Magnesium in PDB 5tzz: Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5tzz 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) 55.72 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.749, 73.119, 91.043, 109.30, 90.91, 91.15
R / Rfree (%) 19.5 / 22.9

Other elements in 5tzz:

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 4 atoms
Bromine (Br) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine (pdb code 5tzz). 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-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5tzz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5tzz

Go back to Magnesium Binding Sites List in 5tzz
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}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 in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:10.0
occ:1.00
O A:HOH1174 2.0 12.4 1.0
OD1 A:ASP697 2.0 9.3 1.0
O A:HOH1164 2.0 10.7 1.0
O A:HOH1220 2.2 10.0 1.0
O A:HOH1216 2.2 8.5 1.0
O A:HOH1222 2.2 10.2 1.0
CG A:ASP697 3.0 9.1 1.0
OD2 A:ASP697 3.3 8.8 1.0
ZN A:ZN1002 3.7 12.3 1.0
O A:HOH1226 4.0 15.5 1.0
O A:HOH1399 4.0 18.7 1.0
NE2 A:HIS730 4.1 10.3 1.0
OE2 A:GLU727 4.2 16.6 1.0
OG1 A:THR768 4.2 11.0 1.0
CD2 A:HIS696 4.2 12.7 1.0
O A:HOH1342 4.2 13.5 1.0
CD2 A:HIS730 4.3 10.0 1.0
O A:HIS696 4.3 10.1 1.0
CB A:ASP697 4.4 12.6 1.0
NE2 A:HIS656 4.4 11.7 1.0
OD2 A:ASP808 4.4 14.9 1.0
CD2 A:HIS656 4.4 9.9 1.0
CB A:THR768 4.5 8.2 1.0
CD2 A:HIS700 4.5 9.6 1.0
NE2 A:HIS696 4.7 10.1 1.0
O A:THR768 4.7 12.7 1.0
CA A:ASP697 4.7 10.1 1.0
NE2 A:HIS700 4.8 10.7 1.0
O A:HOH1119 4.9 22.6 1.0
CG A:GLU727 4.9 13.7 1.0
CD A:GLU727 5.0 10.1 1.0

Magnesium binding site 2 out of 4 in 5tzz

Go back to Magnesium Binding Sites List in 5tzz
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}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 in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:11.4
occ:1.00
O B:HOH1144 2.0 11.2 1.0
OD1 B:ASP697 2.1 8.8 1.0
O B:HOH1286 2.1 9.9 1.0
O B:HOH1147 2.1 11.4 1.0
O B:HOH1209 2.1 14.2 1.0
O B:HOH1178 2.2 12.4 1.0
CG B:ASP697 3.1 7.9 1.0
OD2 B:ASP697 3.4 9.0 1.0
ZN B:ZN1002 3.7 13.9 1.0
O B:HOH1346 4.0 18.7 1.0
O B:HOH1120 4.0 19.2 1.0
OE2 B:GLU727 4.1 17.4 1.0
NE2 B:HIS730 4.1 9.2 1.0
OG1 B:THR768 4.1 11.6 1.0
CD2 B:HIS696 4.2 13.1 1.0
O B:HOH1307 4.2 19.5 1.0
O B:HIS696 4.2 10.9 1.0
CD2 B:HIS730 4.3 13.1 1.0
CB B:ASP697 4.5 13.4 1.0
CB B:THR768 4.5 12.7 1.0
OD2 B:ASP808 4.5 16.6 1.0
NE2 B:HIS656 4.5 12.9 1.0
CD2 B:HIS700 4.5 9.9 1.0
CD2 B:HIS656 4.5 13.4 1.0
NE2 B:HIS696 4.7 8.6 1.0
NE2 B:HIS700 4.8 16.6 1.0
CA B:ASP697 4.8 9.8 1.0
O B:THR768 4.8 13.7 1.0
O B:HOH1125 4.8 21.6 1.0
CG B:GLU727 4.9 9.6 1.0
CD B:GLU727 4.9 14.5 1.0

Magnesium binding site 3 out of 4 in 5tzz

Go back to Magnesium Binding Sites List in 5tzz
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}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 in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:11.8
occ:1.00
OD1 C:ASP697 2.1 10.9 1.0
O C:HOH1136 2.1 10.0 1.0
O C:HOH1175 2.1 12.4 1.0
O C:HOH1235 2.1 10.5 1.0
O C:HOH1132 2.1 10.9 1.0
O C:HOH1251 2.1 12.0 1.0
CG C:ASP697 3.1 10.2 1.0
OD2 C:ASP697 3.4 11.8 1.0
ZN C:ZN1002 3.7 14.2 1.0
OE1 C:GLU727 4.0 15.8 1.0
O C:HOH1221 4.1 18.6 1.0
NE2 C:HIS730 4.2 10.8 1.0
CD2 C:HIS696 4.2 12.0 1.0
OG1 C:THR768 4.2 11.6 1.0
O C:HOH1234 4.2 12.1 1.0
O C:HIS696 4.2 10.4 1.0
CD2 C:HIS700 4.4 12.7 1.0
CD2 C:HIS656 4.4 13.1 1.0
NE2 C:HIS656 4.4 13.8 1.0
OD2 C:ASP808 4.5 16.3 1.0
CB C:ASP697 4.5 11.2 1.0
CD2 C:HIS730 4.5 12.7 1.0
CB C:THR768 4.6 13.2 1.0
NE2 C:HIS700 4.6 10.6 1.0
O C:HOH1104 4.6 20.5 1.0
O C:THR768 4.7 16.9 1.0
NE2 C:HIS696 4.7 12.2 1.0
CA C:ASP697 4.8 9.9 1.0
CD C:GLU727 4.9 13.7 1.0
CG C:GLU727 4.9 13.4 1.0

Magnesium binding site 4 out of 4 in 5tzz

Go back to Magnesium Binding Sites List in 5tzz
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}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 in Complex with 1-[(3- Bromo-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:10.6
occ:1.00
OD1 D:ASP697 2.0 9.5 1.0
O D:HOH1150 2.0 10.1 1.0
O D:HOH1261 2.1 11.0 1.0
O D:HOH1130 2.1 11.1 1.0
O D:HOH1199 2.1 9.3 1.0
O D:HOH1228 2.2 10.9 1.0
CG D:ASP697 3.0 8.8 1.0
OD2 D:ASP697 3.4 11.8 1.0
ZN D:ZN1002 3.7 14.4 1.0
O D:HOH1173 3.9 18.3 1.0
O D:HOH1347 4.0 18.1 1.0
NE2 D:HIS730 4.1 10.2 1.0
OE2 D:GLU727 4.1 11.5 1.0
CD2 D:HIS696 4.2 16.1 1.0
O D:HOH1254 4.2 11.8 1.0
OG1 D:THR768 4.3 11.6 1.0
O D:HIS696 4.4 9.1 1.0
CB D:ASP697 4.4 12.7 1.0
CD2 D:HIS730 4.4 9.1 1.0
CD2 D:HIS700 4.4 14.2 1.0
OD2 D:ASP808 4.4 14.7 1.0
CD2 D:HIS656 4.4 10.6 1.0
NE2 D:HIS656 4.5 11.4 1.0
CB D:THR768 4.5 11.7 1.0
NE2 D:HIS696 4.6 10.8 1.0
NE2 D:HIS700 4.7 13.4 1.0
CA D:ASP697 4.7 11.5 1.0
O D:THR768 4.7 11.9 1.0
O D:HOH1116 4.8 20.7 1.0
CG D:GLU727 4.9 9.3 1.0
CD 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 21:13:40 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy