Atomistry » Zinc » PDB 6ngl-6nl7 » 6njh
Atomistry »
  Zinc »
    PDB 6ngl-6nl7 »
      6njh »

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

Go back to Zinc Binding Sites List in 6njh
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

Go back to Zinc Binding Sites List in 6njh
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

Go back to Zinc Binding Sites List in 6njh
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy