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Magnesium in PDB 6c7j: Crystal Structure of Human Phosphodiesterase 2A with 1-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 1-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 1-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[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-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7j 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) 55.88 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.930, 73.450, 91.030, 109.12, 91.25, 91.56
R / Rfree (%) 17.6 / 23

Other elements in 6c7j:

The structure of Crystal Structure of Human Phosphodiesterase 2A with 1-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[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-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide (pdb code 6c7j). 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-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7j:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6c7j

Go back to Magnesium Binding Sites List in 6c7j
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[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-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:14.2
occ:1.00
 O A:HOH1151 2.1 14.2 1.0
O A:HOH1186 2.1 12.1 1.0
OD1 A:ASP697 2.1 11.2 1.0
O A:HOH1116 2.1 10.4 1.0
O A:HOH1157 2.1 11.2 1.0
O A:HOH1254 2.1 10.9 1.0
CG A:ASP697 3.2 12.6 1.0
OD2 A:ASP697 3.6 16.1 1.0
NE2 A:HIS730 4.0 15.4 1.0
OG1 A:THR768 4.0 13.8 1.0
ZN A:ZN1002 4.1 16.8 1.0
O A:HOH1222 4.1 14.1 1.0
OE2 A:GLU727 4.2 20.5 1.0
O A:HOH1241 4.2 17.7 1.0
CD2 A:HIS696 4.2 9.4 1.0
CD2 A:HIS730 4.2 11.6 1.0
O A:HIS696 4.2 15.0 1.0
CB A:THR768 4.4 15.4 1.0
CB A:ASP697 4.5 12.3 1.0
O A:THR768 4.5 21.0 1.0
CD2 A:HIS700 4.5 16.6 1.0
OD2 A:ASP808 4.6 17.0 1.0
NE2 A:HIS656 4.6 14.6 1.0
NE2 A:HIS696 4.6 9.6 1.0
O A:HOH1117 4.7 20.2 1.0
NE2 A:HIS700 4.7 16.5 1.0
CD2 A:HIS656 4.8 13.4 1.0
CA A:ASP697 4.8 15.0 1.0
CG A:GLU727 4.9 14.3 1.0
C22 A:EPV1001 5.0 19.1 1.0
CD A:GLU727 5.0 20.0 1.0

Magnesium binding site 2 out of 4 in 6c7j

Go back to Magnesium Binding Sites List in 6c7j
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[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-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:14.3
occ:1.00
 OD1 B:ASP697 2.0 13.2 1.0
O B:HOH1131 2.0 13.2 1.0
O B:HOH1173 2.1 12.3 1.0
O B:HOH1197 2.2 15.2 1.0
O B:HOH1147 2.2 15.4 1.0
O B:HOH1102 2.3 12.6 1.0
CG B:ASP697 3.1 10.9 1.0
OD2 B:ASP697 3.5 11.1 1.0
NE2 B:HIS730 4.0 11.5 1.0
ZN B:ZN1002 4.0 18.6 1.0
OG1 B:THR768 4.1 16.7 1.0
OE2 B:GLU727 4.1 21.2 1.0
O B:HOH1218 4.1 19.6 1.0
CD2 B:HIS730 4.2 15.3 1.0
O B:HIS696 4.2 13.2 1.0
O B:HOH1242 4.2 14.5 1.0
CD2 B:HIS696 4.3 12.4 1.0
CB B:ASP697 4.4 12.7 1.0
CD2 B:HIS700 4.5 14.3 1.0
CB B:THR768 4.5 13.8 1.0
O B:THR768 4.5 19.2 1.0
OD2 B:ASP808 4.6 20.7 1.0
NE2 B:HIS656 4.6 15.8 1.0
CA B:ASP697 4.7 12.4 1.0
NE2 B:HIS700 4.7 16.1 1.0
CD2 B:HIS656 4.8 19.1 1.0
NE2 B:HIS696 4.8 9.9 1.0
O B:HOH1134 4.8 30.6 1.0
CG B:GLU727 4.9 14.8 1.0
CD B:GLU727 4.9 23.2 1.0
C22 B:EPV1001 4.9 18.1 1.0

Magnesium binding site 3 out of 4 in 6c7j

Go back to Magnesium Binding Sites List in 6c7j
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[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-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:15.7
occ:1.00
 OD1 C:ASP697 2.0 20.5 1.0
O C:HOH1166 2.1 17.6 1.0
O C:HOH1119 2.1 13.6 1.0
O C:HOH1136 2.2 19.1 1.0
O C:HOH1169 2.2 11.8 1.0
O C:HOH1133 2.2 19.2 1.0
CG C:ASP697 3.1 20.2 1.0
OD2 C:ASP697 3.5 14.1 1.0
NE2 C:HIS730 4.0 12.3 1.0
ZN C:ZN1002 4.1 19.4 1.0
OE2 C:GLU727 4.1 20.4 1.0
OG1 C:THR768 4.1 18.5 1.0
O C:HOH1229 4.2 16.0 1.0
O C:HIS696 4.2 15.1 1.0
CD2 C:HIS696 4.2 14.7 1.0
CD2 C:HIS730 4.3 16.8 1.0
O C:HOH1196 4.3 16.0 1.0
CD2 C:HIS700 4.4 16.1 1.0
CB C:ASP697 4.4 14.9 1.0
NE2 C:HIS656 4.5 21.8 1.0
O C:THR768 4.6 22.7 1.0
CB C:THR768 4.6 17.3 1.0
NE2 C:HIS700 4.6 15.7 1.0
CD2 C:HIS656 4.7 19.1 1.0
CA C:ASP697 4.7 16.2 1.0
OD2 C:ASP808 4.7 19.1 1.0
CG C:GLU727 4.7 18.1 1.0
O C:HOH1107 4.8 27.9 1.0
NE2 C:HIS696 4.8 14.6 1.0
CD C:GLU727 4.9 20.1 1.0

Magnesium binding site 4 out of 4 in 6c7j

Go back to Magnesium Binding Sites List in 6c7j
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[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-(5-Tert-Butoxy- 2-Chloro-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:15.3
occ:1.00
 O D:HOH1143 2.1 16.6 1.0
OD1 D:ASP697 2.1 12.9 1.0
O D:HOH1125 2.1 14.0 1.0
O D:HOH1214 2.1 11.4 1.0
O D:HOH1204 2.2 13.0 1.0
O D:HOH1127 2.2 12.9 1.0
CG D:ASP697 3.1 13.6 1.0
OD2 D:ASP697 3.6 14.6 1.0
OE2 D:GLU727 4.0 16.4 1.0
O D:HOH1238 4.0 13.1 1.0
ZN D:ZN1002 4.1 18.0 1.0
OG1 D:THR768 4.1 18.1 1.0
NE2 D:HIS730 4.1 15.2 1.0
O D:HOH1196 4.1 16.1 1.0
O D:HIS696 4.3 14.8 1.0
CD2 D:HIS696 4.3 13.8 1.0
CD2 D:HIS730 4.3 12.8 1.0
CD2 D:HIS700 4.4 14.3 1.0
CB D:ASP697 4.4 13.4 1.0
O D:THR768 4.5 17.5 1.0
CB D:THR768 4.6 20.4 1.0
OD2 D:ASP808 4.6 20.2 1.0
NE2 D:HIS656 4.6 17.1 1.0
O D:HOH1104 4.7 26.9 1.0
CD2 D:HIS656 4.7 16.8 1.0
CA D:ASP697 4.7 19.1 1.0
NE2 D:HIS696 4.7 14.9 1.0
NE2 D:HIS700 4.7 16.0 1.0
CG D:GLU727 4.8 12.1 1.0
CD D:GLU727 4.8 16.9 1.0
C22 D:EPV1001 4.9 23.4 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 20:21:34 2024

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