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 Dec 14 21:13:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy