Magnesium 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
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound, PDB code: 5tkb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5tkb

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:25.2
occ:1.00
 O A:HOH987 2.0 35.1 1.0
O A:HOH955 2.1 24.1 1.0
OD1 A:ASP367 2.1 26.8 1.0
O A:HOH963 2.1 29.3 1.0
O A:HOH901 2.1 32.5 1.0
O A:HOH902 2.2 22.9 1.0
CG A:ASP367 3.2 26.2 1.0
OD2 A:ASP367 3.6 29.7 1.0
ZN A:ZN801 4.0 29.2 1.0
OE2 A:GLU396 4.1 30.0 1.0
NE2 A:HIS399 4.1 25.3 1.0
O A:HOH974 4.1 34.0 1.0
O A:HIS366 4.1 24.1 1.0
O A:HOH958 4.1 27.3 1.0
OG1 A:THR437 4.2 29.5 1.0
CD2 A:HIS366 4.3 29.4 1.0
CD2 A:HIS399 4.3 25.8 1.0
CB A:ASP367 4.5 21.0 1.0
OD2 A:ASP484 4.5 36.7 1.0
CD2 A:HIS370 4.6 27.3 1.0
O A:THR437 4.6 31.9 1.0
F1 A:7DJ807 4.7 56.3 1.0
O A:HOH911 4.7 47.3 1.0
NE2 A:HIS366 4.7 29.5 1.0
CD2 A:HIS326 4.7 26.0 1.0
NE2 A:HIS326 4.8 25.9 1.0
CB A:THR437 4.8 33.9 1.0
CA A:ASP367 4.8 19.7 1.0
NE2 A:HIS370 4.9 27.2 1.0
CG A:GLU396 4.9 25.6 1.0
CD A:GLU396 4.9 32.5 1.0
C15 A:7DJ807 4.9 57.3 1.0
C A:HIS366 5.0 23.9 1.0

Magnesium binding site 2 out of 4 in 5tkb

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg702

b:27.4
occ:1.00
 O B:HOH826 1.9 33.0 1.0
O B:HOH812 2.0 38.0 1.0
O B:HOH816 2.1 31.6 1.0
OD1 B:ASP367 2.1 30.3 1.0
O B:HOH856 2.1 34.1 1.0
O B:HOH814 2.2 28.4 1.0
CG B:ASP367 3.2 29.2 1.0
OD2 B:ASP367 3.6 35.9 1.0
O B:HOH854 3.9 31.4 1.0
ZN B:ZN701 4.0 35.4 1.0
OE2 B:GLU396 4.1 37.8 1.0
NE2 B:HIS399 4.1 27.5 1.0
O B:HOH850 4.1 32.3 1.0
O B:HIS366 4.1 29.3 1.0
CD2 B:HIS366 4.3 30.1 1.0
OG1 B:THR437 4.3 34.3 1.0
CD2 B:HIS399 4.3 27.9 1.0
CB B:ASP367 4.5 23.9 1.0
F1 B:7DJ707 4.5 72.4 1.0
OD2 B:ASP484 4.5 45.0 1.0
CD2 B:HIS370 4.6 25.8 1.0
O B:THR437 4.7 42.8 1.0
O B:HOH837 4.7 49.4 1.0
NE2 B:HIS326 4.7 30.3 1.0
NE2 B:HIS366 4.7 30.3 1.0
CD2 B:HIS326 4.8 29.8 1.0
C15 B:7DJ707 4.8 72.7 1.0
NE2 B:HIS370 4.8 25.6 1.0
CB B:THR437 4.8 39.6 1.0
CA B:ASP367 4.8 23.2 1.0
C16 B:7DJ707 4.9 73.2 1.0
CD B:GLU396 4.9 42.7 1.0
CG B:GLU396 4.9 27.0 1.0
C B:HIS366 5.0 28.2 1.0

Magnesium binding site 3 out of 4 in 5tkb

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg702

b:26.0
occ:1.00
 O C:HOH814 2.0 38.7 1.0
O C:HOH871 2.0 26.3 1.0
O C:HOH826 2.1 26.8 1.0
OD1 C:ASP367 2.2 26.2 1.0
O C:HOH842 2.2 34.3 1.0
O C:HOH820 2.3 30.0 1.0
CG C:ASP367 3.2 26.2 1.0
OD2 C:ASP367 3.6 29.5 1.0
O C:HOH868 3.9 35.9 1.0
O C:HOH867 4.0 30.4 1.0
ZN C:ZN701 4.0 32.4 1.0
OE2 C:GLU396 4.0 33.3 1.0
NE2 C:HIS399 4.2 22.8 1.0
O C:HIS366 4.3 23.7 1.0
OG1 C:THR437 4.3 33.0 1.0
CD2 C:HIS366 4.3 28.3 1.0
CD2 C:HIS399 4.4 22.7 1.0
CB C:ASP367 4.5 20.8 1.0
O C:HOH818 4.6 45.7 1.0
OD2 C:ASP484 4.6 39.9 1.0
CD2 C:HIS370 4.6 26.2 1.0
O C:THR437 4.6 37.0 1.0
F1 C:7DJ705 4.6 69.4 1.0
NE2 C:HIS326 4.7 27.3 1.0
CD2 C:HIS326 4.7 26.9 1.0
NE2 C:HIS370 4.8 25.8 1.0
C15 C:7DJ705 4.8 70.8 1.0
NE2 C:HIS366 4.8 28.1 1.0
CB C:THR437 4.9 32.1 1.0
CA C:ASP367 4.9 20.0 1.0
CD C:GLU396 4.9 42.0 1.0
C16 C:7DJ705 4.9 70.7 1.0
CG C:GLU396 5.0 28.0 1.0

Magnesium binding site 4 out of 4 in 5tkb

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg702

b:24.2
occ:1.00
 O D:HOH806 2.0 24.7 1.0
O D:HOH891 2.1 34.4 1.0
OD1 D:ASP367 2.1 27.8 1.0
O D:HOH835 2.1 28.3 1.0
O D:HOH801 2.2 38.9 1.0
O D:HOH849 2.3 27.3 1.0
CG D:ASP367 3.1 26.6 1.0
OD2 D:ASP367 3.6 24.1 1.0
ZN D:ZN701 4.0 28.5 1.0
O D:HIS366 4.0 24.3 1.0
NE2 D:HIS399 4.1 26.3 1.0
OE2 D:GLU396 4.1 28.3 1.0
CD2 D:HIS366 4.1 22.2 1.0
OG1 D:THR437 4.2 25.9 1.0
O D:HOH867 4.2 34.3 1.0
O D:HOH872 4.3 33.6 1.0
CD2 D:HIS399 4.3 26.5 1.0
CB D:ASP367 4.5 22.4 1.0
OD2 D:ASP484 4.5 35.5 1.0
F1 D:7DJ704 4.6 66.4 1.0
O D:THR437 4.6 34.7 1.0
CD2 D:HIS370 4.6 24.9 1.0
NE2 D:HIS366 4.6 22.9 1.0
O D:HOH803 4.7 46.9 1.0
CB D:THR437 4.7 31.1 1.0
CA D:ASP367 4.8 20.5 1.0
CD2 D:HIS326 4.8 25.1 1.0
NE2 D:HIS326 4.8 25.1 1.0
C D:HIS366 4.9 23.6 1.0
NE2 D:HIS370 4.9 25.2 1.0
CG D:GLU396 4.9 26.6 1.0
C15 D:7DJ704 4.9 65.2 1.0
CD D:GLU396 5.0 33.0 1.0
C16 D:7DJ704 5.0 65.5 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: Mon Dec 14 21:12:38 2020

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