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Magnesium 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
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 4D with Bound Allosteric Modulator, PDB code: 3iad:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3iad

Go back to Magnesium Binding Sites List in 3iad
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg621

b:17.5
occ:1.00
 O A:HOH190 2.2 21.2 1.0
O A:HOH178 2.2 13.2 1.0
OD1 A:ASP367 2.7 12.4 1.0
CG A:ASP367 3.7 10.6 1.0
OE2 A:GLU396 3.8 10.8 1.0
OD2 A:ASP367 4.0 9.8 1.0
O A:THR437 4.2 16.6 1.0
ZN A:ZN620 4.3 14.6 1.0
OD2 A:ASP484 4.3 15.3 1.0
OG1 A:THR437 4.4 15.3 1.0
CD2 A:HIS366 4.5 10.7 1.0
NE2 A:HIS399 4.5 8.3 1.0
O A:HIS366 4.5 11.0 1.0
CG A:GLU396 4.6 9.2 1.0
CD A:GLU396 4.7 9.6 1.0
CD2 A:HIS399 4.7 8.1 1.0
CB A:THR437 4.8 15.4 1.0
CD2 A:HIS370 4.8 11.5 1.0
NE2 A:HIS370 4.8 12.2 1.0
NE2 A:HIS366 4.9 10.9 1.0
C A:THR437 4.9 16.2 1.0

Magnesium binding site 2 out of 4 in 3iad

Go back to Magnesium Binding Sites List in 3iad
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg621

b:17.2
occ:1.00
 O B:HOH180 2.2 12.1 1.0
O B:HOH181 2.3 13.2 1.0
O B:HOH170 2.3 6.2 1.0
OD1 B:ASP367 2.6 11.4 1.0
O B:HOH31 2.8 19.4 1.0
OE2 B:GLU396 3.5 13.8 1.0
CG B:ASP367 3.7 12.0 1.0
O B:HOH195 3.8 10.9 1.0
OD2 B:ASP367 4.1 12.3 1.0
O B:THR437 4.1 17.4 1.0
OG1 B:THR437 4.2 17.1 1.0
ZN B:ZN620 4.3 13.5 1.0
OD2 B:ASP484 4.3 18.8 1.0
O B:HIS366 4.3 11.8 1.0
NE2 B:HIS399 4.5 11.7 1.0
CD B:GLU396 4.5 14.0 1.0
CD2 B:HIS366 4.5 12.4 1.0
CD2 B:HIS399 4.7 12.3 1.0
CB B:THR437 4.7 17.1 1.0
CG B:GLU396 4.7 13.3 1.0
C B:THR437 4.9 17.5 1.0

Magnesium binding site 3 out of 4 in 3iad

Go back to Magnesium Binding Sites List in 3iad
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg621

b:10.8
occ:1.00
 O C:HOH185 2.0 7.2 1.0
O C:HOH183 2.1 12.2 1.0
O C:HOH182 2.1 12.2 1.0
O C:HOH184 2.2 5.0 1.0
OD1 C:ASP367 2.4 11.5 1.0
CG C:ASP367 3.4 10.3 1.0
OD2 C:ASP367 3.6 8.1 1.0
O C:HOH186 3.7 30.3 1.0
ZN C:ZN620 4.0 16.1 1.0
OE2 C:GLU396 4.1 15.4 1.0
O57 C:15X901 4.3 35.6 1.0
O C:HIS366 4.3 10.2 1.0
O C:THR437 4.4 17.0 1.0
OG1 C:THR437 4.4 16.1 1.0
OD2 C:ASP484 4.4 17.1 1.0
CD2 C:HIS366 4.5 10.2 1.0
NE2 C:HIS399 4.5 9.8 1.0
CD2 C:HIS370 4.6 9.2 1.0
NE2 C:HIS370 4.7 8.7 1.0
CD2 C:HIS399 4.7 10.4 1.0
O C:HOH123 4.7 29.5 1.0
CB C:ASP367 4.8 10.1 1.0
CD2 C:HIS326 4.9 16.5 1.0
NE2 C:HIS366 5.0 10.8 1.0
CB C:THR437 5.0 16.2 1.0
CD C:GLU396 5.0 14.9 1.0
NE2 C:HIS326 5.0 16.5 1.0

Magnesium binding site 4 out of 4 in 3iad

Go back to Magnesium Binding Sites List in 3iad
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg621

b:3.2
occ:1.00
 O D:HOH197 2.1 4.7 1.0
O D:HOH179 2.1 2.0 1.0
O D:HOH189 2.2 4.9 1.0
O D:HOH192 2.2 3.5 1.0
O D:HOH203 2.2 37.2 1.0
OD1 D:ASP367 2.5 8.6 1.0
CG D:ASP367 3.5 8.2 1.0
OD2 D:ASP367 3.7 7.4 1.0
OE2 D:GLU396 3.9 10.5 1.0
O D:HOH196 4.1 13.3 1.0
ZN D:ZN620 4.2 10.7 1.0
NE2 D:HIS399 4.3 7.6 1.0
CD2 D:HIS366 4.5 8.4 1.0
CD2 D:HIS370 4.5 11.7 1.0
O D:HIS366 4.5 8.7 1.0
NE2 D:HIS370 4.5 11.8 1.0
CD2 D:HIS399 4.5 7.8 1.0
OD2 D:ASP484 4.5 8.1 1.0
O D:HOH102 4.6 9.6 1.0
O57 D:15X901 4.6 27.3 1.0
O D:THR437 4.7 12.8 1.0
OG1 D:THR437 4.7 12.6 1.0
NE2 D:HIS326 4.7 12.2 1.0
CD2 D:HIS326 4.8 11.7 1.0
CD D:GLU396 4.8 10.4 1.0
CB D:ASP367 4.8 8.1 1.0
NE2 D:HIS366 4.8 8.4 1.0
CG D:GLU396 4.9 9.9 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: Sun Aug 10 22:30:09 2025

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