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Magnesium in PDB 6hwo: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335, PDB code: 6hwo 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) 80.19 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.465, 110.848, 160.461, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.5

Other elements in 6hwo:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335 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-1335 (pdb code 6hwo). 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-1335, PDB code: 6hwo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6hwo

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg514

b:21.7
occ:1.00
 O A:HOH690 1.9 34.8 1.0
O A:HOH640 2.0 27.7 1.0
O A:HOH631 2.0 28.3 1.0
OD1 A:ASP201 2.1 28.0 1.0
O A:HOH610 2.2 27.7 1.0
O A:HOH638 2.2 29.0 1.0
CG A:ASP201 3.1 28.8 1.0
OD2 A:ASP201 3.3 25.4 1.0
ZN A:ZN510 3.7 34.1 1.0
O A:HOH683 4.0 40.0 1.0
OE2 A:GLU230 4.0 29.2 1.0
CD2 A:HIS200 4.1 27.5 1.0
O A:HOH689 4.1 30.2 1.0
OG1 A:THR271 4.1 28.4 1.0
O A:HIS200 4.2 27.8 1.0
NE2 A:HIS233 4.2 29.2 1.0
C25 A:FFZ513 4.2 69.7 1.0
CD2 A:HIS233 4.3 30.5 1.0
OD2 A:ASP318 4.4 39.4 1.0
CB A:ASP201 4.4 28.8 1.0
NE2 A:HIS200 4.5 28.3 1.0
O A:HOH708 4.5 48.2 1.0
O A:THR271 4.6 36.0 1.0
C24 A:FFZ513 4.6 73.6 1.0
CD2 A:HIS204 4.7 29.8 1.0
CB A:THR271 4.8 35.0 1.0
CA A:ASP201 4.8 27.7 1.0
NE2 A:HIS160 4.8 34.6 1.0
CD2 A:HIS160 4.8 36.8 1.0
NE2 A:HIS204 4.9 29.7 1.0
C A:HIS200 4.9 27.5 1.0

Magnesium binding site 2 out of 4 in 6hwo

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg513

b:18.3
occ:1.00
 OD1 B:ASP201 2.0 29.5 1.0
O B:HOH701 2.0 28.0 1.0
O B:HOH659 2.0 20.9 1.0
O B:HOH625 2.1 26.5 1.0
O B:HOH648 2.3 32.4 1.0
O B:HOH612 2.3 28.4 1.0
CG B:ASP201 3.0 29.3 1.0
OD2 B:ASP201 3.4 29.5 1.0
ZN B:ZN508 3.8 34.6 1.0
O B:HOH691 3.9 25.4 1.0
O B:HIS200 4.0 28.7 1.0
O B:HOH661 4.1 26.8 1.0
OE2 B:GLU230 4.1 30.4 1.0
NE2 B:HIS233 4.2 26.6 1.0
CD2 B:HIS200 4.2 32.5 1.0
OG1 B:THR271 4.3 33.2 1.0
CB B:ASP201 4.4 32.4 1.0
CD2 B:HIS233 4.4 26.7 1.0
C25 B:FFZ512 4.4 51.2 1.0
OD2 B:ASP318 4.5 33.5 1.0
CD2 B:HIS204 4.5 25.3 1.0
O B:THR271 4.5 37.6 1.0
C24 B:FFZ512 4.5 47.7 1.0
NE2 B:HIS200 4.6 29.7 1.0
O B:HOH616 4.6 31.4 1.0
CB B:THR271 4.7 35.5 1.0
CA B:ASP201 4.8 31.1 1.0
CG B:GLU230 4.8 29.4 1.0
NE2 B:HIS204 4.8 25.8 1.0
NE2 B:HIS160 4.8 27.4 1.0
CD2 B:HIS160 4.8 33.8 1.0
C B:HIS200 4.9 25.7 1.0
CD B:GLU230 4.9 30.9 1.0

Magnesium binding site 3 out of 4 in 6hwo

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg512

b:18.4
occ:1.00
 O C:HOH701 2.0 28.4 1.0
OD1 C:ASP201 2.0 26.1 1.0
O C:HOH669 2.0 21.5 1.0
O C:HOH661 2.0 24.1 1.0
O C:HOH618 2.1 26.7 1.0
O C:HOH617 2.3 28.8 1.0
CG C:ASP201 3.0 27.8 1.0
OD2 C:ASP201 3.4 23.4 1.0
ZN C:ZN509 3.8 32.5 1.0
O C:HIS200 4.0 25.9 1.0
O C:HOH680 4.0 27.6 1.0
OE2 C:GLU230 4.1 33.3 1.0
CD2 C:HIS200 4.1 27.7 1.0
NE2 C:HIS233 4.1 21.2 1.0
O C:HOH676 4.2 25.9 1.0
OG1 C:THR271 4.3 26.4 1.0
CD2 C:HIS233 4.3 22.2 1.0
CB C:ASP201 4.4 25.8 1.0
NE2 C:HIS200 4.5 28.7 1.0
C25 C:FFZ510 4.6 52.2 1.0
O C:THR271 4.6 30.4 1.0
CD2 C:HIS204 4.6 22.6 1.0
OD2 C:ASP318 4.6 36.1 1.0
CB C:THR271 4.7 30.4 1.0
O C:HOH705 4.7 33.8 1.0
CA C:ASP201 4.7 27.4 1.0
CD2 C:HIS160 4.7 27.1 1.0
NE2 C:HIS160 4.8 22.5 1.0
C24 C:FFZ510 4.8 52.9 1.0
NE2 C:HIS204 4.9 19.6 1.0
C C:HIS200 4.9 27.7 1.0

Magnesium binding site 4 out of 4 in 6hwo

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg516

b:18.0
occ:1.00
 O D:HOH680 1.9 27.6 1.0
O D:HOH658 1.9 23.4 1.0
OD1 D:ASP201 2.0 22.0 1.0
O D:HOH679 2.0 25.0 1.0
O D:HOH638 2.1 27.5 1.0
O D:HOH647 2.1 26.9 1.0
CG D:ASP201 3.1 24.1 1.0
OD2 D:ASP201 3.6 23.6 1.0
ZN D:ZN512 3.9 29.3 1.0
OE2 D:GLU230 3.9 29.2 1.0
NE2 D:HIS233 4.1 19.2 1.0
O D:HOH706 4.1 27.7 1.0
O D:HOH736 4.1 26.2 1.0
CD2 D:HIS200 4.2 21.0 1.0
O D:HIS200 4.2 25.0 1.0
OG1 D:THR271 4.2 26.2 1.0
C25 D:FFZ515 4.2 42.2 1.0
CD2 D:HIS233 4.3 20.1 1.0
CB D:ASP201 4.5 23.0 1.0
NE2 D:HIS200 4.5 21.5 1.0
C24 D:FFZ515 4.5 46.2 1.0
OD2 D:ASP318 4.5 29.2 1.0
CD2 D:HIS204 4.5 26.9 1.0
CG D:GLU230 4.6 27.1 1.0
O D:THR271 4.6 29.3 1.0
O D:HOH661 4.7 29.8 1.0
CD D:GLU230 4.8 28.4 1.0
NE2 D:HIS204 4.8 29.7 1.0
CB D:THR271 4.8 23.6 1.0
CD2 D:HIS160 4.8 28.6 1.0
NE2 D:HIS160 4.8 30.6 1.0
CA D:ASP201 4.8 21.8 1.0
C D:HIS200 5.0 24.1 1.0

Reference:

E.De Heuvel, A.K.Singh, P.Boronat, A.J.Kooistra, T.Van Der Meer, P.Sadek, A.R.Blaazer, N.C.Shaner, D.S.Bindels, G.Caljon, L.Maes, G.J.Sterk, M.Siderius, M.Oberholzer, I.J.P.De Esch, D.G.Brown, R.Leurs. Alkynamide Phthalazinones As A New Class of TBRPDEB1 Inhibitors (Part 2). Bioorg.Med.Chem. V. 27 4013 2019.
ISSN: ESSN 1464-3391
PubMed: 31378593
DOI: 10.1016/J.BMC.2019.06.026
Page generated: Tue Oct 1 02:47:15 2024

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