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Magnesium in PDB 6njh: Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48, PDB code: 6njh 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) 19.91 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.640, 82.070, 116.530, 90.00, 110.23, 90.00
R / Rfree (%) 17.2 / 21

Other elements in 6njh:

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 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 T-48 (pdb code 6njh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48, PDB code: 6njh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6njh

Go back to Magnesium Binding Sites List in 6njh
Magnesium binding site 1 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48


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 T-48 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:24.1
occ:1.00
 O A:HOH924 2.1 17.6 1.0
OD1 A:ASP367 2.2 15.7 1.0
O A:HOH805 2.3 19.3 1.0
O A:HOH807 2.3 21.3 1.0
O A:HOH869 2.3 16.1 1.0
O A:HOH875 2.3 19.6 1.0
CG A:ASP367 3.3 15.3 1.0
OD2 A:ASP367 3.7 13.2 1.0
ZN A:ZN701 4.0 16.9 1.0
OE2 A:GLU396 4.1 20.2 1.0
O A:HOH850 4.1 24.5 1.0
O A:HIS366 4.1 14.0 1.0
NE2 A:HIS399 4.1 15.6 1.0
CD2 A:HIS366 4.3 11.9 1.0
O A:HOH837 4.3 20.8 1.0
CD2 A:HIS399 4.4 14.6 1.0
OG1 A:THR437 4.5 14.2 1.0
CD2 A:HIS370 4.5 16.1 1.0
OD2 A:ASP484 4.5 18.7 1.0
CB A:ASP367 4.6 15.3 1.0
O A:THR437 4.6 17.6 1.0
NE2 A:HIS366 4.7 12.4 1.0
NE2 A:HIS370 4.7 16.3 1.0
NE2 A:HIS326 4.7 16.8 1.0
CD2 A:HIS326 4.8 16.9 1.0
CA A:ASP367 4.9 15.3 1.0
CG A:GLU396 4.9 16.9 1.0
CD A:GLU396 4.9 18.1 1.0
CB A:THR437 5.0 16.1 1.0
C A:HIS366 5.0 14.9 1.0

Magnesium binding site 2 out of 6 in 6njh

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Magnesium binding site 2 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48


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 T-48 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:10.8
occ:1.00
 OE2 A:GLU384 2.0 43.0 1.0
NE2 C:HIS318 2.1 20.2 1.0
O C:HOH953 2.2 40.0 1.0
O A:HOH937 2.3 28.3 1.0
CD A:GLU384 2.6 42.9 1.0
OE1 A:GLU384 2.7 41.4 1.0
CD2 C:HIS318 3.0 20.3 1.0
CE1 C:HIS318 3.3 19.9 1.0
CG A:GLU384 4.1 36.2 1.0
CG C:HIS318 4.2 19.9 1.0
ND1 C:HIS318 4.3 20.2 1.0
CD2 C:LEU406 4.6 21.5 1.0

Magnesium binding site 3 out of 6 in 6njh

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Magnesium binding site 3 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48


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 T-48 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:28.3
occ:1.00
 O B:HOH840 2.1 20.4 1.0
O B:HOH865 2.1 16.7 1.0
OD1 B:ASP367 2.2 21.4 1.0
O B:HOH910 2.2 29.2 1.0
O B:HOH880 2.2 16.9 1.0
O B:HOH816 2.2 23.2 1.0
CG B:ASP367 3.3 18.3 1.0
OD2 B:ASP367 3.7 16.6 1.0
O B:HOH876 4.0 25.2 1.0
ZN B:ZN701 4.0 20.3 1.0
O B:HIS366 4.1 14.7 1.0
OE2 B:GLU396 4.1 20.1 1.0
NE2 B:HIS399 4.2 17.7 1.0
CD2 B:HIS366 4.2 15.8 1.0
OG1 B:THR437 4.4 17.7 1.0
CD2 B:HIS399 4.4 16.7 1.0
O B:HOH839 4.4 18.8 1.0
O B:THR437 4.5 20.1 1.0
OD2 B:ASP484 4.5 20.0 1.0
CB B:ASP367 4.6 17.4 1.0
NE2 B:HIS366 4.6 15.8 1.0
CD2 B:HIS370 4.7 17.7 1.0
NE2 B:HIS326 4.8 17.8 1.0
CG B:GLU396 4.8 16.1 1.0
CA B:ASP367 4.8 17.1 1.0
CB B:THR437 4.9 19.5 1.0
NE2 B:HIS370 4.9 17.0 1.0
CD2 B:HIS326 4.9 14.9 1.0
CD B:GLU396 4.9 17.6 1.0
C B:HIS366 4.9 16.5 1.0

Magnesium binding site 4 out of 6 in 6njh

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Magnesium binding site 4 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48


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 T-48 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:21.3
occ:1.00
 O C:HOH940 2.1 19.9 1.0
O C:HOH816 2.1 18.7 1.0
OD1 C:ASP367 2.1 15.5 1.0
O C:HOH853 2.1 16.0 1.0
O C:HOH915 2.2 14.0 1.0
O C:HOH873 2.2 24.1 1.0
CG C:ASP367 3.2 15.1 1.0
OD2 C:ASP367 3.6 14.2 1.0
ZN C:ZN700 3.9 16.3 1.0
O C:HOH910 4.1 23.9 1.0
O C:HIS366 4.2 14.2 1.0
OE2 C:GLU396 4.2 22.3 1.0
CD2 C:HIS366 4.2 15.0 1.0
NE2 C:HIS399 4.2 16.5 1.0
OD2 C:ASP484 4.4 18.6 1.0
O C:HOH826 4.4 21.5 1.0
OG1 C:THR437 4.4 18.1 1.0
O C:THR437 4.5 17.6 1.0
CD2 C:HIS399 4.5 16.0 1.0
CB C:ASP367 4.5 13.5 1.0
NE2 C:HIS366 4.6 15.0 1.0
CD2 C:HIS370 4.6 14.2 1.0
NE2 C:HIS326 4.7 18.0 1.0
CD2 C:HIS326 4.8 16.9 1.0
NE2 C:HIS370 4.8 14.8 1.0
CA C:ASP367 4.8 14.3 1.0
CB C:THR437 4.9 18.8 1.0
CG C:GLU396 4.9 16.1 1.0
CD C:GLU396 5.0 16.7 1.0

Magnesium binding site 5 out of 6 in 6njh

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Magnesium binding site 5 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:12.7
occ:1.00
 OE2 D:GLU384 2.0 39.0 1.0
O D:HOH913 2.1 43.0 1.0
NE2 B:HIS318 2.2 23.2 1.0
O D:HOH904 2.3 32.2 1.0
CD D:GLU384 2.6 39.2 1.0
OE1 D:GLU384 2.6 35.6 1.0
CD2 B:HIS318 2.9 23.6 1.0
CE1 B:HIS318 3.3 24.5 1.0
CG D:GLU384 4.0 33.7 1.0
CG B:HIS318 4.2 24.4 1.0
ND1 B:HIS318 4.3 23.5 1.0
CD2 B:LEU406 4.6 22.7 1.0

Magnesium binding site 6 out of 6 in 6njh

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Magnesium binding site 6 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg703

b:30.4
occ:1.00
 O D:HOH818 2.0 15.9 1.0
O D:HOH898 2.2 30.6 1.0
O D:HOH877 2.2 31.0 1.0
OD1 D:ASP367 2.2 24.0 1.0
O D:HOH806 2.2 27.7 1.0
O D:HOH816 2.3 26.6 1.0
CG D:ASP367 3.3 19.3 1.0
OD2 D:ASP367 3.7 19.8 1.0
O D:HIS366 3.9 19.4 1.0
ZN D:ZN702 4.0 22.8 1.0
CD2 D:HIS366 4.1 16.3 1.0
OE2 D:GLU396 4.1 30.5 1.0
NE2 D:HIS399 4.1 16.8 1.0
OG1 D:THR437 4.2 21.1 1.0
CD2 D:HIS399 4.4 15.7 1.0
OD2 D:ASP484 4.4 23.4 1.0
O D:HOH862 4.4 33.2 1.0
O D:THR437 4.4 18.6 1.0
O D:HOH864 4.6 22.2 1.0
NE2 D:HIS366 4.6 17.9 1.0
CB D:ASP367 4.6 17.9 1.0
CB D:THR437 4.7 19.2 1.0
CD2 D:HIS370 4.7 17.9 1.0
CG D:GLU396 4.8 21.9 1.0
CA D:ASP367 4.8 18.0 1.0
C D:HIS366 4.8 18.5 1.0
CD D:GLU396 4.9 24.6 1.0
NE2 D:HIS370 4.9 17.9 1.0
NE2 D:HIS326 5.0 21.9 1.0
O D:HOH822 5.0 29.1 1.0
CD2 D:HIS326 5.0 23.6 1.0

Reference:

M.E.Gurney, R.A.Nugent, X.Mo, J.A.Sindac, T.J.Hagen, D.Fox Iii, 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: Tue Oct 1 12:40:52 2024

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