Atomistry » Magnesium » PDB 6c07-6c7i » 6c7d
Atomistry »
  Magnesium »
    PDB 6c07-6c7i »
      6c7d »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy