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Magnesium in PDB 6rcw: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053, PDB code: 6rcw 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) 91.22 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.894, 110.505, 160.694, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.1

Other elements in 6rcw:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053 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-053 (pdb code 6rcw). 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-053, PDB code: 6rcw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6rcw

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053


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-053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:26.4
occ:1.00
 O A:HOH650 1.9 32.9 1.0
O A:HOH730 2.1 33.0 1.0
OD1 A:ASP201 2.1 31.0 1.0
O A:HOH694 2.1 30.9 1.0
O A:HOH645 2.1 30.4 1.0
O A:HOH629 2.2 28.8 1.0
CG A:ASP201 3.1 31.1 1.0
OD2 A:ASP201 3.4 31.0 1.0
ZN A:ZN501 3.8 35.8 1.0
O A:HOH711 3.8 35.6 1.0
O A:HOH702 4.0 33.4 1.0
OE2 A:GLU230 4.0 37.1 1.0
O A:HOH747 4.1 54.2 1.0
CD2 A:HIS200 4.2 28.7 1.0
O A:HIS200 4.2 26.5 1.0
OG1 A:THR271 4.2 33.8 1.0
NE2 A:HIS233 4.3 31.2 1.0
CD2 A:HIS233 4.3 29.6 1.0
CB A:ASP201 4.5 31.4 1.0
OD2 A:ASP318 4.5 42.0 1.0
O A:HOH620 4.6 50.4 1.0
NE2 A:HIS200 4.6 31.0 1.0
CD2 A:HIS204 4.6 30.6 1.0
O A:THR271 4.7 36.3 1.0
CB A:THR271 4.7 32.3 1.0
CG A:GLU230 4.8 33.4 1.0
CD2 A:HIS160 4.8 35.5 1.0
CA A:ASP201 4.8 28.1 1.0
CD A:GLU230 4.8 35.4 1.0
NE2 A:HIS160 4.9 35.0 1.0
NE2 A:HIS204 4.9 31.0 1.0
C A:HIS200 5.0 25.3 1.0

Magnesium binding site 2 out of 4 in 6rcw

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053


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-053 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:28.7
occ:1.00
 O B:HOH601 2.1 31.2 1.0
O B:HOH645 2.1 32.3 1.0
OD1 B:ASP201 2.1 32.2 1.0
O B:HOH667 2.1 34.9 1.0
O B:HOH644 2.2 31.5 1.0
O B:HOH612 2.2 35.0 1.0
CG B:ASP201 2.8 32.4 1.0
OD2 B:ASP201 2.9 34.1 1.0
ZN B:ZN501 3.8 41.2 1.0
O B:HOH703 3.9 35.7 1.0
C27 B:JX2514 3.9 73.9 1.0
OE2 B:GLU230 4.0 36.2 1.0
NE2 B:HIS233 4.1 34.6 1.0
O B:HOH700 4.1 37.1 1.0
O B:HIS200 4.2 36.0 1.0
OG1 B:THR271 4.2 36.9 1.0
CB B:ASP201 4.3 34.6 1.0
CD2 B:HIS200 4.3 30.6 1.0
CD2 B:HIS233 4.4 34.4 1.0
C26 B:JX2514 4.4 77.5 1.0
O B:THR271 4.4 39.5 1.0
OD2 B:ASP318 4.5 38.3 1.0
CD2 B:HIS204 4.6 35.5 1.0
O B:HOH643 4.6 49.8 1.0
NE2 B:HIS200 4.6 34.1 1.0
CB B:THR271 4.7 45.3 1.0
NE2 B:HIS160 4.7 36.7 1.0
CD2 B:HIS160 4.7 39.4 1.0
CG B:GLU230 4.8 34.6 1.0
CA B:ASP201 4.9 37.7 1.0
NE2 B:HIS204 4.9 31.9 1.0
CD B:GLU230 4.9 34.2 1.0

Magnesium binding site 3 out of 4 in 6rcw

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053


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-053 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:28.6
occ:1.00
 OD1 C:ASP201 2.0 32.9 1.0
O C:HOH706 2.0 31.6 1.0
O C:HOH622 2.0 27.3 1.0
O C:HOH604 2.1 30.1 1.0
O C:HOH651 2.1 30.4 1.0
O C:HOH649 2.1 34.4 1.0
CG C:ASP201 3.0 29.9 1.0
OD2 C:ASP201 3.3 34.3 1.0
ZN C:ZN501 3.7 38.7 1.0
O C:HOH710 3.9 36.8 1.0
O C:HOH699 4.1 34.3 1.0
OE2 C:GLU230 4.1 37.4 1.0
O C:HIS200 4.1 29.2 1.0
NE2 C:HIS233 4.2 30.4 1.0
OG1 C:THR271 4.2 33.1 1.0
CD2 C:HIS200 4.2 29.2 1.0
C27 C:JX2510 4.2 67.8 1.0
CB C:ASP201 4.3 30.8 1.0
CD2 C:HIS233 4.3 28.3 1.0
OD2 C:ASP318 4.4 37.7 1.0
O C:THR271 4.6 36.6 1.0
CD2 C:HIS204 4.6 26.2 1.0
C26 C:JX2510 4.6 75.2 1.0
NE2 C:HIS200 4.6 34.7 1.0
CB C:THR271 4.6 34.2 1.0
CA C:ASP201 4.7 32.5 1.0
O C:HOH629 4.8 43.1 1.0
CD2 C:HIS160 4.8 31.7 1.0
CG C:GLU230 4.9 35.8 1.0
C C:HIS200 4.9 30.8 1.0
NE2 C:HIS160 4.9 32.5 1.0
CD C:GLU230 4.9 37.6 1.0
NE2 C:HIS204 5.0 24.8 1.0

Magnesium binding site 4 out of 4 in 6rcw

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053


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-053 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:26.9
occ:1.00
 O D:HOH630 2.0 26.3 1.0
O D:HOH744 2.0 35.6 1.0
O D:HOH619 2.0 30.2 1.0
OD1 D:ASP201 2.1 31.9 1.0
O D:HOH698 2.1 32.2 1.0
O D:HOH672 2.1 33.3 1.0
CG D:ASP201 3.1 32.7 1.0
OD2 D:ASP201 3.5 31.5 1.0
ZN D:ZN502 3.8 34.8 1.0
O D:HOH736 3.9 35.3 1.0
C27 D:JX2515 4.0 68.4 1.0
OE2 D:GLU230 4.0 36.8 1.0
O D:HOH716 4.1 38.7 1.0
NE2 D:HIS233 4.2 26.8 1.0
O D:HIS200 4.2 29.0 1.0
CD2 D:HIS200 4.2 27.0 1.0
OG1 D:THR271 4.3 33.6 1.0
CB D:ASP201 4.4 30.1 1.0
CD2 D:HIS233 4.4 27.3 1.0
OD2 D:ASP318 4.5 35.6 1.0
C26 D:JX2515 4.5 71.3 1.0
NE2 D:HIS200 4.5 26.8 1.0
O D:HOH745 4.5 41.7 1.0
CD2 D:HIS204 4.6 34.2 1.0
O D:THR271 4.7 33.3 1.0
CB D:THR271 4.8 33.8 1.0
CD2 D:HIS160 4.8 39.5 1.0
CA D:ASP201 4.8 27.1 1.0
NE2 D:HIS160 4.8 38.4 1.0
NE2 D:HIS204 4.9 34.3 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 16:41:48 2024

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