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Zinc in PDB 6c7e: Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[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- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7e 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) 34.31 / 1.43
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.960, 72.650, 90.730, 109.11, 91.28, 91.20
R / Rfree (%) 17.4 / 20.1

Other elements in 6c7e:

The structure of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide (pdb code 6c7e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7e:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6c7e

Go back to Zinc Binding Sites List in 6c7e
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:13.1
occ:1.00
 OD2 A:ASP697 2.1 9.2 1.0
NE2 A:HIS696 2.1 8.8 1.0
NE2 A:HIS660 2.1 11.6 1.0
O A:HOH1260 2.1 11.3 1.0
OD1 A:ASP808 2.2 10.7 1.0
O A:HOH1135 2.4 12.4 1.0
CD2 A:HIS696 3.0 10.0 1.0
CD2 A:HIS660 3.1 11.0 1.0
CG A:ASP808 3.1 13.2 1.0
CE1 A:HIS696 3.1 10.5 1.0
CG A:ASP697 3.1 7.2 1.0
CE1 A:HIS660 3.1 11.0 1.0
OD2 A:ASP808 3.3 17.3 1.0
OD1 A:ASP697 3.7 10.2 1.0
MG A:MG1003 3.9 10.5 1.0
O A:HOH1167 4.0 13.2 1.0
CD2 A:HIS656 4.1 11.7 1.0
CG A:HIS696 4.2 10.2 1.0
ND1 A:HIS696 4.2 10.9 1.0
CG A:HIS660 4.2 11.3 1.0
ND1 A:HIS660 4.2 13.1 1.0
O A:HOH1280 4.2 11.1 1.0
NE2 A:HIS656 4.2 14.8 1.0
CB A:ASP697 4.3 11.5 1.0
CB A:ASP808 4.5 11.5 1.0
O A:HOH1128 4.7 9.3 1.0
CG2 A:VAL664 4.9 11.3 1.0
CA A:ASP808 4.9 11.7 1.0
O A:ASP808 5.0 13.7 1.0

Zinc binding site 2 out of 4 in 6c7e

Go back to Zinc Binding Sites List in 6c7e
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:14.4
occ:1.00
 OD2 B:ASP697 2.1 11.2 1.0
NE2 B:HIS660 2.1 13.9 1.0
NE2 B:HIS696 2.1 10.5 1.0
OD1 B:ASP808 2.1 10.5 1.0
O B:HOH1268 2.2 12.5 1.0
O B:HOH1118 2.4 11.8 1.0
CD2 B:HIS696 3.0 11.9 1.0
CD2 B:HIS660 3.1 11.9 1.0
CE1 B:HIS660 3.1 11.9 1.0
CG B:ASP808 3.1 13.6 1.0
CE1 B:HIS696 3.1 13.8 1.0
CG B:ASP697 3.2 11.1 1.0
OD2 B:ASP808 3.4 17.2 1.0
OD1 B:ASP697 3.7 11.1 1.0
MG B:MG1003 4.0 12.9 1.0
O B:HOH1147 4.0 14.4 1.0
CD2 B:HIS656 4.1 14.5 1.0
O B:HOH1267 4.1 12.0 1.0
ND1 B:HIS660 4.2 13.3 1.0
CG B:HIS696 4.2 11.8 1.0
ND1 B:HIS696 4.2 13.3 1.0
CG B:HIS660 4.2 13.9 1.0
NE2 B:HIS656 4.3 13.7 1.0
CB B:ASP697 4.3 11.2 1.0
CB B:ASP808 4.5 13.8 1.0
O B:HOH1127 4.8 10.4 1.0
CG2 B:VAL664 4.8 11.5 1.0
CA B:ASP808 4.9 12.2 1.0
O B:ASP808 5.0 14.4 1.0

Zinc binding site 3 out of 4 in 6c7e

Go back to Zinc Binding Sites List in 6c7e
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:15.4
occ:1.00
 NE2 C:HIS660 2.1 14.0 1.0
OD2 C:ASP697 2.1 13.2 1.0
O C:HOH1226 2.1 13.1 1.0
OD1 C:ASP808 2.1 13.8 1.0
NE2 C:HIS696 2.2 11.9 1.0
O C:HOH1107 2.4 15.2 1.0
CG C:ASP808 3.0 20.0 1.0
CD2 C:HIS660 3.0 11.0 1.0
CE1 C:HIS660 3.0 11.8 1.0
CD2 C:HIS696 3.0 17.6 1.0
CG C:ASP697 3.2 12.9 1.0
CE1 C:HIS696 3.2 13.3 1.0
OD2 C:ASP808 3.3 20.2 1.0
OD1 C:ASP697 3.7 12.8 1.0
MG C:MG1003 4.0 13.5 1.0
O C:HOH1160 4.0 15.2 1.0
CD2 C:HIS656 4.1 15.2 1.0
ND1 C:HIS660 4.2 15.4 1.0
O C:HOH1246 4.2 12.3 1.0
CG C:HIS660 4.2 12.3 1.0
CG C:HIS696 4.2 14.4 1.0
NE2 C:HIS656 4.2 16.2 1.0
ND1 C:HIS696 4.3 14.2 1.0
CB C:ASP697 4.3 13.9 1.0
CB C:ASP808 4.4 13.6 1.0
O C:HOH1142 4.8 13.1 1.0
CA C:ASP808 4.8 15.7 1.0
CG2 C:VAL664 4.9 14.1 1.0
O C:ASP808 4.9 14.8 1.0

Zinc binding site 4 out of 4 in 6c7e

Go back to Zinc Binding Sites List in 6c7e
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:14.4
occ:1.00
 NE2 D:HIS696 2.1 10.1 1.0
OD2 D:ASP697 2.1 12.2 1.0
NE2 D:HIS660 2.1 10.9 1.0
O D:HOH1227 2.1 12.4 1.0
OD1 D:ASP808 2.2 14.2 1.0
O D:HOH1116 2.4 13.5 1.0
CD2 D:HIS696 3.0 10.4 1.0
CG D:ASP808 3.1 16.4 1.0
CE1 D:HIS696 3.1 14.0 1.0
CD2 D:HIS660 3.1 13.1 1.0
CE1 D:HIS660 3.1 11.4 1.0
CG D:ASP697 3.1 11.3 1.0
OD2 D:ASP808 3.3 18.7 1.0
OD1 D:ASP697 3.7 11.5 1.0
MG D:MG1003 3.9 11.9 1.0
O D:HOH1161 4.1 14.1 1.0
CD2 D:HIS656 4.1 11.9 1.0
O D:HOH1272 4.2 11.6 1.0
ND1 D:HIS696 4.2 14.5 1.0
CG D:HIS696 4.2 11.3 1.0
ND1 D:HIS660 4.2 14.6 1.0
NE2 D:HIS656 4.2 13.2 1.0
CG D:HIS660 4.2 11.9 1.0
CB D:ASP697 4.3 11.3 1.0
CB D:ASP808 4.5 11.2 1.0
O D:HOH1127 4.7 11.4 1.0
CA D:ASP808 4.9 11.6 1.0
CG2 D:VAL664 4.9 13.6 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 Oct 28 18:31:59 2024

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