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Magnesium in PDB 5tz3: Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide, PDB code: 5tz3 was solved by R.Xu, K.Aertgeerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.65 / 1.72
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.754, 72.727, 90.517, 109.21, 90.70, 91.19
R / Rfree (%) 19.1 / 23.3

Other elements in 5tz3:

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide 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 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide (pdb code 5tz3). 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 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide, PDB code: 5tz3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5tz3

Go back to Magnesium Binding Sites List in 5tz3
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide


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 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:12.7
occ:1.00
 O A:HOH1135 2.0 11.6 1.0
OD1 A:ASP697 2.0 11.4 1.0
O A:HOH1139 2.1 12.6 1.0
O A:HOH1221 2.2 13.5 1.0
O A:HOH1182 2.2 10.5 1.0
O A:HOH1177 2.2 11.2 1.0
CG A:ASP697 3.0 15.2 1.0
OD2 A:ASP697 3.3 15.4 1.0
ZN A:ZN1002 3.7 16.2 1.0
O A:HOH1285 3.9 26.2 1.0
O A:HOH1203 4.0 20.8 1.0
NE2 A:HIS730 4.1 14.4 1.0
OG1 A:THR768 4.1 16.1 1.0
CD2 A:HIS696 4.1 18.9 1.0
OE2 A:GLU727 4.2 14.8 1.0
O A:HOH1230 4.3 15.3 1.0
O A:HIS696 4.3 12.2 1.0
CD2 A:HIS730 4.3 11.2 1.0
CB A:ASP697 4.4 20.2 1.0
OD2 A:ASP808 4.5 21.2 1.0
CB A:THR768 4.5 11.3 1.0
CD2 A:HIS700 4.5 13.1 1.0
CD2 A:HIS656 4.5 15.6 1.0
NE2 A:HIS696 4.6 17.5 1.0
NE2 A:HIS656 4.6 17.7 1.0
CA A:ASP697 4.7 10.2 1.0
O A:THR768 4.7 18.9 1.0
NE2 A:HIS700 4.8 15.3 1.0
CG A:GLU727 4.8 17.4 1.0
CD A:GLU727 5.0 14.7 1.0

Magnesium binding site 2 out of 4 in 5tz3

Go back to Magnesium Binding Sites List in 5tz3
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide


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 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:12.1
occ:1.00
 OD1 B:ASP697 2.1 9.9 1.0
O B:HOH1129 2.1 14.3 1.0
O B:HOH1127 2.1 15.4 1.0
O B:HOH1220 2.1 15.5 1.0
O B:HOH1175 2.1 13.4 1.0
O B:HOH1121 2.2 12.3 1.0
CG B:ASP697 3.0 10.6 1.0
OD2 B:ASP697 3.3 12.1 1.0
ZN B:ZN1002 3.7 17.0 1.0
O B:HOH1190 4.0 25.5 1.0
NE2 B:HIS730 4.1 13.9 1.0
OE2 B:GLU727 4.1 19.3 1.0
O B:HOH1280 4.1 29.8 1.0
CD2 B:HIS696 4.2 12.3 1.0
O B:HIS696 4.2 12.1 1.0
OG1 B:THR768 4.2 13.3 1.0
CD2 B:HIS730 4.3 16.9 1.0
O B:HOH1231 4.4 18.6 1.0
CB B:ASP697 4.4 17.0 1.0
CD2 B:HIS700 4.4 13.6 1.0
OD2 B:ASP808 4.5 21.6 1.0
NE2 B:HIS656 4.5 15.1 1.0
CD2 B:HIS656 4.5 14.3 1.0
CB B:THR768 4.6 10.9 1.0
NE2 B:HIS696 4.6 10.6 1.0
CA B:ASP697 4.7 18.3 1.0
NE2 B:HIS700 4.7 17.8 1.0
O B:THR768 4.8 15.9 1.0
O B:HOH1157 4.9 28.4 1.0
CD B:GLU727 4.9 18.1 1.0
CG B:GLU727 5.0 13.7 1.0
C B:HIS696 5.0 14.8 1.0

Magnesium binding site 3 out of 4 in 5tz3

Go back to Magnesium Binding Sites List in 5tz3
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide


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 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:14.6
occ:1.00
 O C:HOH1121 2.1 14.3 1.0
O C:HOH1211 2.1 14.9 1.0
OD1 C:ASP697 2.1 15.2 1.0
O C:HOH1176 2.1 14.9 1.0
O C:HOH1187 2.1 13.1 1.0
O C:HOH1114 2.2 14.5 1.0
CG C:ASP697 3.1 10.8 1.0
OD2 C:ASP697 3.4 14.8 1.0
ZN C:ZN1002 3.7 17.9 1.0
O C:HOH1240 3.9 30.2 1.0
O C:HOH1139 4.0 27.0 1.0
OE2 C:GLU727 4.1 20.2 1.0
OG1 C:THR768 4.2 17.0 1.0
O C:HOH1207 4.2 19.2 1.0
CD2 C:HIS696 4.2 14.4 1.0
NE2 C:HIS730 4.2 14.2 1.0
O C:HIS696 4.3 10.7 1.0
CD2 C:HIS700 4.3 17.5 1.0
OD2 C:ASP808 4.4 23.1 1.0
CB C:ASP697 4.4 14.3 1.0
CD2 C:HIS730 4.4 12.3 1.0
CD2 C:HIS656 4.5 18.1 1.0
CB C:THR768 4.6 14.4 1.0
NE2 C:HIS656 4.6 20.8 1.0
NE2 C:HIS696 4.6 12.2 1.0
NE2 C:HIS700 4.6 14.3 1.0
O C:HOH1122 4.7 27.1 1.0
CA C:ASP697 4.7 13.3 1.0
O C:THR768 4.8 14.7 1.0
CG C:GLU727 4.9 18.1 1.0
CD C:GLU727 4.9 19.7 1.0

Magnesium binding site 4 out of 4 in 5tz3

Go back to Magnesium Binding Sites List in 5tz3
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide


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 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:14.2
occ:1.00
 O D:HOH1168 1.9 15.8 1.0
OD1 D:ASP697 2.0 11.9 1.0
O D:HOH1151 2.0 13.2 1.0
O D:HOH1213 2.1 14.3 1.0
O D:HOH1194 2.2 13.6 1.0
O D:HOH1234 2.2 14.4 1.0
CG D:ASP697 2.9 12.6 1.0
OD2 D:ASP697 3.3 17.2 1.0
ZN D:ZN1002 3.6 18.1 1.0
O D:HOH1122 3.8 18.5 1.0
O D:HOH1280 4.0 26.4 1.0
CD2 D:HIS696 4.1 14.4 1.0
NE2 D:HIS730 4.1 12.9 1.0
OE2 D:GLU727 4.2 15.3 1.0
OG1 D:THR768 4.3 14.4 1.0
O D:HOH1200 4.3 15.4 1.0
O D:HIS696 4.3 11.8 1.0
OD2 D:ASP808 4.3 19.7 1.0
CB D:ASP697 4.3 13.1 1.0
CD2 D:HIS700 4.3 19.0 1.0
CD2 D:HIS730 4.4 10.7 1.0
NE2 D:HIS656 4.4 13.2 1.0
NE2 D:HIS696 4.5 13.3 1.0
CD2 D:HIS656 4.5 14.3 1.0
CB D:THR768 4.5 16.6 1.0
NE2 D:HIS700 4.6 14.8 1.0
CA D:ASP697 4.7 12.9 1.0
O D:THR768 4.8 14.7 1.0
O D:HOH1156 5.0 20.6 1.0
CD D:GLU727 5.0 14.4 1.0
CG D:GLU727 5.0 9.8 1.0

Reference:

L.Gomez, M.E.Massari, T.Vickers, G.Freestone, W.Vernier, K.Ly, R.Xu, M.Mccarrick, T.Marrone, M.Metz, Y.G.Yan, Z.W.Yoder, R.Lemus, N.J.Broadbent, R.Barido, N.Warren, K.Schmelzer, D.Neul, D.Lee, C.B.Andersen, K.Sebring, K.Aertgeerts, X.Zhou, A.Tabatabaei, M.Peters, J.G.Breitenbucher. Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2A) Inhibitors For the Treatment of Memory Disorders. J. Med. Chem. V. 60 2037 2017.
ISSN: ISSN 1520-4804
PubMed: 28165743
DOI: 10.1021/ACS.JMEDCHEM.6B01793
Page generated: Mon Sep 30 05:06:26 2024

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