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Magnesium in PDB 3g4l: Crystal Structure of Human Phosphodiesterase 4D with Roflumilast

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D with Roflumilast

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D with Roflumilast:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D with Roflumilast, PDB code: 3g4l was solved by B.L.Staker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.665, 111.952, 161.701, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.9

Other elements in 3g4l:

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

Fluorine (F) 8 atoms
Chlorine (Cl) 8 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 4D with Roflumilast (pdb code 3g4l). 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 Roflumilast, PDB code: 3g4l:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3g4l

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Roflumilast


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 Roflumilast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:19.9
occ:1.00
 O A:HOH61 2.0 23.5 1.0
O A:HOH188 2.0 19.0 1.0
OD1 A:ASP367 2.1 17.1 1.0
O A:HOH27 2.1 7.7 1.0
O A:HOH22 2.2 13.2 1.0
O A:HOH187 2.3 13.8 1.0
CG A:ASP367 3.1 18.6 1.0
OD2 A:ASP367 3.5 16.6 1.0
O A:HOH1 3.8 16.3 1.0
OE2 A:GLU396 3.8 22.8 1.0
N3 A:ROF901 3.9 34.1 1.0
ZN A:ZN801 3.9 20.6 1.0
O A:HOH156 4.2 17.7 1.0
CD2 A:HIS366 4.2 20.2 1.0
C4 A:ROF901 4.2 34.8 1.0
OG1 A:THR437 4.3 22.0 1.0
O A:HIS366 4.3 19.3 1.0
NE2 A:HIS399 4.3 21.7 1.0
OD2 A:ASP484 4.3 20.0 1.0
C2 A:ROF901 4.4 34.4 1.0
CD2 A:HIS399 4.4 21.4 1.0
CB A:ASP367 4.5 19.2 1.0
NE2 A:HIS366 4.6 20.5 1.0
CD2 A:HIS370 4.6 21.1 1.0
CB A:THR437 4.7 23.3 1.0
O A:THR437 4.7 24.9 1.0
NE2 A:HIS326 4.7 23.1 1.0
CD A:GLU396 4.7 21.7 1.0
CG A:GLU396 4.7 21.1 1.0
NE2 A:HIS370 4.8 22.0 1.0
CA A:ASP367 4.9 19.0 1.0
CD2 A:HIS326 4.9 22.4 1.0

Magnesium binding site 2 out of 4 in 3g4l

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Roflumilast


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 Roflumilast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:27.1
occ:1.00
 O B:HOH104 2.1 12.7 1.0
O B:HOH78 2.1 21.5 1.0
O B:HOH152 2.2 15.2 1.0
O B:HOH137 2.3 13.1 1.0
OD1 B:ASP367 2.3 15.2 1.0
CG B:ASP367 3.4 19.9 1.0
OE2 B:GLU396 3.6 23.4 1.0
N3 B:ROF902 3.8 41.1 1.0
OD2 B:ASP367 3.8 20.6 1.0
C4 B:ROF902 4.1 43.1 1.0
O B:THR437 4.1 24.7 1.0
O B:HOH103 4.1 22.9 1.0
OG1 B:THR437 4.2 21.4 1.0
ZN B:ZN803 4.3 25.9 1.0
O B:HIS366 4.3 21.7 1.0
C2 B:ROF902 4.4 39.5 1.0
OD2 B:ASP484 4.4 24.6 1.0
CD2 B:HIS366 4.5 20.1 1.0
CD B:GLU396 4.5 21.3 1.0
CB B:THR437 4.5 23.4 1.0
CG B:GLU396 4.5 21.6 1.0
NE2 B:HIS399 4.7 23.7 1.0
C B:THR437 4.8 24.3 1.0
CD2 B:HIS399 4.8 22.2 1.0
CB B:ASP367 4.8 20.3 1.0
C5 B:ROF902 4.9 43.5 1.0
NE2 B:HIS326 4.9 22.0 1.0
CD2 B:HIS370 5.0 20.6 1.0

Magnesium binding site 3 out of 4 in 3g4l

Go back to Magnesium Binding Sites List in 3g4l
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Roflumilast


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 Roflumilast within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg806

b:18.7
occ:1.00
 O C:HOH151 2.0 12.0 1.0
OD1 C:ASP367 2.0 18.2 1.0
O C:HOH71 2.1 17.7 1.0
O C:HOH102 2.1 13.4 1.0
O C:HOH44 2.1 13.9 1.0
O C:HOH183 2.2 21.4 1.0
CG C:ASP367 3.1 20.0 1.0
OD2 C:ASP367 3.5 19.4 1.0
NE2 C:HIS399 4.0 21.6 1.0
OE2 C:GLU396 4.0 22.6 1.0
O C:HOH106 4.1 21.8 1.0
O C:HIS366 4.1 20.7 1.0
ZN C:ZN805 4.1 21.8 1.0
CD2 C:HIS399 4.2 20.7 1.0
OG1 C:THR437 4.2 23.9 1.0
O C:HOH60 4.2 9.6 1.0
CD2 C:HIS366 4.2 20.3 1.0
N3 C:ROF903 4.3 41.5 1.0
CD2 C:HIS370 4.5 20.6 1.0
CB C:ASP367 4.5 19.8 1.0
C4 C:ROF903 4.6 42.0 1.0
OD2 C:ASP484 4.6 23.3 1.0
CG C:GLU396 4.7 21.8 1.0
CD2 C:HIS326 4.7 23.3 1.0
NE2 C:HIS326 4.7 23.7 1.0
NE2 C:HIS366 4.7 22.0 1.0
CD C:GLU396 4.8 22.3 1.0
O C:THR437 4.8 24.3 1.0
CA C:ASP367 4.8 19.9 1.0
CB C:THR437 4.8 23.9 1.0
NE2 C:HIS370 4.8 19.7 1.0
C2 C:ROF903 4.8 40.2 1.0
C C:HIS366 4.9 20.3 1.0

Magnesium binding site 4 out of 4 in 3g4l

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with Roflumilast


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 Roflumilast within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg808

b:16.4
occ:1.00
 O D:HOH175 1.9 18.7 1.0
OD1 D:ASP367 2.0 18.4 1.0
O D:HOH146 2.0 9.0 1.0
O D:HOH11 2.0 15.2 1.0
O D:HOH73 2.1 18.2 1.0
O D:HOH126 2.1 14.6 1.0
CG D:ASP367 3.0 18.1 1.0
OD2 D:ASP367 3.4 14.8 1.0
OE2 D:GLU396 3.9 23.6 1.0
O D:HIS366 4.0 18.4 1.0
OG1 D:THR437 4.0 22.9 1.0
N3 D:ROF904 4.0 28.1 1.0
ZN D:ZN807 4.0 20.6 1.0
NE2 D:HIS399 4.1 21.3 1.0
CD2 D:HIS366 4.2 19.0 1.0
O D:HOH21 4.3 18.9 1.0
CD2 D:HIS399 4.3 20.9 1.0
C4 D:ROF904 4.3 30.4 1.0
CB D:ASP367 4.4 18.3 1.0
OD2 D:ASP484 4.4 22.4 1.0
NE2 D:HIS366 4.6 19.3 1.0
C2 D:ROF904 4.6 28.5 1.0
CD2 D:HIS370 4.6 22.1 1.0
CG D:GLU396 4.6 21.1 1.0
CD D:GLU396 4.6 21.6 1.0
CB D:THR437 4.7 23.0 1.0
CA D:ASP367 4.7 18.4 1.0
NE2 D:HIS370 4.8 22.8 1.0
NE2 D:HIS326 4.8 22.2 1.0
CD2 D:HIS326 4.8 20.9 1.0
O D:THR437 4.8 23.4 1.0
C D:HIS366 4.9 18.6 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: Wed Aug 14 14:03:59 2024

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