Zinc in PDB 5tkb: Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound, PDB code: 5tkb was solved by J.S.Sack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.62 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.000, 112.700, 159.880, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 20.9

Other elements in 5tkb:

The structure of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound (pdb code 5tkb). 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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound, PDB code: 5tkb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5tkb

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:29.2
occ:1.00
 NE2 A:HIS330 2.0 25.1 1.0
NE2 A:HIS366 2.1 29.5 1.0
OD2 A:ASP367 2.2 29.7 1.0
OD1 A:ASP484 2.2 30.7 1.0
O A:HOH901 2.4 32.5 1.0
O A:HOH974 2.4 34.0 1.0
CD2 A:HIS366 3.0 29.4 1.0
CE1 A:HIS330 3.0 24.9 1.0
CD2 A:HIS330 3.1 25.1 1.0
CG A:ASP367 3.1 26.2 1.0
CG A:ASP484 3.1 32.0 1.0
CE1 A:HIS366 3.2 28.9 1.0
OD2 A:ASP484 3.4 36.7 1.0
OD1 A:ASP367 3.6 26.8 1.0
MG A:MG802 4.0 25.2 1.0
O A:HOH987 4.1 35.1 1.0
O A:HOH919 4.1 30.8 1.0
CD2 A:HIS326 4.1 26.0 1.0
ND1 A:HIS330 4.1 25.7 1.0
CG A:HIS366 4.2 26.8 1.0
CG A:HIS330 4.2 24.7 1.0
ND1 A:HIS366 4.3 28.8 1.0
CB A:ASP367 4.3 21.0 1.0
NE2 A:HIS326 4.4 25.9 1.0
CB A:ASP484 4.5 28.3 1.0
CG2 A:VAL334 4.6 24.9 1.0
CA A:ASP484 5.0 27.4 1.0
O A:HOH902 5.0 22.9 1.0

Zinc binding site 2 out of 4 in 5tkb

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:35.4
occ:1.00
 NE2 B:HIS330 2.1 34.0 1.0
NE2 B:HIS366 2.1 30.3 1.0
OD1 B:ASP484 2.2 39.2 1.0
OD2 B:ASP367 2.2 35.9 1.0
O B:HOH854 2.3 31.4 1.0
O B:HOH812 2.4 38.0 1.0
CD2 B:HIS366 3.0 30.1 1.0
CE1 B:HIS330 3.0 33.8 1.0
CG B:ASP484 3.1 41.7 1.0
CG B:ASP367 3.1 29.2 1.0
CD2 B:HIS330 3.1 34.7 1.0
CE1 B:HIS366 3.2 29.8 1.0
OD2 B:ASP484 3.4 45.0 1.0
OD1 B:ASP367 3.6 30.3 1.0
MG B:MG702 4.0 27.4 1.0
O B:HOH806 4.1 34.3 1.0
CG B:HIS366 4.2 28.6 1.0
O B:HOH856 4.2 34.1 1.0
CD2 B:HIS326 4.2 29.8 1.0
ND1 B:HIS330 4.2 34.7 1.0
CG B:HIS330 4.2 33.6 1.0
ND1 B:HIS366 4.3 30.1 1.0
CB B:ASP367 4.3 23.9 1.0
NE2 B:HIS326 4.5 30.3 1.0
CB B:ASP484 4.5 35.8 1.0
CG2 B:VAL334 4.6 34.3 1.0
O B:HOH816 4.8 31.6 1.0
CA B:ASP484 5.0 34.4 1.0

Zinc binding site 3 out of 4 in 5tkb

Go back to Zinc Binding Sites List in 5tkb
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:32.4
occ:1.00
 NE2 C:HIS330 2.0 27.2 1.0
NE2 C:HIS366 2.1 28.1 1.0
OD2 C:ASP367 2.2 29.5 1.0
OD1 C:ASP484 2.2 31.2 1.0
O C:HOH868 2.4 35.9 1.0
O C:HOH814 2.5 38.7 1.0
CD2 C:HIS366 3.0 28.3 1.0
CE1 C:HIS330 3.0 26.1 1.0
CD2 C:HIS330 3.1 26.7 1.0
CG C:ASP484 3.1 33.8 1.0
CG C:ASP367 3.1 26.2 1.0
CE1 C:HIS366 3.2 28.1 1.0
OD2 C:ASP484 3.3 39.9 1.0
OD1 C:ASP367 3.6 26.2 1.0
O C:HOH801 4.0 36.3 1.0
MG C:MG702 4.0 26.0 1.0
O C:HOH871 4.1 26.3 1.0
CD2 C:HIS326 4.1 26.9 1.0
ND1 C:HIS330 4.2 26.1 1.0
CG C:HIS366 4.2 25.9 1.0
CG C:HIS330 4.2 25.7 1.0
ND1 C:HIS366 4.3 27.8 1.0
CB C:ASP367 4.3 20.8 1.0
NE2 C:HIS326 4.4 27.3 1.0
CB C:ASP484 4.5 33.8 1.0
CG2 C:VAL334 4.6 26.4 1.0
O C:HOH826 4.8 26.8 1.0
CA C:ASP484 5.0 32.4 1.0

Zinc binding site 4 out of 4 in 5tkb

Go back to Zinc Binding Sites List in 5tkb
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:28.5
occ:1.00
 NE2 D:HIS330 2.0 27.3 1.0
NE2 D:HIS366 2.1 22.9 1.0
OD2 D:ASP367 2.2 24.1 1.0
OD1 D:ASP484 2.2 30.2 1.0
O D:HOH801 2.4 38.9 1.0
O D:HOH867 2.4 34.3 1.0
CD2 D:HIS366 3.0 22.2 1.0
CE1 D:HIS330 3.0 26.7 1.0
CD2 D:HIS330 3.1 27.8 1.0
CG D:ASP367 3.1 26.6 1.0
CG D:ASP484 3.1 31.7 1.0
CE1 D:HIS366 3.2 22.9 1.0
OD2 D:ASP484 3.4 35.5 1.0
OD1 D:ASP367 3.6 27.8 1.0
MG D:MG702 4.0 24.2 1.0
O D:HOH891 4.1 34.4 1.0
O D:HOH805 4.1 30.3 1.0
CD2 D:HIS326 4.1 25.1 1.0
CG D:HIS366 4.1 20.8 1.0
ND1 D:HIS330 4.2 27.0 1.0
CG D:HIS330 4.2 25.9 1.0
ND1 D:HIS366 4.3 22.2 1.0
CB D:ASP367 4.3 22.4 1.0
NE2 D:HIS326 4.4 25.1 1.0
CB D:ASP484 4.5 25.9 1.0
CG2 D:VAL334 4.6 25.2 1.0
O D:HOH806 4.9 24.7 1.0
CA D:ASP484 4.9 25.5 1.0

Reference:

R.Moslin, D.Gardner, J.Santella, Y.Zhang, J.V.Duncia, C.Liu, J.Lin, J.S.Tokarski, J.Strnad, D.Pedicord, J.Chen, Y.Blat, A.Zupa-Fernandez, L.Cheng, H.Sun, C.Chaudhry, C.Huang, C.D'arienzo, J.S.Sack, J.K.Muckelbauer, C.Chang, J.Tredup, D.Xie, N.Aranibar, J.R.Burke, P.H.Carter, D.S.Weinstein. Identification of Imidazo[1,2-B]Pyridazine TYK2 Pseudokinase Ligands As Potent and Selective Allosteric Inhibitors of TYK2 Signalling. Medchemcomm V. 8 700 2017.
ISSN: ISSN 2040-2503
PubMed: 30108788
DOI: 10.1039/C6MD00560H
Page generated: Wed Dec 16 10:56:02 2020

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