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Zinc in PDB 6blf: PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid

Enzymatic activity of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid

All present enzymatic activity of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid:
3.1.4.17;

Protein crystallography data

The structure of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid, PDB code: 6blf was solved by H.P.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 2.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.030, 95.830, 104.130, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.8

Other elements in 6blf:

The structure of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid (pdb code 6blf). 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 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid, PDB code: 6blf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6blf

Go back to Zinc Binding Sites List in 6blf
Zinc binding site 1 out of 2 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:22.0
occ:1.00
 OD2 A:ASP697 2.0 17.8 1.0
NE2 A:HIS696 2.1 19.7 1.0
NE2 A:HIS660 2.2 18.7 1.0
OD1 A:ASP808 2.2 20.6 1.0
O A:HOH1147 2.3 20.4 1.0
O A:HOH1137 2.4 17.2 1.0
CD2 A:HIS696 2.9 18.9 1.0
CG A:ASP697 3.1 18.5 1.0
CE1 A:HIS660 3.1 18.1 1.0
CG A:ASP808 3.1 24.6 1.0
CE1 A:HIS696 3.2 19.3 1.0
CD2 A:HIS660 3.2 19.1 1.0
OD2 A:ASP808 3.4 26.9 1.0
OD1 A:ASP697 3.6 15.7 1.0
MG A:MG1002 3.9 17.3 1.0
O A:HOH1136 4.0 16.5 1.0
CG A:HIS696 4.1 17.6 1.0
CD2 A:HIS656 4.1 17.3 1.0
NE2 A:HIS656 4.2 17.6 1.0
ND1 A:HIS696 4.2 18.5 1.0
CB A:ASP697 4.2 15.2 1.0
O A:HOH1167 4.3 17.9 1.0
ND1 A:HIS660 4.3 19.1 1.0
CG A:HIS660 4.3 17.9 1.0
CB A:ASP808 4.5 21.0 1.0
CG2 A:VAL664 4.8 17.3 1.0
O A:HOH1102 4.8 18.8 1.0
CA A:ASP808 4.9 19.8 1.0
O A:ASP808 5.0 21.6 1.0

Zinc binding site 2 out of 2 in 6blf

Go back to Zinc Binding Sites List in 6blf
Zinc binding site 2 out of 2 in the PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PDE2 Complexed with 2-[6-Fluoro-8-Methylsulfonyl-9-[(1R)-1-[4- (Trifluoromethyl)Phenyl]Ethyl]-1,2,3,4-Tetrahydrocarbazol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:22.1
occ:1.00
 OD2 B:ASP697 2.0 20.8 1.0
OD1 B:ASP808 2.1 19.9 1.0
NE2 B:HIS696 2.2 17.4 1.0
NE2 B:HIS660 2.2 15.3 1.0
O B:HOH1176 2.4 20.6 1.0
O B:HOH1111 2.4 21.9 1.0
CD2 B:HIS696 3.0 17.1 1.0
CG B:ASP808 3.1 21.2 1.0
CG B:ASP697 3.1 19.4 1.0
CE1 B:HIS660 3.2 14.7 1.0
CD2 B:HIS660 3.2 16.1 1.0
CE1 B:HIS696 3.3 16.8 1.0
OD2 B:ASP808 3.4 28.2 1.0
OD1 B:ASP697 3.7 17.7 1.0
MG B:MG1002 4.0 18.8 1.0
O B:HOH1158 4.1 18.4 1.0
CG B:HIS696 4.2 15.8 1.0
CD2 B:HIS656 4.2 20.8 1.0
O B:HOH1183 4.2 15.7 1.0
NE2 B:HIS656 4.3 20.9 1.0
CB B:ASP697 4.3 15.4 1.0
ND1 B:HIS696 4.3 16.3 1.0
ND1 B:HIS660 4.3 15.5 1.0
CG B:HIS660 4.4 15.5 1.0
CB B:ASP808 4.5 16.7 1.0
CG2 B:VAL664 4.8 13.3 1.0
CA B:ASP808 4.8 16.2 1.0
O B:HOH1103 4.9 14.5 1.0
O B:ASP808 4.9 15.0 1.0

Reference:

H.P.Su, H.P.Su. N/A N/A.
Page generated: Mon Oct 28 18:01:02 2024

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