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Magnesium in PDB 6ftw: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048, PDB code: 6ftw was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.00 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.140, 111.430, 160.060, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.3

Other elements in 6ftw:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048 (pdb code 6ftw). 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 4D2 Catalytic Domain with Inhibitor Npd-048, PDB code: 6ftw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ftw

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048


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 4D2 Catalytic Domain with Inhibitor Npd-048 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:26.9
occ:1.00
 OD1 A:ASP201 2.0 32.3 1.0
O A:HOH626 2.1 32.5 1.0
O A:HOH717 2.1 31.7 1.0
O A:HOH688 2.1 29.7 1.0
O A:HOH628 2.2 33.5 1.0
O A:HOH613 2.3 29.9 1.0
CG A:ASP201 3.0 29.0 1.0
OD2 A:ASP201 3.4 28.1 1.0
ZN A:ZN501 3.7 36.7 1.0
O A:HOH649 4.0 36.2 1.0
OE2 A:GLU230 4.0 31.7 1.0
O A:HOH669 4.1 29.9 1.0
CD2 A:HIS200 4.1 30.1 1.0
OG1 A:THR271 4.1 31.2 1.0
NE2 A:HIS233 4.2 27.9 1.0
O A:HIS200 4.2 26.9 1.0
C22 A:E6Z517 4.3 49.2 1.0
CD2 A:HIS233 4.4 28.9 1.0
CB A:ASP201 4.4 30.0 1.0
OD2 A:ASP318 4.5 37.5 1.0
C21 A:E6Z517 4.6 56.6 1.0
NE2 A:HIS200 4.6 33.7 1.0
O A:THR271 4.6 35.8 1.0
O A:HOH611 4.6 31.5 1.0
CD2 A:HIS204 4.6 28.7 1.0
CB A:THR271 4.7 32.8 1.0
NE2 A:HIS160 4.8 27.6 1.0
CG A:GLU230 4.8 30.0 1.0
CA A:ASP201 4.8 28.8 1.0
CD2 A:HIS160 4.8 30.0 1.0
CD A:GLU230 4.9 30.1 1.0
NE2 A:HIS204 5.0 32.6 1.0
C A:HIS200 5.0 27.2 1.0

Magnesium binding site 2 out of 4 in 6ftw

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048


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 4D2 Catalytic Domain with Inhibitor Npd-048 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:33.0
occ:1.00
 O B:HOH654 2.0 31.6 1.0
OD1 B:ASP201 2.0 32.1 1.0
O B:HOH658 2.0 38.0 1.0
O B:HOH614 2.1 33.4 1.0
O B:HOH646 2.2 32.3 1.0
O B:HOH626 2.2 39.5 1.0
CG B:ASP201 3.1 34.6 1.0
OD2 B:ASP201 3.5 39.2 1.0
ZN B:ZN501 3.7 44.2 1.0
OE2 B:GLU230 3.9 38.6 1.0
O B:HOH673 4.0 36.4 1.0
O B:HIS200 4.0 42.7 1.0
NE2 B:HIS233 4.0 39.3 1.0
C22 B:E6Z509 4.2 60.2 1.0
CD2 B:HIS200 4.2 34.2 1.0
O B:HOH669 4.2 35.3 1.0
CD2 B:HIS233 4.2 36.7 1.0
OG1 B:THR271 4.3 40.9 1.0
CB B:ASP201 4.5 40.2 1.0
OD2 B:ASP318 4.6 41.3 1.0
CD2 B:HIS204 4.6 31.3 1.0
NE2 B:HIS200 4.6 40.6 1.0
O B:THR271 4.7 44.7 1.0
O B:HOH642 4.7 43.8 1.0
C21 B:E6Z509 4.7 59.1 1.0
CG B:GLU230 4.8 37.0 1.0
CB B:THR271 4.8 42.2 1.0
CA B:ASP201 4.8 41.0 1.0
NE2 B:HIS204 4.8 31.3 1.0
CD B:GLU230 4.8 37.2 1.0
CD2 B:HIS160 4.8 36.6 1.0
C B:HIS200 4.9 36.5 1.0
NE2 B:HIS160 4.9 33.3 1.0

Magnesium binding site 3 out of 4 in 6ftw

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048


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 4D2 Catalytic Domain with Inhibitor Npd-048 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:28.0
occ:1.00
 O C:HOH675 2.0 30.8 1.0
OD1 C:ASP201 2.0 32.1 1.0
O C:HOH645 2.1 34.6 1.0
O C:HOH607 2.1 26.4 1.0
O C:HOH625 2.1 33.8 1.0
O C:HOH657 2.2 31.2 1.0
CG C:ASP201 3.1 35.4 1.0
OD2 C:ASP201 3.4 35.9 1.0
ZN C:ZN501 3.7 41.6 1.0
O C:HOH658 4.0 27.7 1.0
O C:HIS200 4.0 32.3 1.0
OE2 C:GLU230 4.1 36.9 1.0
OG1 C:THR271 4.1 45.3 1.0
O C:HOH695 4.2 35.2 1.0
CD2 C:HIS200 4.2 28.5 1.0
NE2 C:HIS233 4.2 30.8 1.0
C22 C:E6Z512 4.4 54.4 1.0
CD2 C:HIS233 4.4 29.3 1.0
CB C:ASP201 4.4 37.0 1.0
O C:THR271 4.6 37.2 1.0
OD2 C:ASP318 4.6 45.8 1.0
ND1 C:HIS204 4.6 32.2 1.0
C21 C:E6Z512 4.7 51.0 1.0
CB C:THR271 4.7 41.8 1.0
NE2 C:HIS200 4.7 34.6 1.0
CE1 C:HIS204 4.7 28.7 1.0
CG C:GLU230 4.7 35.0 1.0
O C:HOH611 4.8 36.1 1.0
CA C:ASP201 4.8 36.0 1.0
CD2 C:HIS160 4.8 33.0 1.0
CD C:GLU230 4.9 36.4 1.0
NE2 C:HIS160 4.9 30.8 1.0
C C:HIS200 4.9 35.2 1.0

Magnesium binding site 4 out of 4 in 6ftw

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048


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 4D2 Catalytic Domain with Inhibitor Npd-048 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:29.1
occ:1.00
 O D:HOH709 2.0 37.3 1.0
O D:HOH652 2.0 31.5 1.0
O D:HOH617 2.0 35.3 1.0
OD1 D:ASP201 2.1 32.6 1.0
O D:HOH689 2.2 34.3 1.0
O D:HOH671 2.2 31.6 1.0
CG D:ASP201 3.1 33.5 1.0
OD2 D:ASP201 3.5 29.6 1.0
ZN D:ZN501 3.8 38.2 1.0
O D:HOH654 4.0 33.4 1.0
OE2 D:GLU230 4.1 34.8 1.0
O D:HIS200 4.2 30.6 1.0
NE2 D:HIS233 4.2 31.6 1.0
O D:HOH706 4.2 39.5 1.0
CD2 D:HIS200 4.2 27.4 1.0
OG1 D:THR271 4.2 33.6 1.0
C22 D:E6Z516 4.3 57.7 1.0
CD2 D:HIS233 4.4 32.1 1.0
CB D:ASP201 4.5 32.4 1.0
OD2 D:ASP318 4.5 39.1 1.0
NE2 D:HIS200 4.6 30.4 1.0
CG D:GLU230 4.6 33.0 1.0
C21 D:E6Z516 4.6 57.4 1.0
CD2 D:HIS204 4.6 34.0 1.0
O D:HOH631 4.6 40.2 1.0
O D:THR271 4.7 34.2 1.0
NE2 D:HIS160 4.8 36.0 1.0
CB D:THR271 4.8 35.5 1.0
CD D:GLU230 4.8 35.3 1.0
CD2 D:HIS160 4.8 36.9 1.0
CA D:ASP201 4.8 30.1 1.0
NE2 D:HIS204 4.9 32.2 1.0
C D:HIS200 5.0 30.6 1.0

Reference:

E.De Heuvel, A.K.Singh, E.Edink, T.Van Der Meer, M.Van Der Woude, P.Sadek, M.P.Krell-Jorgensen, T.Van Den Bergh, J.Veerman, G.Caljon, T.D.Kalejaiye, M.Wijtmans, L.Maes, H.P.De Koning, G.Jan Sterk, M.Siderius, I.J.P.De Esch, D.G.Brown, R.Leurs. Alkynamide Phthalazinones As A New Class of TBRPDEB1 Inhibitors. Bioorg.Med.Chem. V. 27 3998 2019.
ISSN: ESSN 1464-3391
PubMed: 31327675
DOI: 10.1016/J.BMC.2019.06.027
Page generated: Wed Aug 13 06:22:11 2025

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