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Zinc in PDB 3iad: Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator, PDB code: 3iad was solved by B.L.Staker, A.B.Burgin Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.551, 111.997, 162.384, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.7

Other elements in 3iad:

The structure of Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator also contains other interesting chemical elements:

Fluorine (F) 5 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator (pdb code 3iad). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator, PDB code: 3iad:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3iad

Go back to Zinc Binding Sites List in 3iad
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator


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 Human Phosphodiesterase 4D with Bound Allosteric Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn620

b:14.6
occ:1.00
 NE2 A:HIS366 2.1 10.9 1.0
O A:HOH178 2.1 13.2 1.0
NE2 A:HIS330 2.2 9.9 1.0
OD2 A:ASP367 2.2 9.8 1.0
OD1 A:ASP484 2.2 15.7 1.0
CG A:ASP484 3.0 16.0 1.0
CD2 A:HIS366 3.0 10.7 1.0
CE1 A:HIS366 3.1 11.4 1.0
CD2 A:HIS330 3.1 10.3 1.0
OD2 A:ASP484 3.1 15.3 1.0
CE1 A:HIS330 3.2 9.7 1.0
CG A:ASP367 3.2 10.6 1.0
OD1 A:ASP367 3.7 12.4 1.0
CG A:HIS366 4.2 10.5 1.0
ND1 A:HIS366 4.2 10.5 1.0
MG A:MG621 4.3 17.5 1.0
ND1 A:HIS330 4.3 10.3 1.0
CG A:HIS330 4.3 10.3 1.0
CD2 A:HIS326 4.3 13.5 1.0
CG2 A:VAL334 4.4 11.3 1.0
CB A:ASP484 4.4 16.2 1.0
CB A:ASP367 4.4 10.2 1.0
NE2 A:HIS326 4.6 13.6 1.0
CA A:ASP484 4.9 16.4 1.0

Zinc binding site 2 out of 4 in 3iad

Go back to Zinc Binding Sites List in 3iad
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator


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 Human Phosphodiesterase 4D with Bound Allosteric Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn620

b:13.5
occ:1.00
 OD2 B:ASP367 2.1 12.3 1.0
O B:HOH180 2.1 12.1 1.0
NE2 B:HIS330 2.2 15.3 1.0
NE2 B:HIS366 2.2 12.9 1.0
OD1 B:ASP484 2.2 17.8 1.0
O B:HOH195 2.7 10.9 1.0
CD2 B:HIS366 3.0 12.4 1.0
CG B:ASP484 3.0 17.6 1.0
CE1 B:HIS330 3.1 15.4 1.0
CG B:ASP367 3.1 12.0 1.0
CD2 B:HIS330 3.2 15.6 1.0
OD2 B:ASP484 3.2 18.8 1.0
CE1 B:HIS366 3.3 12.9 1.0
OD1 B:ASP367 3.6 11.4 1.0
CG B:HIS366 4.2 11.9 1.0
ND1 B:HIS330 4.2 15.9 1.0
MG B:MG621 4.3 17.2 1.0
CG B:HIS330 4.3 15.6 1.0
CD2 B:HIS326 4.3 14.1 1.0
ND1 B:HIS366 4.3 12.5 1.0
CB B:ASP367 4.3 11.5 1.0
O B:HOH28 4.3 7.5 1.0
CB B:ASP484 4.4 17.3 1.0
CG2 B:VAL334 4.5 16.4 1.0
O B:HOH31 4.6 19.4 1.0
NE2 B:HIS326 4.7 13.8 1.0
CA B:ASP484 4.9 17.3 1.0

Zinc binding site 3 out of 4 in 3iad

Go back to Zinc Binding Sites List in 3iad
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn620

b:16.1
occ:1.00
 OD2 C:ASP367 2.1 8.1 1.0
OD1 C:ASP484 2.2 17.4 1.0
NE2 C:HIS366 2.2 10.8 1.0
NE2 C:HIS330 2.2 14.7 1.0
O C:HOH182 2.2 12.2 1.0
O C:HOH186 2.6 30.3 1.0
CG C:ASP484 3.0 17.3 1.0
CD2 C:HIS366 3.0 10.2 1.0
CD2 C:HIS330 3.1 13.9 1.0
OD2 C:ASP484 3.1 17.1 1.0
CG C:ASP367 3.2 10.3 1.0
CE1 C:HIS330 3.3 14.6 1.0
CE1 C:HIS366 3.3 10.4 1.0
OD1 C:ASP367 3.7 11.5 1.0
MG C:MG621 4.0 10.8 1.0
CG C:HIS366 4.3 10.2 1.0
CD2 C:HIS326 4.3 16.5 1.0
CG C:HIS330 4.3 13.6 1.0
ND1 C:HIS330 4.3 14.8 1.0
O C:HOH63 4.3 15.2 1.0
ND1 C:HIS366 4.4 9.8 1.0
CB C:ASP367 4.4 10.1 1.0
CB C:ASP484 4.5 17.0 1.0
O C:HOH185 4.6 7.2 1.0
CG2 C:VAL334 4.6 14.0 1.0
NE2 C:HIS326 4.8 16.5 1.0
CA C:ASP484 5.0 17.0 1.0

Zinc binding site 4 out of 4 in 3iad

Go back to Zinc Binding Sites List in 3iad
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn620

b:10.7
occ:1.00
 NE2 D:HIS366 2.0 8.4 1.0
OD2 D:ASP367 2.1 7.4 1.0
NE2 D:HIS330 2.2 5.9 1.0
OD1 D:ASP484 2.3 8.4 1.0
O D:HOH179 2.3 2.0 1.0
O D:HOH196 2.4 13.3 1.0
CD2 D:HIS366 3.0 8.4 1.0
CE1 D:HIS366 3.0 8.6 1.0
CG D:ASP484 3.0 8.4 1.0
CE1 D:HIS330 3.1 6.5 1.0
OD2 D:ASP484 3.1 8.1 1.0
CG D:ASP367 3.2 8.2 1.0
CD2 D:HIS330 3.2 6.4 1.0
OD1 D:ASP367 3.7 8.6 1.0
O D:HOH153 4.0 11.2 1.0
ND1 D:HIS366 4.1 7.7 1.0
CG D:HIS366 4.1 8.1 1.0
MG D:MG621 4.2 3.2 1.0
ND1 D:HIS330 4.2 6.9 1.0
O D:HOH203 4.2 37.2 1.0
CD2 D:HIS326 4.3 11.7 1.0
CG D:HIS330 4.3 7.7 1.0
CB D:ASP367 4.3 8.1 1.0
CB D:ASP484 4.4 8.5 1.0
CG2 D:VAL334 4.5 6.4 1.0
NE2 D:HIS326 4.5 12.2 1.0
O D:HOH192 4.7 3.5 1.0

Reference:

A.B.Burgin, O.T.Magnusson, J.Singh, P.Witte, B.L.Staker, J.M.Bjornsson, M.Thorsteinsdottir, S.Hrafnsdottir, T.Hagen, A.S.Kiselyov, L.J.Stewart, M.E.Gurney. Design of Phosphodiesterase 4D (PDE4D) Allosteric Modulators For Enhancing Cognition with Improved Safety. Nat.Biotechnol. V. 28 63 2010.
ISSN: ISSN 1087-0156
PubMed: 20037581
DOI: 10.1038/NBT.1598
Page generated: Sat Oct 26 06:50:52 2024

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