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Magnesium in PDB 5tza: Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine, PDB code: 5tza 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) 55.77 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.799, 73.444, 91.614, 109.36, 91.17, 91.14
R / Rfree (%) 16.5 / 19.7

Other elements in 5tza:

The structure of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine 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 with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine (pdb code 5tza). 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 with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine, PDB code: 5tza:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5tza

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


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 with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:8.7
occ:1.00
 O A:HOH1174 2.0 10.0 1.0
O A:HOH1201 2.1 10.6 1.0
O A:HOH1234 2.1 10.2 1.0
O A:HOH1154 2.1 8.3 1.0
OD1 A:ASP697 2.1 7.8 1.0
O A:HOH1226 2.2 9.6 1.0
CG A:ASP697 3.1 7.7 1.0
OD2 A:ASP697 3.4 9.2 1.0
ZN A:ZN1002 3.7 11.8 1.0
O A:HOH1370 3.9 15.9 1.0
O A:HOH1277 3.9 14.8 1.0
OE2 A:GLU727 4.1 14.8 1.0
CD2 A:HIS696 4.1 11.1 1.0
NE2 A:HIS730 4.1 8.4 1.0
OG1 A:THR768 4.2 8.9 1.0
O A:HOH1257 4.3 11.6 1.0
O A:HIS696 4.4 8.4 1.0
CD2 A:HIS730 4.4 9.6 1.0
OD2 A:ASP808 4.4 13.6 1.0
CD2 A:HIS656 4.5 11.1 1.0
CB A:ASP697 4.5 10.2 1.0
NE2 A:HIS656 4.5 12.9 1.0
CB A:THR768 4.5 8.0 1.0
NE2 A:HIS696 4.5 7.6 1.0
CD2 A:HIS700 4.6 9.6 1.0
O A:THR768 4.7 11.7 1.0
CA A:ASP697 4.8 7.6 1.0
NE2 A:HIS700 4.9 10.6 1.0
CG A:GLU727 4.9 10.2 1.0
CD A:GLU727 4.9 13.4 1.0

Magnesium binding site 2 out of 4 in 5tza

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


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 with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:10.2
occ:1.00
 O B:HOH1130 2.0 10.8 1.0
O B:HOH1156 2.1 9.8 1.0
OD1 B:ASP697 2.1 9.7 1.0
O B:HOH1249 2.1 10.7 1.0
O B:HOH1229 2.1 11.8 1.0
O B:HOH1208 2.2 11.4 1.0
CG B:ASP697 3.1 10.0 1.0
OD2 B:ASP697 3.4 10.3 1.0
ZN B:ZN1002 3.7 12.7 1.0
O B:HOH1235 3.9 17.6 1.0
O B:HOH1341 4.0 19.9 1.0
CD2 B:HIS696 4.1 9.5 1.0
OG1 B:THR768 4.1 10.3 1.0
OE2 B:GLU727 4.1 14.2 1.0
NE2 B:HIS730 4.2 10.1 1.0
O B:HIS696 4.3 9.9 1.0
O B:HOH1261 4.3 14.4 1.0
OD2 B:ASP808 4.3 13.3 1.0
CD2 B:HIS730 4.4 11.3 1.0
CB B:ASP697 4.5 10.9 1.0
NE2 B:HIS696 4.5 9.4 1.0
CB B:THR768 4.5 11.9 1.0
CD2 B:HIS656 4.5 14.5 1.0
NE2 B:HIS656 4.5 14.7 1.0
CD2 B:HIS700 4.6 14.6 1.0
O B:THR768 4.7 11.6 1.0
CA B:ASP697 4.8 10.3 1.0
O B:HOH1118 4.9 26.4 1.0
NE2 B:HIS700 4.9 13.5 1.0
CG B:GLU727 5.0 10.4 1.0
CD B:GLU727 5.0 11.5 1.0

Magnesium binding site 3 out of 4 in 5tza

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


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

b:11.1
occ:1.00
 O C:HOH1167 2.1 11.5 1.0
O C:HOH1229 2.1 11.0 1.0
OD1 C:ASP697 2.1 10.1 1.0
O C:HOH1132 2.1 12.3 1.0
O C:HOH1121 2.1 11.5 1.0
O C:HOH1215 2.1 10.6 1.0
CG C:ASP697 3.1 13.1 1.0
OD2 C:ASP697 3.4 11.2 1.0
ZN C:ZN1002 3.7 13.3 1.0
O C:HOH1319 3.8 19.9 1.0
OE2 C:GLU727 4.0 13.2 1.0
O C:HOH1231 4.1 19.2 1.0
OG1 C:THR768 4.2 9.8 1.0
NE2 C:HIS730 4.2 10.0 1.0
CD2 C:HIS696 4.2 13.1 1.0
O C:HOH1251 4.2 12.4 1.0
O C:HIS696 4.3 9.8 1.0
CD2 C:HIS656 4.4 14.2 1.0
CD2 C:HIS700 4.4 10.9 1.0
CB C:ASP697 4.4 12.9 1.0
OD2 C:ASP808 4.4 15.5 1.0
CD2 C:HIS730 4.5 9.1 1.0
NE2 C:HIS656 4.5 18.0 1.0
CB C:THR768 4.6 10.7 1.0
O C:THR768 4.6 12.9 1.0
NE2 C:HIS696 4.7 10.2 1.0
NE2 C:HIS700 4.7 11.1 1.0
CA C:ASP697 4.8 11.7 1.0
CD C:GLU727 4.9 13.9 1.0
CG C:GLU727 5.0 9.5 1.0
O C:HOH1136 5.0 24.1 1.0

Magnesium binding site 4 out of 4 in 5tza

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


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

b:9.5
occ:1.00
 O D:HOH1167 2.0 11.7 1.0
O D:HOH1278 2.1 10.7 1.0
OD1 D:ASP697 2.1 9.1 1.0
O D:HOH1143 2.1 9.3 1.0
O D:HOH1169 2.2 11.0 1.0
O D:HOH1237 2.2 10.2 1.0
CG D:ASP697 3.0 9.4 1.0
OD2 D:ASP697 3.3 10.1 1.0
ZN D:ZN1002 3.7 13.0 1.0
O D:HOH1350 3.9 18.8 1.0
O D:HOH1252 4.0 16.0 1.0
OE2 D:GLU727 4.1 12.3 1.0
CD2 D:HIS696 4.1 11.6 1.0
NE2 D:HIS730 4.2 8.8 1.0
O D:HOH1241 4.2 12.9 1.0
OG1 D:THR768 4.2 10.1 1.0
O D:HIS696 4.3 8.8 1.0
CD2 D:HIS700 4.4 13.2 1.0
CB D:ASP697 4.4 11.5 1.0
OD2 D:ASP808 4.4 14.3 1.0
CD2 D:HIS656 4.5 12.3 1.0
CD2 D:HIS730 4.5 8.8 1.0
NE2 D:HIS656 4.5 13.3 1.0
NE2 D:HIS696 4.5 10.0 1.0
CB D:THR768 4.5 9.8 1.0
NE2 D:HIS700 4.7 11.0 1.0
CA D:ASP697 4.8 9.2 1.0
O D:THR768 4.8 11.4 1.0
O D:HOH1140 4.8 20.8 1.0
CD D:GLU727 5.0 12.3 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 05:06:28 2024

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