure of PDE2 in Complex with Complex 9

All present enzymatic activity of Crystal Structure of PDE2 in Complex with Complex 9:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE2 in Complex with Complex 9, PDB code: 6b97 was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.06 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.270, 96.070, 102.060, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22

Other elements in 6b97:

The structure of Crystal Structure of PDE2 in Complex with Complex 9 also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE2 in Complex with Complex 9 (pdb code 6b97). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE2 in Complex with Complex 9, PDB code: 6b97:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6b97

Go back to Zinc Binding Sites List in 6b97
Zinc binding site 1 out of 2 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:25.2
occ:1.00
OD2 A:ASP697 2.0 20.4 1.0
NE2 A:HIS660 2.1 21.8 1.0
NE2 A:HIS696 2.1 21.6 1.0
OD1 A:ASP808 2.2 21.0 1.0
O A:HOH1199 2.3 21.0 1.0
O A:HOH1106 2.4 20.4 1.0
CE1 A:HIS660 3.1 20.6 1.0
CD2 A:HIS660 3.1 21.4 1.0
CD2 A:HIS696 3.1 22.4 1.0
CG A:ASP808 3.1 23.2 1.0
CE1 A:HIS696 3.1 21.5 1.0
CG A:ASP697 3.1 19.9 1.0
OD2 A:ASP808 3.4 22.5 1.0
OD1 A:ASP697 3.7 19.4 1.0
MG A:MG1002 4.0 18.8 1.0
O A:HOH1184 4.2 24.2 1.0
CD2 A:HIS656 4.2 20.9 1.0
CG A:HIS660 4.2 19.5 1.0
ND1 A:HIS660 4.2 21.2 1.0
CG A:HIS696 4.2 21.2 1.0
ND1 A:HIS696 4.3 22.7 1.0
CB A:ASP697 4.3 18.3 1.0
O A:HOH1209 4.3 18.4 1.0
NE2 A:HIS656 4.4 21.1 1.0
CB A:ASP808 4.5 17.4 1.0
CG2 A:VAL664 4.8 20.3 1.0
O A:HOH1120 4.8 21.4 1.0
CA A:ASP808 4.9 18.1 1.0
O A:ASP808 4.9 23.2 1.0

Zinc binding site 2 out of 2 in 6b97

Go back to Zinc Binding Sites List in 6b97
Zinc binding site 2 out of 2 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:26.1
occ:1.00
OD2 B:ASP697 2.1 21.1 1.0
NE2 B:HIS696 2.1 19.6 1.0
NE2 B:HIS660 2.1 20.9 1.0
OD1 B:ASP808 2.2 20.9 1.0
O B:HOH1181 2.4 23.3 1.0
O B:HOH1105 2.4 18.6 1.0
CD2 B:HIS696 3.0 20.1 1.0
CE1 B:HIS660 3.1 19.6 1.0
CG B:ASP808 3.1 24.0 1.0
CD2 B:HIS660 3.1 20.7 1.0
CE1 B:HIS696 3.1 19.1 1.0
CG B:ASP697 3.2 22.0 1.0
OD2 B:ASP808 3.4 23.6 1.0
OD1 B:ASP697 3.7 20.3 1.0
MG B:MG1002 4.0 20.0 1.0
O B:HOH1211 4.2 25.2 1.0
CG B:HIS696 4.2 18.8 1.0
CD2 B:HIS656 4.2 20.8 1.0
ND1 B:HIS696 4.2 20.2 1.0
CG B:HIS660 4.3 18.6 1.0
ND1 B:HIS660 4.3 19.3 1.0
CB B:ASP697 4.3 17.8 1.0
O B:HOH1242 4.3 19.9 1.0
NE2 B:HIS656 4.3 20.6 1.0
CB B:ASP808 4.5 17.7 1.0
CG2 B:VAL664 4.8 17.3 1.0
O B:HOH1134 4.8 18.6 1.0
O B:ASP808 4.8 19.8 1.0
CA B:ASP808 4.9 16.8 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 11:31:36 2020

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