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Magnesium in PDB 5laq: Crystal Structure of Human Phosphodiesterase 4B Catalytic Domain with Inhibitor Npd-001

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4B Catalytic Domain with Inhibitor Npd-001

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4B Catalytic Domain with Inhibitor Npd-001:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4B Catalytic Domain with Inhibitor Npd-001, PDB code: 5laq 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) 82.91 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.737, 95.737, 85.113, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 24.1

Other elements in 5laq:

The structure of Crystal Structure of Human Phosphodiesterase 4B Catalytic Domain with Inhibitor Npd-001 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 4B Catalytic Domain with Inhibitor Npd-001 (pdb code 5laq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Human Phosphodiesterase 4B Catalytic Domain with Inhibitor Npd-001, PDB code: 5laq:

Magnesium binding site 1 out of 1 in 5laq

Go back to Magnesium Binding Sites List in 5laq
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Phosphodiesterase 4B Catalytic Domain with Inhibitor Npd-001


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 4B Catalytic Domain with Inhibitor Npd-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:52.4
occ:1.00
 O A:HOH1168 2.0 53.0 1.0
OD1 A:ASP447 2.1 45.6 1.0
O A:HOH1133 2.2 48.5 1.0
O A:HOH1104 2.2 38.1 1.0
O A:HOH1141 2.4 39.0 1.0
O A:HOH1136 2.6 42.7 1.0
CG A:ASP447 3.2 38.7 1.0
OD2 A:ASP447 3.7 36.8 1.0
OE2 A:GLU476 4.0 49.6 1.0
O A:HIS446 4.1 36.1 1.0
NE2 A:HIS479 4.2 38.8 1.0
ZN A:ZN1001 4.2 35.9 1.0
O A:HOH1154 4.2 53.0 1.0
CD2 A:HIS446 4.3 37.0 1.0
CD2 A:HIS450 4.3 42.6 1.0
CD2 A:HIS479 4.4 33.1 1.0
OG1 A:THR517 4.4 39.5 1.0
CB A:ASP447 4.5 36.0 1.0
C29 A:6M51005 4.5 50.3 1.0
NE2 A:HIS450 4.6 40.1 1.0
C28 A:6M51005 4.6 48.1 1.0
CA A:ASP447 4.8 35.0 1.0
NE2 A:HIS406 4.8 39.9 1.0
OD2 A:ASP564 4.8 41.9 1.0
NE2 A:HIS446 4.8 35.6 1.0
CD A:GLU476 4.9 51.5 1.0
CG A:GLU476 4.9 46.5 1.0
CD2 A:HIS406 4.9 40.9 1.0
CB A:THR517 4.9 37.9 1.0
O A:THR517 5.0 46.6 1.0
O A:HOH1156 5.0 41.9 1.0

Reference:

A.R.Blaazer, A.K.Singh, E.De Heuvel, E.Edink, K.M.Orrling, J.J.N.Veerman, T.Van Den Bergh, C.Jansen, E.Balasubramaniam, W.J.Mooij, H.Custers, M.Sijm, D.N.A.Tagoe, T.D.Kalejaiye, J.C.Munday, H.Tenor, A.Matheeussen, M.Wijtmans, M.Siderius, C.De Graaf, L.Maes, H.P.De Koning, D.S.Bailey, G.J.Sterk, I.J.P.De Esch, D.G.Brown, R.Leurs. Targeting A Subpocket in Trypanosoma Brucei Phosphodiesterase B1 (TBRPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. J. Med. Chem. V. 61 3870 2018.
ISSN: ISSN 1520-4804
PubMed: 29672041
DOI: 10.1021/ACS.JMEDCHEM.7B01670
Page generated: Tue Aug 12 13:45:51 2025

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