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Magnesium in PDB 5lbo: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001, PDB code: 5lbo 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) 91.40 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.223, 111.092, 160.798, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21

Other elements in 5lbo:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 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-001 (pdb code 5lbo). 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-001, PDB code: 5lbo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5lbo

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 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 4D2 Catalytic Domain with Inhibitor Npd-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:23.6
occ:1.00
 O A:HOH1191 2.0 28.1 1.0
O A:HOH1108 2.0 30.6 1.0
OD1 A:ASP201 2.0 30.6 1.0
O A:HOH1110 2.1 28.5 1.0
O A:HOH1169 2.1 26.8 1.0
O A:HOH1134 2.2 27.3 1.0
CG A:ASP201 3.1 30.0 1.0
OD2 A:ASP201 3.5 26.7 1.0
ZN A:ZN1001 3.8 35.6 1.0
OE2 A:GLU230 4.0 31.5 1.0
O A:HOH1160 4.0 33.2 1.0
O A:HOH1124 4.0 32.2 1.0
O A:HIS200 4.1 26.2 1.0
NE2 A:HIS233 4.1 31.7 1.0
OG1 A:THR271 4.2 30.2 1.0
CD2 A:HIS200 4.2 28.2 1.0
CD2 A:HIS233 4.3 28.0 1.0
CB A:ASP201 4.5 29.4 1.0
CD2 A:HIS204 4.5 29.6 1.0
OD2 A:ASP318 4.5 31.6 1.0
C29 A:6M51011 4.6 41.1 1.0
O A:THR271 4.6 38.2 1.0
O A:HOH1127 4.7 38.9 1.0
NE2 A:HIS200 4.7 30.4 1.0
C28 A:6M51011 4.7 44.4 1.0
CB A:THR271 4.7 35.0 1.0
NE2 A:HIS204 4.7 29.7 1.0
CD2 A:HIS160 4.8 32.6 1.0
CG A:GLU230 4.8 28.1 1.0
NE2 A:HIS160 4.8 34.3 1.0
CA A:ASP201 4.8 28.2 1.0
CD A:GLU230 4.8 33.1 1.0
C A:HIS200 4.9 25.9 1.0

Magnesium binding site 2 out of 4 in 5lbo

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 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 2 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:24.2
occ:1.00
 OD1 B:ASP201 2.0 25.8 1.0
O B:HOH1154 2.0 27.1 1.0
O B:HOH1116 2.0 28.1 1.0
O B:HOH1182 2.1 23.6 1.0
O B:HOH1162 2.2 28.5 1.0
O B:HOH1108 2.2 25.5 1.0
CG B:ASP201 3.1 28.4 1.0
OD2 B:ASP201 3.5 30.5 1.0
ZN B:ZN1001 3.8 39.3 1.0
OE2 B:GLU230 4.0 29.1 1.0
O B:HIS200 4.0 35.5 1.0
O B:HOH1149 4.0 26.8 1.0
NE2 B:HIS233 4.1 28.8 1.0
OG1 B:THR271 4.1 33.3 1.0
O B:HOH1163 4.2 27.3 1.0
CD2 B:HIS200 4.2 32.4 1.0
CD2 B:HIS233 4.3 29.1 1.0
CB B:ASP201 4.4 29.1 1.0
CD2 B:HIS204 4.5 29.3 1.0
OD2 B:ASP318 4.5 38.5 1.0
C29 B:6M51011 4.6 38.2 1.0
O B:THR271 4.6 34.8 1.0
C28 B:6M51011 4.6 39.0 1.0
NE2 B:HIS200 4.6 36.0 1.0
O B:HOH1114 4.7 34.2 1.0
CB B:THR271 4.7 34.8 1.0
CA B:ASP201 4.7 32.9 1.0
CG B:GLU230 4.8 29.5 1.0
NE2 B:HIS204 4.8 27.9 1.0
NE2 B:HIS160 4.8 33.9 1.0
CD B:GLU230 4.8 34.1 1.0
CD2 B:HIS160 4.9 34.0 1.0
C B:HIS200 4.9 30.9 1.0

Magnesium binding site 3 out of 4 in 5lbo

Go back to Magnesium Binding Sites List in 5lbo
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 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 3 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:22.6
occ:1.00
 O C:HOH1114 2.0 27.5 1.0
OD1 C:ASP201 2.0 29.1 1.0
O C:HOH1167 2.0 24.7 1.0
O C:HOH1105 2.0 28.3 1.0
O C:HOH1123 2.1 27.8 1.0
O C:HOH1144 2.2 29.3 1.0
CG C:ASP201 3.1 32.1 1.0
OD2 C:ASP201 3.4 30.9 1.0
ZN C:ZN1001 3.8 38.8 1.0
O C:HOH1126 4.0 34.5 1.0
OE2 C:GLU230 4.0 32.9 1.0
O C:HIS200 4.1 27.6 1.0
O C:HOH1160 4.1 30.8 1.0
OG1 C:THR271 4.2 34.7 1.0
NE2 C:HIS233 4.2 24.8 1.0
CD2 C:HIS200 4.2 28.6 1.0
C29 C:6M51008 4.3 38.8 1.0
CB C:ASP201 4.4 31.0 1.0
CD2 C:HIS233 4.5 25.5 1.0
OD2 C:ASP318 4.5 37.9 1.0
CD2 C:HIS204 4.5 25.4 1.0
O C:THR271 4.5 34.3 1.0
C28 C:6M51008 4.6 37.9 1.0
CB C:THR271 4.7 34.8 1.0
NE2 C:HIS200 4.7 27.3 1.0
NE2 C:HIS160 4.7 28.6 1.0
CD2 C:HIS160 4.7 29.0 1.0
NE2 C:HIS204 4.7 23.1 1.0
O C:HOH1124 4.8 31.5 1.0
CA C:ASP201 4.8 29.1 1.0
CG C:GLU230 4.8 32.8 1.0
CD C:GLU230 4.9 36.1 1.0
C C:HIS200 5.0 30.6 1.0

Magnesium binding site 4 out of 4 in 5lbo

Go back to Magnesium Binding Sites List in 5lbo
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 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 4 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:20.5
occ:1.00
 O D:HOH1124 2.0 21.9 1.0
O D:HOH1206 2.0 24.2 1.0
O D:HOH1122 2.1 22.9 1.0
O D:HOH1165 2.1 23.0 1.0
OD1 D:ASP201 2.1 25.1 1.0
O D:HOH1173 2.1 27.1 1.0
CG D:ASP201 3.2 27.2 1.0
OD2 D:ASP201 3.6 26.6 1.0
ZN D:ZN1001 3.9 32.2 1.0
OE2 D:GLU230 3.9 33.6 1.0
NE2 D:HIS233 4.1 23.9 1.0
O D:HIS200 4.1 26.0 1.0
OG1 D:THR271 4.2 30.3 1.0
O D:HOH1202 4.2 32.1 1.0
O D:HOH1174 4.3 28.1 1.0
CD2 D:HIS200 4.3 25.1 1.0
CD2 D:HIS233 4.4 21.9 1.0
O D:HOH1116 4.4 43.7 1.0
C29 D:6M51015 4.5 37.3 1.0
CD2 D:HIS204 4.5 33.4 1.0
CB D:ASP201 4.5 26.3 1.0
OD2 D:ASP318 4.5 27.7 1.0
O D:THR271 4.6 29.1 1.0
C28 D:6M51015 4.6 34.8 1.0
NE2 D:HIS204 4.7 31.4 1.0
CG D:GLU230 4.7 33.3 1.0
CB D:THR271 4.7 31.1 1.0
NE2 D:HIS200 4.8 28.1 1.0
CD D:GLU230 4.8 35.8 1.0
NE2 D:HIS160 4.8 40.4 1.0
CD2 D:HIS160 4.8 37.0 1.0
CA D:ASP201 4.8 25.6 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: Sun Sep 29 19:49:04 2024

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