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Magnesium in PDB 6c7e: Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7e 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) 34.31 / 1.43
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.960, 72.650, 90.730, 109.11, 91.28, 91.20
R / Rfree (%) 17.4 / 20.1

Other elements in 6c7e:

The structure of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide (pdb code 6c7e). 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 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7e:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6c7e

Go back to Magnesium Binding Sites List in 6c7e
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- 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 with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:10.5
occ:1.00
 OD1 A:ASP697 2.0 10.2 1.0
O A:HOH1128 2.0 9.3 1.0
O A:HOH1205 2.1 10.5 1.0
O A:HOH1135 2.1 12.4 1.0
O A:HOH1280 2.1 11.1 1.0
O A:HOH1180 2.1 10.4 1.0
CG A:ASP697 3.0 7.2 1.0
OD2 A:ASP697 3.4 9.2 1.0
ZN A:ZN1002 3.9 13.1 1.0
NE2 A:HIS730 4.0 10.3 1.0
O A:HOH1260 4.1 11.3 1.0
OE2 A:GLU727 4.1 14.7 1.0
OG1 A:THR768 4.1 11.8 1.0
CD2 A:HIS696 4.2 10.0 1.0
O A:HOH1298 4.2 13.4 1.0
CD2 A:HIS730 4.2 11.3 1.0
O A:HIS696 4.2 9.9 1.0
CB A:ASP697 4.4 11.5 1.0
C20 A:EOG1001 4.4 16.9 1.0
CB A:THR768 4.5 10.3 1.0
CD2 A:HIS700 4.5 12.2 1.0
NE2 A:HIS656 4.5 14.8 1.0
O A:THR768 4.6 12.6 1.0
OD2 A:ASP808 4.6 17.3 1.0
NE2 A:HIS696 4.6 8.8 1.0
CD2 A:HIS656 4.7 11.7 1.0
CA A:ASP697 4.8 8.7 1.0
CG A:GLU727 4.8 10.5 1.0
NE2 A:HIS700 4.8 14.8 1.0
CD A:GLU727 4.9 11.3 1.0

Magnesium binding site 2 out of 4 in 6c7e

Go back to Magnesium Binding Sites List in 6c7e
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- 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 with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:12.9
occ:1.00
 O B:HOH1127 2.0 10.4 1.0
O B:HOH1267 2.1 12.0 1.0
OD1 B:ASP697 2.1 11.1 1.0
O B:HOH1151 2.1 11.6 1.0
O B:HOH1165 2.1 12.7 1.0
O B:HOH1118 2.2 11.8 1.0
CG B:ASP697 3.1 11.1 1.0
OD2 B:ASP697 3.5 11.2 1.0
ZN B:ZN1002 4.0 14.4 1.0
OE2 B:GLU727 4.0 16.8 1.0
NE2 B:HIS730 4.0 10.9 1.0
OG1 B:THR768 4.1 12.2 1.0
O B:HOH1268 4.1 12.5 1.0
CD2 B:HIS696 4.2 11.9 1.0
O B:HOH1280 4.2 13.5 1.0
O B:HIS696 4.2 9.6 1.0
CD2 B:HIS730 4.2 11.3 1.0
CB B:ASP697 4.4 11.2 1.0
C20 B:EOG1001 4.5 14.1 1.0
CB B:THR768 4.5 12.6 1.0
CD2 B:HIS700 4.6 13.1 1.0
O B:THR768 4.6 14.2 1.0
OD2 B:ASP808 4.6 17.2 1.0
NE2 B:HIS696 4.6 10.5 1.0
NE2 B:HIS656 4.6 13.7 1.0
O B:HOH1152 4.7 23.7 1.0
CG B:GLU727 4.8 10.6 1.0
CA B:ASP697 4.8 9.9 1.0
CD2 B:HIS656 4.8 14.5 1.0
CD B:GLU727 4.8 12.9 1.0
NE2 B:HIS700 4.9 14.4 1.0

Magnesium binding site 3 out of 4 in 6c7e

Go back to Magnesium Binding Sites List in 6c7e
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- 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 with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:13.5
occ:1.00
 O C:HOH1142 2.0 13.1 1.0
O C:HOH1246 2.0 12.3 1.0
OD1 C:ASP697 2.0 12.8 1.0
O C:HOH1164 2.1 13.6 1.0
O C:HOH1134 2.1 13.6 1.0
O C:HOH1107 2.2 15.2 1.0
CG C:ASP697 3.1 12.9 1.0
OD2 C:ASP697 3.5 13.2 1.0
ZN C:ZN1002 4.0 15.4 1.0
OE2 C:GLU727 4.0 17.1 1.0
NE2 C:HIS730 4.0 12.0 1.0
O C:HOH1226 4.1 13.1 1.0
O C:HOH1233 4.1 14.7 1.0
OG1 C:THR768 4.2 13.9 1.0
CD2 C:HIS696 4.2 17.6 1.0
O C:HIS696 4.2 12.4 1.0
CD2 C:HIS730 4.3 14.5 1.0
CD2 C:HIS700 4.4 13.4 1.0
CB C:ASP697 4.4 13.9 1.0
O C:THR768 4.5 16.7 1.0
CB C:THR768 4.5 14.9 1.0
C20 C:EOG1001 4.6 18.9 1.0
NE2 C:HIS656 4.6 16.2 1.0
OD2 C:ASP808 4.6 20.2 1.0
NE2 C:HIS696 4.7 11.9 1.0
NE2 C:HIS700 4.7 14.8 1.0
O C:HOH1119 4.7 23.7 1.0
CD2 C:HIS656 4.7 15.2 1.0
CA C:ASP697 4.7 11.9 1.0
CG C:GLU727 4.8 13.6 1.0
CD C:GLU727 4.8 14.1 1.0

Magnesium binding site 4 out of 4 in 6c7e

Go back to Magnesium Binding Sites List in 6c7e
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- 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 with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:11.9
occ:1.00
 O D:HOH1127 2.0 11.4 1.0
OD1 D:ASP697 2.0 11.5 1.0
O D:HOH1272 2.0 11.6 1.0
O D:HOH1219 2.0 12.2 1.0
O D:HOH1116 2.1 13.5 1.0
O D:HOH1195 2.2 11.8 1.0
CG D:ASP697 3.1 11.3 1.0
OD2 D:ASP697 3.4 12.2 1.0
ZN D:ZN1002 3.9 14.4 1.0
O D:HOH1227 4.1 12.4 1.0
OE2 D:GLU727 4.1 12.3 1.0
NE2 D:HIS730 4.1 10.5 1.0
O D:HOH1254 4.1 14.2 1.0
CD2 D:HIS696 4.2 10.4 1.0
OG1 D:THR768 4.2 13.6 1.0
O D:HIS696 4.3 12.0 1.0
CD2 D:HIS730 4.3 11.9 1.0
CB D:ASP697 4.4 11.3 1.0
CD2 D:HIS700 4.5 12.2 1.0
CB D:THR768 4.5 13.7 1.0
C20 D:EOG1001 4.5 16.1 1.0
OD2 D:ASP808 4.5 18.7 1.0
O D:THR768 4.6 13.1 1.0
NE2 D:HIS696 4.6 10.1 1.0
NE2 D:HIS656 4.6 13.2 1.0
CA D:ASP697 4.8 10.9 1.0
CG D:GLU727 4.8 11.3 1.0
NE2 D:HIS700 4.8 13.7 1.0
CD2 D:HIS656 4.8 11.9 1.0
O D:HOH1112 4.8 21.8 1.0
CD D:GLU727 4.9 11.8 1.0

Reference:

L.Gomez, R.Xu, W.Sinko, B.Selfridge, W.Vernier, K.Ly, R.Truong, M.Metz, T.Marrone, K.Sebring, Y.Yan, B.Appleton, K.Aertgeerts, M.E.Massari, J.G.Breitenbucher. Mathematical and Structural Characterization of Strong Nonadditive Structure-Activity Relationship Caused By Protein Conformational Changes. J. Med. Chem. V. 61 7754 2018.
ISSN: ISSN 1520-4804
PubMed: 30070482
DOI: 10.1021/ACS.JMEDCHEM.8B00713
Page generated: Mon Sep 30 20:14:47 2024

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