Atomistry » Zinc » PDB 6c6t-6cee » 6c7e
Atomistry »
  Zinc »
    PDB 6c6t-6cee »
      6c7e »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy