Magnesium in PDB 6c7f: Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7f 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) 71.73 / 1.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.248, 73.004, 91.953, 90.00, 110.33, 90.00
R / Rfree (%) 19.5 / 24.6

Other elements in 6c7f:

The structure of Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide (pdb code 6c7f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7f:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6c7f

Go back to Magnesium Binding Sites List in 6c7f
Magnesium binding site 1 out of 3 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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:18.3
occ:1.00
 O A:HOH1144 2.0 18.0 1.0
OD1 A:ASP697 2.1 16.4 1.0
O A:HOH1216 2.1 14.8 1.0
O A:HOH1133 2.1 13.7 1.0
O A:HOH1112 2.2 20.8 1.0
O A:HOH1206 2.2 17.2 1.0
CG A:ASP697 3.1 15.2 1.0
OD2 A:ASP697 3.4 16.3 1.0
ZN A:ZN1002 4.0 20.6 1.0
OE2 A:GLU727 4.0 26.1 1.0
O A:HOH1190 4.1 16.9 1.0
NE2 A:HIS730 4.1 21.5 1.0
OG1 A:THR768 4.1 21.7 1.0
O A:HOH1253 4.2 16.9 1.0
CD2 A:HIS696 4.2 14.0 1.0
CD2 A:HIS730 4.3 22.9 1.0
O A:HIS696 4.3 16.4 1.0
CB A:ASP697 4.4 16.6 1.0
CD2 A:HIS700 4.5 18.4 1.0
OD2 A:ASP808 4.5 20.5 1.0
CB A:THR768 4.5 20.9 1.0
NE2 A:HIS696 4.6 14.4 1.0
O A:THR768 4.6 23.5 1.0
NE2 A:HIS656 4.7 17.7 1.0
C20 A:EOS1001 4.7 24.2 1.0
CA A:ASP697 4.8 17.3 1.0
NE2 A:HIS700 4.8 19.3 1.0
CD2 A:HIS656 4.8 22.4 1.0
CG A:GLU727 4.8 21.0 1.0
CD A:GLU727 4.8 26.5 1.0

Magnesium binding site 2 out of 3 in 6c7f

Go back to Magnesium Binding Sites List in 6c7f
Magnesium binding site 2 out of 3 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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:16.5
occ:1.00
 O B:HOH1234 2.0 14.2 1.0
OD1 B:ASP697 2.1 14.7 1.0
O B:HOH1189 2.1 19.3 1.0
O B:HOH1120 2.1 16.0 1.0
O B:HOH1117 2.1 19.2 1.0
O B:HOH1134 2.2 18.3 1.0
CG B:ASP697 3.1 16.8 1.0
OD2 B:ASP697 3.4 17.3 1.0
ZN B:ZN1002 4.0 21.5 1.0
O B:HOH1211 4.0 17.0 1.0
NE2 B:HIS730 4.0 17.5 1.0
OE2 B:GLU727 4.1 22.5 1.0
OG1 B:THR768 4.2 23.2 1.0
O B:HOH1208 4.2 16.7 1.0
CD2 B:HIS696 4.2 14.1 1.0
CD2 B:HIS730 4.3 16.2 1.0
O B:HIS696 4.3 19.4 1.0
CB B:ASP697 4.4 18.9 1.0
CD2 B:HIS700 4.4 17.9 1.0
OD2 B:ASP808 4.5 19.5 1.0
CB B:THR768 4.5 23.6 1.0
O B:THR768 4.6 18.2 1.0
NE2 B:HIS656 4.6 19.7 1.0
NE2 B:HIS696 4.6 15.2 1.0
CA B:ASP697 4.7 17.7 1.0
NE2 B:HIS700 4.7 18.1 1.0
CD2 B:HIS656 4.7 19.8 1.0
O B:HOH1121 4.8 26.2 1.0
CG B:GLU727 4.9 18.0 1.0
CD B:GLU727 5.0 27.0 1.0
C20 B:EOS1001 5.0 25.8 1.0

Magnesium binding site 3 out of 3 in 6c7f

Go back to Magnesium Binding Sites List in 6c7f
Magnesium binding site 3 out of 3 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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:18.0
occ:1.00
 O C:HOH1122 2.0 17.9 1.0
O C:HOH1119 2.0 16.6 1.0
O C:HOH1126 2.1 19.0 1.0
OD1 C:ASP697 2.1 20.0 1.0
O C:HOH1158 2.1 20.2 1.0
O C:HOH1189 2.2 16.9 1.0
CG C:ASP697 3.1 19.4 1.0
OD2 C:ASP697 3.5 19.4 1.0
OE2 C:GLU727 4.0 24.8 1.0
ZN C:ZN1002 4.0 23.2 1.0
OG1 C:THR768 4.1 20.6 1.0
NE2 C:HIS730 4.1 21.9 1.0
O C:HOH1209 4.2 25.4 1.0
CD2 C:HIS730 4.2 21.1 1.0
CD2 C:HIS696 4.2 18.0 1.0
O C:HIS696 4.2 21.1 1.0
O C:HOH1181 4.3 18.3 1.0
CB C:THR768 4.5 15.1 1.0
CB C:ASP697 4.5 21.1 1.0
C20 C:EOS1001 4.5 34.1 1.0
OD2 C:ASP808 4.5 18.6 1.0
O C:THR768 4.5 22.2 1.0
CG C:GLU727 4.7 25.4 1.0
NE2 C:HIS696 4.7 17.7 1.0
NE2 C:HIS656 4.7 23.1 1.0
CD C:GLU727 4.7 28.4 1.0
CD2 C:HIS700 4.7 23.7 1.0
O24 C:EOS1001 4.8 32.8 1.0
CA C:ASP697 4.8 18.8 1.0
O C:HOH1107 4.8 33.9 1.0
CD2 C:HIS656 4.9 20.6 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 Dec 14 22:26:41 2020

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