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Zinc 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:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48, PDB code: 6njh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6njh

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Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn701

b:16.9
occ:1.00
 OD1 A:ASP484 2.1 14.8 1.0
OD2 A:ASP367 2.1 13.2 1.0
NE2 A:HIS330 2.1 13.6 1.0
NE2 A:HIS366 2.2 12.4 1.0
O A:HOH805 2.2 19.3 1.0
O A:HOH850 2.7 24.5 1.0
CG A:ASP484 3.0 18.3 1.0
CD2 A:HIS366 3.1 11.9 1.0
CE1 A:HIS330 3.1 13.0 1.0
CG A:ASP367 3.1 15.3 1.0
CD2 A:HIS330 3.2 13.9 1.0
CE1 A:HIS366 3.2 12.2 1.0
OD2 A:ASP484 3.3 18.7 1.0
OD1 A:ASP367 3.5 15.7 1.0
MG A:MG702 4.0 24.1 1.0
CD2 A:HIS326 4.2 16.9 1.0
O A:HOH924 4.2 17.6 1.0
ND1 A:HIS330 4.2 14.6 1.0
CG A:HIS366 4.2 12.1 1.0
ND1 A:HIS366 4.3 12.6 1.0
CG A:HIS330 4.3 13.5 1.0
CB A:ASP367 4.4 15.3 1.0
CB A:ASP484 4.4 19.1 1.0
NE2 A:HIS326 4.5 16.8 1.0
O A:HOH871 4.5 15.9 1.0
CG2 A:VAL334 4.6 15.6 1.0
O A:HOH807 4.8 21.3 1.0
CA A:ASP484 4.9 17.2 1.0

Zinc binding site 2 out of 4 in 6njh

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Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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
B:Zn701

b:20.3
occ:1.00
 OD1 B:ASP484 2.1 19.6 1.0
NE2 B:HIS366 2.1 15.8 1.0
NE2 B:HIS330 2.1 20.6 1.0
OD2 B:ASP367 2.2 16.6 1.0
O B:HOH816 2.2 23.2 1.0
O B:HOH876 2.4 25.2 1.0
CG B:ASP484 3.0 19.3 1.0
CD2 B:HIS366 3.1 15.8 1.0
CE1 B:HIS330 3.1 19.5 1.0
CG B:ASP367 3.1 18.3 1.0
CD2 B:HIS330 3.2 20.9 1.0
CE1 B:HIS366 3.2 17.1 1.0
OD2 B:ASP484 3.3 20.0 1.0
OD1 B:ASP367 3.5 21.4 1.0
MG B:MG702 4.0 28.3 1.0
CD2 B:HIS326 4.2 14.9 1.0
ND1 B:HIS330 4.2 19.9 1.0
CG B:HIS366 4.2 15.5 1.0
ND1 B:HIS366 4.2 18.2 1.0
CG B:HIS330 4.3 20.6 1.0
O B:HOH910 4.3 29.2 1.0
CB B:ASP367 4.4 17.4 1.0
CB B:ASP484 4.4 21.0 1.0
O B:HOH885 4.5 22.2 1.0
NE2 B:HIS326 4.5 17.8 1.0
CG2 B:VAL334 4.6 17.6 1.0
O B:HOH840 4.8 20.4 1.0
CA B:ASP484 4.9 19.8 1.0

Zinc binding site 3 out of 4 in 6njh

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Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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
C:Zn700

b:16.3
occ:1.00
 OD2 C:ASP367 2.1 14.2 1.0
NE2 C:HIS330 2.1 14.2 1.0
OD1 C:ASP484 2.1 17.0 1.0
NE2 C:HIS366 2.2 15.0 1.0
O C:HOH816 2.3 18.7 1.0
O C:HOH910 2.5 23.9 1.0
CG C:ASP484 3.0 18.4 1.0
CD2 C:HIS366 3.1 15.0 1.0
CE1 C:HIS330 3.1 14.9 1.0
CG C:ASP367 3.1 15.1 1.0
CD2 C:HIS330 3.1 14.5 1.0
CE1 C:HIS366 3.2 15.5 1.0
OD2 C:ASP484 3.3 18.6 1.0
OD1 C:ASP367 3.5 15.5 1.0
MG C:MG701 3.9 21.3 1.0
CD2 C:HIS326 4.2 16.9 1.0
ND1 C:HIS330 4.2 16.2 1.0
CG C:HIS366 4.2 15.0 1.0
CG C:HIS330 4.3 15.1 1.0
O C:HOH940 4.3 19.9 1.0
ND1 C:HIS366 4.3 13.9 1.0
CB C:ASP367 4.3 13.5 1.0
O C:HOH855 4.4 23.5 1.0
NE2 C:HIS326 4.5 18.0 1.0
CB C:ASP484 4.5 18.4 1.0
CG2 C:VAL334 4.6 17.8 1.0
O C:HOH853 4.8 16.0 1.0
CA C:ASP484 5.0 17.2 1.0

Zinc binding site 4 out of 4 in 6njh

Go back to Zinc Binding Sites List in 6njh
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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
D:Zn702

b:22.8
occ:1.00
 OD1 D:ASP484 2.1 18.6 1.0
OD2 D:ASP367 2.1 19.8 1.0
NE2 D:HIS366 2.1 17.9 1.0
NE2 D:HIS330 2.1 22.4 1.0
O D:HOH806 2.3 27.7 1.0
O D:HOH862 2.8 33.2 1.0
CG D:ASP484 3.0 23.7 1.0
CD2 D:HIS366 3.1 16.3 1.0
CE1 D:HIS330 3.1 19.7 1.0
CG D:ASP367 3.1 19.3 1.0
CD2 D:HIS330 3.1 20.2 1.0
CE1 D:HIS366 3.1 19.0 1.0
OD2 D:ASP484 3.3 23.4 1.0
OD1 D:ASP367 3.5 24.0 1.0
MG D:MG703 4.0 30.4 1.0
O D:HOH898 4.1 30.6 1.0
CD2 D:HIS326 4.2 23.6 1.0
CG D:HIS366 4.2 17.2 1.0
ND1 D:HIS366 4.2 19.3 1.0
ND1 D:HIS330 4.2 20.6 1.0
CG D:HIS330 4.3 20.2 1.0
CB D:ASP367 4.4 17.9 1.0
CB D:ASP484 4.5 20.6 1.0
NE2 D:HIS326 4.5 21.9 1.0
O D:HOH871 4.5 22.3 1.0
CG2 D:VAL334 4.6 20.6 1.0
CA D:ASP484 4.9 20.0 1.0
O D:HOH818 5.0 15.9 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 29 03:53:00 2024

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