Magnesium in PDB 6njj: Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770, PDB code: 6njj was solved by D.Fox Iii, J.W.Fairman, M.E.Gurney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.49 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.330, 82.050, 116.350, 90.00, 110.01, 90.00
R / Rfree (%) 16.7 / 21.4

Other elements in 6njj:

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770 also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 6 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770 (pdb code 6njj). 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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770, PDB code: 6njj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6njj

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Magnesium binding site 1 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770


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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:12.2
occ:1.00
 O A:HOH823 1.9 14.2 1.0
OD1 A:ASP367 2.0 15.6 1.0
O A:HOH894 2.1 19.7 1.0
O A:HOH807 2.2 10.7 1.0
O A:HOH869 2.2 15.2 1.0
O A:HOH907 2.3 22.8 1.0
CG A:ASP367 3.1 16.5 1.0
OD2 A:ASP367 3.5 16.2 1.0
ZN A:ZN701 3.7 23.5 1.0
O A:HOH805 3.8 18.2 1.0
O A:HIS366 4.0 14.4 1.0
CD2 A:HIS366 4.1 15.9 1.0
OE2 A:GLU396 4.1 22.7 1.0
NE2 A:HIS399 4.2 16.6 1.0
OG1 A:THR437 4.4 15.2 1.0
OD2 A:ASP484 4.4 20.2 1.0
CD2 A:HIS399 4.4 14.8 1.0
CB A:ASP367 4.5 17.5 1.0
NE2 A:HIS366 4.5 16.2 1.0
O A:HOH871 4.6 31.2 1.0
O A:THR437 4.6 20.6 1.0
CD2 A:HIS370 4.6 15.0 1.0
CA A:ASP367 4.8 16.5 1.0
CD2 A:HIS326 4.8 18.0 1.0
CB A:THR437 4.9 18.2 1.0
CG A:GLU396 4.9 17.0 1.0
NE2 A:HIS326 4.9 18.9 1.0
CD A:GLU396 4.9 18.6 1.0
C A:HIS366 4.9 15.8 1.0
NE2 A:HIS370 5.0 16.5 1.0

Magnesium binding site 2 out of 4 in 6njj

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Magnesium binding site 2 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770


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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:15.7
occ:1.00
 O B:HOH817 1.8 20.6 1.0
O B:HOH829 2.0 19.8 1.0
OD1 B:ASP367 2.1 21.9 1.0
O B:HOH874 2.1 18.8 1.0
O B:HOH847 2.2 23.5 1.0
O B:HOH883 2.4 35.1 1.0
CG B:ASP367 3.2 21.5 1.0
OD2 B:ASP367 3.5 25.5 1.0
O B:HOH830 3.6 22.9 1.0
ZN B:ZN701 3.8 26.1 1.0
CD2 B:HIS366 4.1 19.2 1.0
O B:HIS366 4.1 17.9 1.0
OE2 B:GLU396 4.2 22.1 1.0
O B:HOH855 4.2 34.0 1.0
NE2 B:HIS399 4.2 19.1 1.0
OG1 B:THR437 4.4 20.7 1.0
OD2 B:ASP484 4.4 23.4 1.0
CD2 B:HIS399 4.5 18.5 1.0
CB B:ASP367 4.5 20.3 1.0
O B:THR437 4.5 24.0 1.0
NE2 B:HIS366 4.6 18.8 1.0
O B:HOH810 4.6 45.3 1.0
CD2 B:HIS370 4.7 19.8 1.0
CD2 B:HIS326 4.7 18.6 1.0
O B:HOH862 4.8 29.5 1.0
NE2 B:HIS326 4.8 20.3 1.0
CA B:ASP367 4.8 17.9 1.0
CB B:THR437 4.9 21.0 1.0
CG B:GLU396 5.0 18.4 1.0
NE2 B:HIS370 5.0 17.7 1.0
CD B:GLU396 5.0 20.4 1.0

Magnesium binding site 3 out of 4 in 6njj

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Magnesium binding site 3 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770


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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:13.0
occ:1.00
 O C:HOH833 2.0 17.5 1.0
OD1 C:ASP367 2.1 14.5 1.0
O C:HOH828 2.1 18.3 1.0
O C:HOH912 2.1 18.9 1.0
O C:HOH849 2.3 16.4 1.0
O C:HOH903 2.4 23.2 1.0
CG C:ASP367 3.1 13.5 1.0
OD2 C:ASP367 3.6 12.7 1.0
ZN C:ZN701 3.7 22.7 1.0
O C:HOH867 3.8 16.1 1.0
CD2 C:HIS366 4.0 14.4 1.0
O C:HIS366 4.0 18.4 1.0
OE2 C:GLU396 4.2 23.8 1.0
NE2 C:HIS399 4.2 17.0 1.0
OG1 C:THR437 4.3 20.8 1.0
OD2 C:ASP484 4.3 17.2 1.0
CD2 C:HIS399 4.4 15.7 1.0
O C:THR437 4.5 22.3 1.0
CB C:ASP367 4.5 14.4 1.0
NE2 C:HIS366 4.5 14.5 1.0
O C:HOH899 4.6 27.3 1.0
CB C:THR437 4.8 20.6 1.0
CD2 C:HIS370 4.8 15.8 1.0
CA C:ASP367 4.8 15.1 1.0
CD2 C:HIS326 4.9 18.4 1.0
CG C:GLU396 4.9 19.4 1.0
C C:HIS366 4.9 15.4 1.0
NE2 C:HIS326 4.9 18.3 1.0

Magnesium binding site 4 out of 4 in 6njj

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Magnesium binding site 4 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770


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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:19.8
occ:1.00
 OD1 D:ASP367 2.0 21.6 1.0
O D:HOH817 2.0 27.2 1.0
O D:HOH856 2.1 22.5 1.0
O D:HOH857 2.1 24.4 1.0
O D:HOH804 2.2 17.5 1.0
O D:HOH895 2.2 38.7 1.0
CG D:ASP367 3.1 21.2 1.0
OD2 D:ASP367 3.6 21.1 1.0
O D:HOH870 3.8 28.6 1.0
ZN D:ZN701 3.8 28.9 1.0
O D:HIS366 3.9 20.9 1.0
NE2 D:HIS399 4.0 16.1 1.0
CD2 D:HIS366 4.1 17.8 1.0
OE2 D:GLU396 4.1 35.1 1.0
CD2 D:HIS399 4.3 15.9 1.0
OG1 D:THR437 4.3 23.7 1.0
CB D:ASP367 4.4 20.4 1.0
OD2 D:ASP484 4.5 28.9 1.0
NE2 D:HIS366 4.5 17.6 1.0
CD2 D:HIS370 4.6 18.2 1.0
O D:THR437 4.6 26.4 1.0
CA D:ASP367 4.7 19.8 1.0
O D:HOH878 4.7 37.6 1.0
CD2 D:HIS326 4.9 25.5 1.0
CG D:GLU396 4.9 21.0 1.0
C D:HIS366 4.9 20.5 1.0
CB D:THR437 4.9 25.6 1.0
CD D:GLU396 4.9 23.8 1.0
NE2 D:HIS370 5.0 17.9 1.0
NE2 D:HIS326 5.0 25.6 1.0

Reference:

M.E.Gurney, R.A.Nugent, X.Mo, J.A.Sindac, T.J.Hagen, D.Fox 3Rd, J.M.O'donnell, C.Zhang, Y.Xu, H.T.Zhang, V.E.Groppi, M.Bailie, R.E.White, D.L.Romero, A.S.Vellekoop, J.R.Walker, M.D.Surman, L.Zhu, R.F.Campbell. Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors For the Treatment of Fragile X Syndrome and Other Brain Disorders. J.Med.Chem. V. 62 4884 2019.
ISSN: ISSN 0022-2623
PubMed: 31013090
DOI: 10.1021/ACS.JMEDCHEM.9B00193
Page generated: Mon Dec 14 23:40:19 2020

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