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Magnesium in PDB 6c7i: Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-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-(2-Chloro-5- Methoxy-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-(2-Chloro-5- Methoxy-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-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7i 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) 47.40 / 1.71
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.902, 72.682, 90.816, 109.33, 91.13, 91.06
R / Rfree (%) 17.1 / 21.4

Other elements in 6c7i:

The structure of Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-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-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide (pdb code 6c7i). 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-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6c7i

Go back to Magnesium Binding Sites List in 6c7i
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-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-(2-Chloro-5- Methoxy-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:13.3
occ:1.00
 O A:HOH1134 2.1 10.5 1.0
OD1 A:ASP697 2.1 12.3 1.0
O A:HOH1265 2.1 13.3 1.0
O A:HOH1176 2.1 11.9 1.0
O A:HOH1136 2.1 15.4 1.0
O A:HOH1191 2.1 13.2 1.0
CG A:ASP697 3.1 11.5 1.0
OD2 A:ASP697 3.4 13.6 1.0
ZN A:ZN1002 3.9 16.8 1.0
OE2 A:GLU727 4.0 16.8 1.0
NE2 A:HIS730 4.1 10.7 1.0
O A:HOH1249 4.1 12.3 1.0
OG1 A:THR768 4.1 13.3 1.0
CD2 A:HIS696 4.1 11.9 1.0
O A:HOH1208 4.2 15.0 1.0
O A:HIS696 4.2 14.1 1.0
CD2 A:HIS730 4.3 10.4 1.0
CB A:ASP697 4.4 13.1 1.0
CB A:THR768 4.5 15.3 1.0
C18 A:EP71001 4.5 18.6 1.0
OD2 A:ASP808 4.5 16.2 1.0
CD2 A:HIS700 4.5 13.8 1.0
O A:THR768 4.6 18.2 1.0
NE2 A:HIS696 4.6 8.9 1.0
O25 A:EP71001 4.6 24.4 1.0
NE2 A:HIS656 4.7 16.3 1.0
CG A:GLU727 4.7 13.8 1.0
CA A:ASP697 4.8 9.4 1.0
NE2 A:HIS700 4.8 14.3 1.0
CD2 A:HIS656 4.8 11.7 1.0
CD A:GLU727 4.8 15.1 1.0
O A:HOH1114 4.9 29.1 1.0
C17 A:EP71001 4.9 21.1 1.0

Magnesium binding site 2 out of 4 in 6c7i

Go back to Magnesium Binding Sites List in 6c7i
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-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-(2-Chloro-5- Methoxy-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:13.4
occ:1.00
 O B:HOH1119 2.0 11.6 1.0
O B:HOH1154 2.1 11.5 1.0
OD1 B:ASP697 2.1 12.2 1.0
O B:HOH1260 2.1 13.0 1.0
O B:HOH1165 2.1 13.9 1.0
O B:HOH1110 2.2 12.5 1.0
CG B:ASP697 3.1 13.3 1.0
OD2 B:ASP697 3.5 13.4 1.0
ZN B:ZN1002 3.9 16.9 1.0
OE2 B:GLU727 3.9 16.2 1.0
NE2 B:HIS730 4.0 11.1 1.0
OG1 B:THR768 4.0 14.3 1.0
CD2 B:HIS696 4.1 11.1 1.0
O B:HOH1254 4.2 13.0 1.0
O B:HIS696 4.2 11.7 1.0
O B:HOH1269 4.2 14.1 1.0
CD2 B:HIS730 4.2 15.1 1.0
CB B:ASP697 4.4 13.3 1.0
OD2 B:ASP808 4.5 17.5 1.0
CB B:THR768 4.5 14.9 1.0
CD2 B:HIS700 4.6 13.0 1.0
NE2 B:HIS696 4.6 8.8 1.0
O25 B:EP71001 4.6 20.2 1.0
C18 B:EP71001 4.6 13.1 1.0
O B:THR768 4.7 15.6 1.0
NE2 B:HIS656 4.7 13.2 1.0
CA B:ASP697 4.8 12.2 1.0
CG B:GLU727 4.8 11.0 1.0
O B:HOH1126 4.8 25.2 1.0
CD B:GLU727 4.8 14.3 1.0
CD2 B:HIS656 4.8 13.9 1.0
NE2 B:HIS700 4.9 15.5 1.0
C17 B:EP71001 4.9 16.1 1.0

Magnesium binding site 3 out of 4 in 6c7i

Go back to Magnesium Binding Sites List in 6c7i
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-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-(2-Chloro-5- Methoxy-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:13.4
occ:1.00
 O C:HOH1134 2.0 14.6 1.0
O C:HOH1246 2.1 12.9 1.0
OD1 C:ASP697 2.1 12.7 1.0
O C:HOH1192 2.1 13.6 1.0
O C:HOH1147 2.1 15.5 1.0
O C:HOH1103 2.2 15.9 1.0
CG C:ASP697 3.1 15.1 1.0
OD2 C:ASP697 3.4 13.2 1.0
ZN C:ZN1002 4.0 18.3 1.0
OE2 C:GLU727 4.0 17.9 1.0
NE2 C:HIS730 4.1 13.5 1.0
O C:HOH1193 4.1 14.6 1.0
O C:HOH1232 4.1 17.8 1.0
CD2 C:HIS696 4.2 17.2 1.0
OG1 C:THR768 4.2 16.6 1.0
O C:HIS696 4.3 12.2 1.0
CD2 C:HIS730 4.3 13.3 1.0
CB C:ASP697 4.4 13.9 1.0
CD2 C:HIS700 4.4 18.8 1.0
O C:THR768 4.5 15.7 1.0
OD2 C:ASP808 4.5 20.4 1.0
CB C:THR768 4.6 16.3 1.0
C18 C:EP71001 4.6 19.6 1.0
NE2 C:HIS696 4.6 13.8 1.0
NE2 C:HIS656 4.6 18.7 1.0
O C:HOH1129 4.7 31.1 1.0
NE2 C:HIS700 4.7 16.6 1.0
CA C:ASP697 4.7 14.5 1.0
CD2 C:HIS656 4.7 20.9 1.0
CD C:GLU727 4.8 18.1 1.0
CG C:GLU727 4.8 14.0 1.0
O25 C:EP71001 4.9 29.7 1.0

Magnesium binding site 4 out of 4 in 6c7i

Go back to Magnesium Binding Sites List in 6c7i
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-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-(2-Chloro-5- Methoxy-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:12.4
occ:1.00
 O D:HOH1140 2.0 11.5 1.0
OD1 D:ASP697 2.0 11.1 1.0
O D:HOH1251 2.1 12.6 1.0
O D:HOH1144 2.1 18.1 1.0
O D:HOH1168 2.1 13.0 1.0
O D:HOH1169 2.1 17.3 1.0
CG D:ASP697 3.1 13.4 1.0
OD2 D:ASP697 3.5 14.8 1.0
ZN D:ZN1002 3.9 17.0 1.0
OE2 D:GLU727 4.0 13.9 1.0
NE2 D:HIS730 4.1 13.2 1.0
O D:HOH1184 4.1 13.2 1.0
CD2 D:HIS696 4.1 11.9 1.0
O D:HIS696 4.2 13.6 1.0
OG1 D:THR768 4.2 14.8 1.0
O D:HOH1240 4.2 15.7 1.0
CD2 D:HIS730 4.3 14.3 1.0
CB D:ASP697 4.4 14.5 1.0
CD2 D:HIS700 4.5 14.3 1.0
NE2 D:HIS696 4.5 12.5 1.0
OD2 D:ASP808 4.5 20.0 1.0
CB D:THR768 4.6 16.6 1.0
O D:THR768 4.6 17.4 1.0
NE2 D:HIS656 4.6 14.4 1.0
CA D:ASP697 4.7 15.4 1.0
C18 D:EP71001 4.7 18.6 1.0
O25 D:EP71001 4.7 30.9 1.0
CG D:GLU727 4.8 10.3 1.0
CD2 D:HIS656 4.8 15.3 1.0
NE2 D:HIS700 4.8 16.1 1.0
CD D:GLU727 4.8 13.4 1.0
O D:HOH1129 4.9 29.0 1.0
C D:HIS696 5.0 12.5 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 20:17:31 2024

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