Atomistry » Magnesium » PDB 6r5k-6rde » 6rcw
Atomistry »
  Magnesium »
    PDB 6r5k-6rde »
      6rcw »

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

Go back to Magnesium Binding Sites List in 6rcw
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

Go back to Magnesium Binding Sites List in 6rcw
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

Go back to Magnesium Binding Sites List in 6rcw
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

Go back to Magnesium Binding Sites List in 6rcw
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy