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Magnesium in PDB 5tzh: Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-5-{5-Methyl-[1,2,4]Triazolo[1, 5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5tzh 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) 68.78 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.838, 72.841, 90.706, 109.15, 90.93, 91.18
R / Rfree (%) 21.4 / 25.6

Other elements in 5tzh:

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5tzh

Go back to Magnesium Binding Sites List in 5tzh
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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:8.8
occ:1.00
 O A:HOH1153 1.9 9.6 1.0
O A:HOH1157 2.0 13.1 1.0
OD1 A:ASP697 2.0 8.4 1.0
O A:HOH1238 2.1 11.0 1.0
O A:HOH1231 2.1 9.4 1.0
O A:HOH1239 2.2 14.3 1.0
CG A:ASP697 3.0 11.1 1.0
OD2 A:ASP697 3.2 10.4 1.0
ZN A:ZN1002 3.7 14.0 1.0
O A:HOH1316 3.8 24.6 1.0
O A:HOH1229 3.9 15.1 1.0
CD2 A:HIS696 4.1 12.3 1.0
OG1 A:THR768 4.1 9.3 1.0
NE2 A:HIS730 4.1 9.3 1.0
OE2 A:GLU727 4.1 14.8 1.0
O A:HIS696 4.2 10.1 1.0
O A:HOH1217 4.3 16.9 1.0
CB A:ASP697 4.3 9.6 1.0
CD2 A:HIS730 4.3 10.4 1.0
OD2 A:ASP808 4.4 17.1 1.0
CB A:THR768 4.4 11.4 1.0
NE2 A:HIS656 4.5 17.8 1.0
CD2 A:HIS656 4.6 15.2 1.0
CD2 A:HIS700 4.6 11.0 1.0
NE2 A:HIS696 4.6 8.6 1.0
CG A:GLU727 4.7 10.1 1.0
O A:THR768 4.7 16.1 1.0
CA A:ASP697 4.8 7.9 1.0
NE2 A:HIS700 4.8 13.6 1.0
CD A:GLU727 4.9 9.2 1.0
C A:HIS696 5.0 8.3 1.0

Magnesium binding site 2 out of 4 in 5tzh

Go back to Magnesium Binding Sites List in 5tzh
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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:11.8
occ:1.00
 O B:HOH1161 2.0 9.1 1.0
O B:HOH1214 2.0 14.6 1.0
OD1 B:ASP697 2.0 8.8 1.0
O B:HOH1172 2.1 12.7 1.0
O B:HOH1229 2.1 10.2 1.0
O B:HOH1113 2.2 9.1 1.0
CG B:ASP697 3.0 9.6 1.0
OD2 B:ASP697 3.2 11.6 1.0
ZN B:ZN1002 3.7 15.1 1.0
O B:HOH1286 4.0 25.3 1.0
NE2 B:HIS730 4.0 11.6 1.0
OE2 B:GLU727 4.1 15.0 1.0
O B:HOH1240 4.1 21.3 1.0
CD2 B:HIS696 4.1 12.7 1.0
OG1 B:THR768 4.2 11.8 1.0
O B:HIS696 4.2 10.7 1.0
CD2 B:HIS730 4.3 11.9 1.0
O B:HOH1227 4.3 15.2 1.0
CB B:ASP697 4.4 13.4 1.0
OD2 B:ASP808 4.4 18.1 1.0
CB B:THR768 4.5 11.8 1.0
CD2 B:HIS700 4.5 14.1 1.0
NE2 B:HIS656 4.5 12.8 1.0
CD2 B:HIS656 4.6 12.9 1.0
NE2 B:HIS696 4.6 9.6 1.0
CA B:ASP697 4.7 12.7 1.0
NE2 B:HIS700 4.8 15.0 1.0
O B:THR768 4.8 14.3 1.0
CD B:GLU727 4.9 13.1 1.0
C B:HIS696 5.0 11.2 1.0
CG B:GLU727 5.0 9.3 1.0

Magnesium binding site 3 out of 4 in 5tzh

Go back to Magnesium Binding Sites List in 5tzh
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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:12.5
occ:1.00
 O C:HOH1189 2.0 13.7 1.0
O C:HOH1198 2.0 12.5 1.0
OD1 C:ASP697 2.1 12.0 1.0
O C:HOH1134 2.1 10.9 1.0
O C:HOH1154 2.1 15.2 1.0
O C:HOH1144 2.1 13.5 1.0
CG C:ASP697 3.0 12.5 1.0
OD2 C:ASP697 3.3 13.4 1.0
ZN C:ZN1002 3.7 16.6 1.0
O C:HOH1257 3.7 27.6 1.0
OE2 C:GLU727 4.0 18.1 1.0
O C:HOH1234 4.1 22.9 1.0
NE2 C:HIS730 4.2 12.2 1.0
CD2 C:HIS696 4.2 24.2 1.0
O C:HOH1161 4.3 17.2 1.0
O C:HIS696 4.3 11.2 1.0
OG1 C:THR768 4.4 13.7 1.0
CB C:ASP697 4.4 13.3 1.0
CD2 C:HIS656 4.4 18.8 1.0
OD2 C:ASP808 4.4 20.0 1.0
CD2 C:HIS700 4.4 15.8 1.0
NE2 C:HIS656 4.5 22.1 1.0
CD2 C:HIS730 4.5 9.9 1.0
CB C:THR768 4.6 10.5 1.0
NE2 C:HIS696 4.6 13.2 1.0
O C:THR768 4.7 18.8 1.0
NE2 C:HIS700 4.7 14.9 1.0
CA C:ASP697 4.7 18.8 1.0
CD C:GLU727 4.9 17.0 1.0
O C:HOH1126 5.0 24.6 1.0

Magnesium binding site 4 out of 4 in 5tzh

Go back to Magnesium Binding Sites List in 5tzh
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluorophenyl)Carbonyl]-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:12.2
occ:1.00
 O D:HOH1140 2.0 17.4 1.0
OD1 D:ASP697 2.0 11.4 1.0
O D:HOH1129 2.0 10.4 1.0
O D:HOH1224 2.0 11.7 1.0
O D:HOH1211 2.1 14.2 1.0
O D:HOH1206 2.1 10.1 1.0
CG D:ASP697 3.0 12.1 1.0
OD2 D:ASP697 3.3 13.8 1.0
ZN D:ZN1002 3.7 16.0 1.0
O D:HOH1281 3.8 23.7 1.0
O D:HOH1160 3.9 19.5 1.0
OE2 D:GLU727 4.1 14.1 1.0
NE2 D:HIS730 4.1 11.1 1.0
CD2 D:HIS696 4.1 17.1 1.0
OG1 D:THR768 4.2 10.8 1.0
O D:HIS696 4.2 10.6 1.0
O D:HOH1198 4.3 16.2 1.0
CB D:ASP697 4.4 13.7 1.0
CD2 D:HIS700 4.4 13.9 1.0
CD2 D:HIS730 4.4 11.3 1.0
OD2 D:ASP808 4.4 17.1 1.0
NE2 D:HIS656 4.4 12.8 1.0
NE2 D:HIS696 4.5 12.9 1.0
CB D:THR768 4.5 12.4 1.0
CD2 D:HIS656 4.5 12.9 1.0
NE2 D:HIS700 4.6 14.3 1.0
CA D:ASP697 4.7 11.5 1.0
O D:THR768 4.7 16.2 1.0
CG D:GLU727 4.8 11.8 1.0
CD D:GLU727 4.9 13.3 1.0
O D:HOH1136 4.9 27.4 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 05:06:49 2024

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