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Chlorine 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
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 4 in 6njh

Go back to Chlorine Binding Sites List in 6njh
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl703

b:30.9
occ:1.00
CL A:KRD703 0.0 30.9 1.0
C17 A:KRD703 1.8 29.3 1.0
C16 A:KRD703 2.7 27.0 1.0
C18 A:KRD703 2.7 27.3 1.0
CD2 A:PHE599 3.4 26.2 1.0
CB A:PHE538 3.6 20.4 1.0
CE2 A:PHE599 3.6 28.7 1.0
CD1 A:PHE538 3.7 20.5 1.0
CG1 A:ILE600 3.8 28.1 1.0
CA A:PHE538 3.9 22.2 1.0
CG A:PHE538 3.9 19.5 1.0
C15 A:KRD703 4.0 27.7 1.0
C13 A:KRD703 4.0 24.7 1.0
CD1 A:ILE600 4.2 30.1 1.0
N A:PHE538 4.3 22.8 1.0
O A:SER534 4.4 22.2 1.0
CG A:PHE599 4.5 25.8 1.0
CE2 A:PHE604 4.5 24.3 1.0
C14 A:KRD703 4.5 25.4 1.0
CE1 A:PHE538 4.7 20.6 1.0
CZ A:PHE599 4.8 27.8 1.0
O A:VAL596 4.9 36.1 1.0
CB A:PHE599 5.0 28.1 1.0
CG1 A:VAL596 5.0 34.2 1.0

Chlorine binding site 2 out of 4 in 6njh

Go back to Chlorine Binding Sites List in 6njh
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl703

b:43.6
occ:1.00
CL B:KRD703 0.0 43.6 1.0
C17 B:KRD703 1.8 35.0 1.0
C18 B:KRD703 2.8 32.4 1.0
C16 B:KRD703 2.8 33.8 1.0
CD2 B:PHE599 3.3 34.4 1.0
CE2 B:PHE599 3.6 37.5 1.0
CG1 B:ILE600 3.7 44.0 1.0
CB B:PHE538 3.7 28.7 1.0
CD1 B:PHE538 3.7 29.6 1.0
CA B:PHE538 3.9 27.9 1.0
CG B:PHE538 4.0 30.6 1.0
CD1 B:ILE600 4.0 50.4 1.0
C13 B:KRD703 4.1 31.6 1.0
C15 B:KRD703 4.1 37.7 1.0
N B:PHE538 4.3 29.7 1.0
CE2 B:PHE604 4.3 29.9 1.0
CG B:PHE599 4.4 35.9 1.0
O B:SER534 4.6 31.8 1.0
C14 B:KRD703 4.6 30.8 1.0
CE1 B:PHE538 4.7 27.8 1.0
CZ B:PHE599 4.8 34.9 1.0
O B:VAL596 4.9 41.8 1.0
CB B:PHE599 5.0 36.8 1.0

Chlorine binding site 3 out of 4 in 6njh

Go back to Chlorine Binding Sites List in 6njh
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl702

b:32.2
occ:1.00
CL C:KRD702 0.0 32.2 1.0
C17 C:KRD702 1.8 30.9 1.0
C18 C:KRD702 2.7 31.1 1.0
C16 C:KRD702 2.8 30.2 1.0
CD2 C:PHE599 3.3 34.1 1.0
CE2 C:PHE599 3.5 32.7 1.0
CB C:PHE538 3.6 18.9 1.0
CD1 C:PHE538 3.7 18.4 1.0
CG1 C:ILE600 3.8 36.0 1.0
CA C:PHE538 3.8 17.1 1.0
CG C:PHE538 4.0 17.5 1.0
C13 C:KRD702 4.0 31.1 1.0
C15 C:KRD702 4.1 32.7 1.0
CD1 C:ILE600 4.1 38.1 1.0
N C:PHE538 4.2 18.3 1.0
CE2 C:PHE604 4.4 24.5 1.0
O C:SER534 4.4 25.0 1.0
CG C:PHE599 4.4 34.1 1.0
C14 C:KRD702 4.6 30.4 1.0
CE1 C:PHE538 4.8 18.0 1.0
CZ C:PHE599 4.8 32.3 1.0
O C:VAL596 5.0 38.8 1.0
CB C:PHE599 5.0 30.7 1.0

Chlorine binding site 4 out of 4 in 6njh

Go back to Chlorine Binding Sites List in 6njh
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl704

b:40.5
occ:0.80
CL D:KRD704 0.0 40.5 0.8
C17 D:KRD704 1.8 31.5 0.8
C16 D:KRD704 2.7 33.8 0.8
C18 D:KRD704 2.7 32.0 0.8
CD2 D:PHE599 3.4 38.7 1.0
CB D:PHE538 3.6 25.9 1.0
CE2 D:PHE599 3.6 40.7 1.0
CD1 D:PHE538 3.8 29.8 1.0
CA D:PHE538 3.9 26.1 1.0
CG1 D:ILE600 3.9 40.3 1.0
CG D:PHE538 4.0 24.8 1.0
C15 D:KRD704 4.0 33.4 0.8
C13 D:KRD704 4.0 30.2 0.8
N D:PHE538 4.3 26.6 1.0
CD1 D:ILE600 4.3 44.5 1.0
O D:SER534 4.3 27.2 1.0
CG D:PHE599 4.4 38.3 1.0
C14 D:KRD704 4.5 33.1 0.8
CE2 D:PHE604 4.6 32.7 1.0
CE1 D:PHE538 4.8 29.5 1.0
CZ D:PHE599 4.8 41.0 1.0
O D:VAL596 4.9 56.8 1.0
CB D:PHE599 4.9 42.5 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: Sat Jul 12 17:18:59 2025

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