Atomistry » Magnesium » PDB 5l5u-5lcd » 5lbo
Atomistry »
  Magnesium »
    PDB 5l5u-5lcd »
      5lbo »

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

Go back to Magnesium Binding Sites List in 5lbo
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

Go back to Magnesium Binding Sites List in 5lbo
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

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