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Magnesium in PDB 6c7d: Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-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-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7d 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) 65.84 / 1.79
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.914, 73.703, 91.108, 109.56, 91.24, 91.03
R / Rfree (%) 18.7 / 23.2

Other elements in 6c7d:

The structure of Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide (pdb code 6c7d). 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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6c7d

Go back to Magnesium Binding Sites List in 6c7d
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:15.2
occ:1.00
 OD1 A:ASP697 2.0 15.5 1.0
O A:HOH2152 2.1 17.3 1.0
O A:HOH2114 2.1 16.8 1.0
O A:HOH2125 2.1 16.1 1.0
O A:HOH2222 2.1 12.0 1.0
O A:HOH2182 2.2 14.7 1.0
CG A:ASP697 3.1 15.2 1.0
OD2 A:ASP697 3.4 21.0 1.0
ZN A:ZN2002 4.0 19.9 1.0
OE2 A:GLU727 4.0 22.2 1.0
OG1 A:THR768 4.1 17.8 1.0
NE2 A:HIS730 4.1 17.9 1.0
O A:HOH2211 4.2 16.1 1.0
O A:HIS696 4.2 16.1 1.0
CD2 A:HIS696 4.2 17.3 1.0
O A:HOH2158 4.2 17.5 1.0
CD2 A:HIS730 4.2 18.1 1.0
CB A:ASP697 4.4 12.8 1.0
C29 A:EOJ2001 4.4 20.7 1.0
CD2 A:HIS700 4.5 14.5 1.0
CB A:THR768 4.5 20.4 1.0
O A:THR768 4.5 17.8 1.0
NE2 A:HIS656 4.6 19.8 1.0
OD2 A:ASP808 4.6 21.8 1.0
NE2 A:HIS696 4.7 13.4 1.0
CG A:GLU727 4.7 12.6 1.0
CD2 A:HIS656 4.7 14.6 1.0
CA A:ASP697 4.7 14.6 1.0
NE2 A:HIS700 4.7 16.1 1.0
CD A:GLU727 4.8 19.3 1.0

Magnesium binding site 2 out of 4 in 6c7d

Go back to Magnesium Binding Sites List in 6c7d
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2003

b:18.2
occ:1.00
 O B:HOH2113 2.0 15.0 1.0
OD1 B:ASP697 2.1 15.4 1.0
O B:HOH2161 2.2 14.3 1.0
O B:HOH2193 2.2 14.9 1.0
O B:HOH2110 2.2 14.8 1.0
O B:HOH2107 2.4 17.9 1.0
CG B:ASP697 3.1 15.3 1.0
OD2 B:ASP697 3.5 15.9 1.0
ZN B:ZN2002 4.0 19.5 1.0
OE2 B:GLU727 4.0 19.7 1.0
OG1 B:THR768 4.1 16.1 1.0
O B:HIS696 4.1 11.9 1.0
NE2 B:HIS730 4.1 13.8 1.0
CD2 B:HIS696 4.2 15.0 1.0
O B:HOH2239 4.2 19.2 1.0
CD2 B:HIS730 4.3 14.4 1.0
O B:HOH2180 4.3 15.2 1.0
CB B:ASP697 4.4 15.6 1.0
CB B:THR768 4.5 18.8 1.0
CD2 B:HIS700 4.6 13.2 1.0
O B:THR768 4.6 15.7 1.0
OD2 B:ASP808 4.6 19.2 1.0
NE2 B:HIS656 4.6 21.3 1.0
NE2 B:HIS696 4.6 11.1 1.0
C29 B:EOJ2001 4.6 23.8 1.0
CA B:ASP697 4.7 14.9 1.0
CD2 B:HIS656 4.8 15.0 1.0
CG B:GLU727 4.8 12.3 1.0
CD B:GLU727 4.8 17.0 1.0
O B:HOH2160 4.9 25.3 1.0
NE2 B:HIS700 4.9 22.0 1.0
C B:HIS696 4.9 18.1 1.0

Magnesium binding site 3 out of 4 in 6c7d

Go back to Magnesium Binding Sites List in 6c7d
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:19.9
occ:1.00
 OD1 C:ASP697 2.0 18.5 1.0
O C:HOH2118 2.0 25.0 1.0
O C:HOH2125 2.1 20.9 1.0
O C:HOH2123 2.1 17.0 1.0
O C:HOH2169 2.1 21.5 1.0
O C:HOH2156 2.2 16.6 1.0
CG C:ASP697 3.0 24.7 1.0
OD2 C:ASP697 3.4 20.8 1.0
ZN C:ZN2002 4.0 24.1 1.0
OE2 C:GLU727 4.0 23.6 1.0
O C:HOH2144 4.1 19.9 1.0
CD2 C:HIS696 4.1 22.0 1.0
NE2 C:HIS730 4.2 14.0 1.0
OG1 C:THR768 4.2 20.1 1.0
O C:HOH2185 4.2 17.7 1.0
O C:HIS696 4.2 19.3 1.0
CD2 C:HIS730 4.3 14.3 1.0
CB C:ASP697 4.4 18.5 1.0
O C:THR768 4.4 25.9 1.0
NE2 C:HIS656 4.5 21.0 1.0
CD2 C:HIS700 4.5 23.1 1.0
OD2 C:ASP808 4.5 24.4 1.0
CB C:THR768 4.6 15.2 1.0
NE2 C:HIS696 4.6 17.5 1.0
C29 C:EOJ2001 4.6 24.3 1.0
O C:HOH2120 4.7 32.4 1.0
CD2 C:HIS656 4.7 23.0 1.0
CA C:ASP697 4.7 17.6 1.0
CG C:GLU727 4.8 17.8 1.0
NE2 C:HIS700 4.8 21.8 1.0
CD C:GLU727 4.8 23.0 1.0

Magnesium binding site 4 out of 4 in 6c7d

Go back to Magnesium Binding Sites List in 6c7d
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:18.3
occ:1.00
 O D:HOH2119 1.9 18.6 1.0
OD1 D:ASP697 2.0 17.9 1.0
O D:HOH2115 2.1 16.0 1.0
O D:HOH2207 2.1 17.1 1.0
O D:HOH2141 2.2 19.3 1.0
O D:HOH2193 2.2 17.7 1.0
CG D:ASP697 3.0 22.7 1.0
OD2 D:ASP697 3.4 25.9 1.0
ZN D:ZN2002 3.9 23.1 1.0
O D:HOH2124 4.1 19.8 1.0
OE2 D:GLU727 4.1 22.2 1.0
CD2 D:HIS696 4.1 22.0 1.0
NE2 D:HIS730 4.1 16.4 1.0
OG1 D:THR768 4.1 18.6 1.0
O D:HOH2184 4.1 17.6 1.0
O D:HIS696 4.2 20.2 1.0
CD2 D:HIS730 4.3 15.7 1.0
CB D:ASP697 4.4 19.4 1.0
CB D:THR768 4.4 20.4 1.0
OD2 D:ASP808 4.4 28.0 1.0
CD2 D:HIS700 4.4 21.8 1.0
O D:THR768 4.5 16.9 1.0
NE2 D:HIS696 4.6 19.2 1.0
NE2 D:HIS656 4.6 18.8 1.0
CA D:ASP697 4.7 17.7 1.0
C29 D:EOJ2001 4.7 28.8 1.0
CG D:GLU727 4.7 14.5 1.0
NE2 D:HIS700 4.8 19.8 1.0
CD2 D:HIS656 4.8 16.8 1.0
CD D:GLU727 4.9 20.7 1.0
O D:HOH2123 4.9 24.8 1.0
C D:HIS696 4.9 18.2 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 20:14:32 2024

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