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Magnesium in PDB 6c7g: Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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 N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7g 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) 66.13 / 1.68
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.141, 73.992, 91.743, 109.48, 91.49, 91.04
R / Rfree (%) 19.7 / 23.4

Other elements in 6c7g:

The structure of Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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 N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide (pdb code 6c7g). 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 N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7g:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6c7g

Go back to Magnesium Binding Sites List in 6c7g
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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 N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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:7.8
occ:1.00
 O A:HOH1128 2.0 6.3 1.0
OD1 A:ASP697 2.0 8.4 1.0
O A:HOH1129 2.1 8.8 1.0
O A:HOH1121 2.1 8.0 1.0
O A:HOH1138 2.2 7.5 1.0
O A:HOH1161 2.2 7.2 1.0
CG A:ASP697 3.1 6.6 1.0
OD2 A:ASP697 3.4 7.5 1.0
ZN A:ZN1002 4.0 10.9 1.0
OE2 A:GLU727 4.0 12.1 1.0
NE2 A:HIS730 4.0 8.4 1.0
OG1 A:THR768 4.1 8.0 1.0
O A:HOH1197 4.2 8.0 1.0
CD2 A:HIS696 4.2 5.7 1.0
O A:HOH1242 4.2 11.6 1.0
O A:HIS696 4.2 9.7 1.0
CD2 A:HIS730 4.2 6.8 1.0
CB A:ASP697 4.4 10.2 1.0
C20 A:EOY1001 4.5 17.5 1.0
CB A:THR768 4.5 7.9 1.0
OD2 A:ASP808 4.5 11.5 1.0
NE2 A:HIS656 4.5 10.9 1.0
O A:THR768 4.6 12.6 1.0
NE2 A:HIS696 4.6 5.9 1.0
CD2 A:HIS700 4.6 12.6 1.0
O A:HOH1113 4.7 18.8 1.0
CG A:GLU727 4.7 7.6 1.0
CA A:ASP697 4.7 7.1 1.0
CD2 A:HIS656 4.8 9.3 1.0
CD A:GLU727 4.8 12.3 1.0
NE2 A:HIS700 4.9 11.8 1.0
O24 A:EOY1001 4.9 22.6 1.0

Magnesium binding site 2 out of 4 in 6c7g

Go back to Magnesium Binding Sites List in 6c7g
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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 N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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:6.4
occ:1.00
 O B:HOH1140 1.9 8.1 1.0
O B:HOH1225 2.0 6.0 1.0
OD1 B:ASP697 2.0 6.0 1.0
O B:HOH1156 2.2 8.0 1.0
O B:HOH1151 2.2 7.5 1.0
O B:HOH1118 2.3 8.2 1.0
CG B:ASP697 3.1 6.0 1.0
OD2 B:ASP697 3.4 8.7 1.0
ZN B:ZN1002 4.0 11.6 1.0
NE2 B:HIS730 4.0 8.9 1.0
OG1 B:THR768 4.1 9.6 1.0
OE2 B:GLU727 4.1 12.4 1.0
O B:HOH1199 4.1 9.6 1.0
CD2 B:HIS696 4.2 5.6 1.0
O B:HIS696 4.2 8.1 1.0
CD2 B:HIS730 4.2 6.4 1.0
O B:HOH1244 4.3 8.4 1.0
CB B:ASP697 4.4 8.0 1.0
CB B:THR768 4.5 9.4 1.0
NE2 B:HIS696 4.5 6.4 1.0
NE2 B:HIS656 4.6 11.9 1.0
CD2 B:HIS700 4.6 8.3 1.0
OD2 B:ASP808 4.6 12.5 1.0
C20 B:EOY1001 4.6 11.8 1.0
O B:THR768 4.7 10.0 1.0
CA B:ASP697 4.8 6.1 1.0
CD2 B:HIS656 4.8 11.9 1.0
CG B:GLU727 4.8 6.7 1.0
NE2 B:HIS700 4.9 12.7 1.0
CD B:GLU727 4.9 9.8 1.0
O24 B:EOY1001 4.9 24.3 1.0

Magnesium binding site 3 out of 4 in 6c7g

Go back to Magnesium Binding Sites List in 6c7g
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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 N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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:9.2
occ:1.00
 OD1 C:ASP697 2.0 8.8 1.0
O C:HOH1160 2.0 9.8 1.0
O C:HOH1116 2.0 10.2 1.0
O C:HOH1197 2.1 8.5 1.0
O C:HOH1182 2.1 9.2 1.0
O C:HOH1137 2.1 13.7 1.0
CG C:ASP697 3.1 9.4 1.0
OD2 C:ASP697 3.5 12.8 1.0
ZN C:ZN1002 4.0 12.8 1.0
NE2 C:HIS730 4.1 8.1 1.0
OE2 C:GLU727 4.1 9.5 1.0
O C:HOH1179 4.1 11.9 1.0
O C:HOH1161 4.1 13.2 1.0
CD2 C:HIS696 4.2 16.2 1.0
OG1 C:THR768 4.2 12.3 1.0
CD2 C:HIS730 4.3 7.9 1.0
O C:HIS696 4.4 8.8 1.0
CB C:ASP697 4.4 9.7 1.0
CD2 C:HIS700 4.4 10.6 1.0
NE2 C:HIS656 4.6 10.1 1.0
CB C:THR768 4.6 10.0 1.0
NE2 C:HIS696 4.6 10.2 1.0
O C:THR768 4.6 14.2 1.0
OD2 C:ASP808 4.6 16.2 1.0
NE2 C:HIS700 4.6 9.3 1.0
CD2 C:HIS656 4.7 9.2 1.0
CA C:ASP697 4.7 11.5 1.0
O C:HOH1102 4.8 16.9 1.0
CG C:GLU727 4.9 10.2 1.0
C20 C:EOY1001 4.9 23.8 1.0
CD C:GLU727 4.9 7.6 1.0

Magnesium binding site 4 out of 4 in 6c7g

Go back to Magnesium Binding Sites List in 6c7g
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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 N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-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:8.6
occ:1.00
 OD1 D:ASP697 2.0 11.9 1.0
O D:HOH1132 2.0 7.4 1.0
O D:HOH1190 2.1 11.7 1.0
O D:HOH1216 2.1 7.5 1.0
O D:HOH1130 2.2 11.7 1.0
O D:HOH1107 2.2 15.8 1.0
CG D:ASP697 3.0 10.9 1.0
OD2 D:ASP697 3.4 11.9 1.0
ZN D:ZN1002 4.0 13.5 1.0
O D:HOH1193 4.1 8.2 1.0
NE2 D:HIS730 4.1 10.2 1.0
CD2 D:HIS696 4.1 13.8 1.0
OE2 D:GLU727 4.2 15.5 1.0
O D:HIS696 4.2 10.9 1.0
OG1 D:THR768 4.2 12.6 1.0
O D:HOH1200 4.2 11.6 1.0
CD2 D:HIS730 4.3 9.2 1.0
CB D:ASP697 4.4 11.3 1.0
CD2 D:HIS700 4.5 10.7 1.0
OD2 D:ASP808 4.5 14.9 1.0
NE2 D:HIS696 4.6 12.3 1.0
O D:THR768 4.6 14.0 1.0
CB D:THR768 4.7 13.9 1.0
NE2 D:HIS656 4.7 13.6 1.0
CA D:ASP697 4.7 11.4 1.0
C20 D:EOY1001 4.7 22.2 1.0
CD2 D:HIS656 4.7 10.3 1.0
NE2 D:HIS700 4.8 11.1 1.0
O D:HOH1122 4.9 19.4 1.0
CG D:GLU727 4.9 10.9 1.0
C D:HIS696 5.0 9.8 1.0
CD D:GLU727 5.0 12.1 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 20:16:14 2024

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