Atomistry » Zinc » PDB 6c6t-6cee » 6c7i
Atomistry »
  Zinc »
    PDB 6c6t-6cee »
      6c7i »

Zinc in PDB 6c7i: Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-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 1-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7i 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) 47.40 / 1.71
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.902, 72.682, 90.816, 109.33, 91.13, 91.06
R / Rfree (%) 17.1 / 21.4

Other elements in 6c7i:

The structure of Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[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-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide (pdb code 6c7i). 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-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6c7i

Go back to Zinc Binding Sites List in 6c7i
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[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-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:16.8
occ:1.00
 OD2 A:ASP697 2.1 13.6 1.0
NE2 A:HIS696 2.1 8.9 1.0
OD1 A:ASP808 2.1 14.7 1.0
NE2 A:HIS660 2.2 18.1 1.0
O A:HOH1136 2.2 15.4 1.0
O A:HOH1249 2.2 12.3 1.0
CG A:ASP808 3.0 14.2 1.0
CD2 A:HIS696 3.0 11.9 1.0
CG A:ASP697 3.1 11.5 1.0
CD2 A:HIS660 3.1 13.8 1.0
CE1 A:HIS696 3.1 8.8 1.0
CE1 A:HIS660 3.2 13.8 1.0
OD2 A:ASP808 3.3 16.2 1.0
OD1 A:ASP697 3.7 12.3 1.0
MG A:MG1003 3.9 13.3 1.0
O A:HOH1142 4.0 15.3 1.0
CD2 A:HIS656 4.2 11.7 1.0
O A:HOH1265 4.2 13.3 1.0
CG A:HIS696 4.2 10.1 1.0
ND1 A:HIS696 4.2 10.7 1.0
ND1 A:HIS660 4.3 15.7 1.0
CB A:ASP697 4.3 13.1 1.0
CG A:HIS660 4.3 14.4 1.0
NE2 A:HIS656 4.4 16.3 1.0
CB A:ASP808 4.5 14.1 1.0
O A:HOH1134 4.8 10.5 1.0
CG2 A:VAL664 4.8 14.0 1.0
CA A:ASP808 4.9 14.5 1.0
O A:ASP808 4.9 16.0 1.0

Zinc binding site 2 out of 4 in 6c7i

Go back to Zinc Binding Sites List in 6c7i
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[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-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:16.9
occ:1.00
 OD2 B:ASP697 2.0 13.4 1.0
OD1 B:ASP808 2.1 13.9 1.0
NE2 B:HIS696 2.1 8.8 1.0
NE2 B:HIS660 2.1 14.6 1.0
O B:HOH1254 2.2 13.0 1.0
O B:HOH1110 2.4 12.5 1.0
CG B:ASP808 3.1 19.2 1.0
CD2 B:HIS696 3.1 11.1 1.0
CD2 B:HIS660 3.1 12.2 1.0
CG B:ASP697 3.1 13.3 1.0
CE1 B:HIS696 3.1 13.1 1.0
CE1 B:HIS660 3.1 12.8 1.0
OD2 B:ASP808 3.3 17.5 1.0
OD1 B:ASP697 3.6 12.2 1.0
MG B:MG1003 3.9 13.4 1.0
O B:HOH1151 4.1 17.6 1.0
O B:HOH1260 4.1 13.0 1.0
CD2 B:HIS656 4.1 13.9 1.0
ND1 B:HIS696 4.2 13.0 1.0
CG B:HIS696 4.2 11.6 1.0
ND1 B:HIS660 4.2 13.7 1.0
CG B:HIS660 4.2 13.4 1.0
CB B:ASP697 4.3 13.3 1.0
NE2 B:HIS656 4.3 13.2 1.0
CB B:ASP808 4.5 16.7 1.0
O B:HOH1119 4.8 11.6 1.0
CA B:ASP808 4.8 15.8 1.0
CG2 B:VAL664 4.8 11.4 1.0
O B:ASP808 4.9 18.2 1.0

Zinc binding site 3 out of 4 in 6c7i

Go back to Zinc Binding Sites List in 6c7i
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[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-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:18.3
occ:1.00
 OD2 C:ASP697 2.0 13.2 1.0
OD1 C:ASP808 2.1 15.3 1.0
NE2 C:HIS660 2.1 15.8 1.0
NE2 C:HIS696 2.1 13.8 1.0
O C:HOH1193 2.2 14.6 1.0
O C:HOH1103 2.3 15.9 1.0
CG C:ASP808 3.0 15.7 1.0
CD2 C:HIS696 3.1 17.2 1.0
CD2 C:HIS660 3.1 13.2 1.0
CE1 C:HIS660 3.1 14.5 1.0
CG C:ASP697 3.1 15.1 1.0
CE1 C:HIS696 3.1 14.7 1.0
OD2 C:ASP808 3.2 20.4 1.0
OD1 C:ASP697 3.7 12.7 1.0
MG C:MG1003 4.0 13.4 1.0
O C:HOH1169 4.1 18.2 1.0
CD2 C:HIS656 4.1 20.9 1.0
ND1 C:HIS660 4.2 16.4 1.0
O C:HOH1246 4.2 12.9 1.0
CG C:HIS696 4.2 12.2 1.0
ND1 C:HIS696 4.2 12.8 1.0
CG C:HIS660 4.2 15.8 1.0
CB C:ASP697 4.3 13.9 1.0
NE2 C:HIS656 4.3 18.7 1.0
CB C:ASP808 4.4 15.8 1.0
O C:HOH1134 4.7 14.6 1.0
CA C:ASP808 4.8 18.9 1.0
CG2 C:VAL664 4.9 12.5 1.0

Zinc binding site 4 out of 4 in 6c7i

Go back to Zinc Binding Sites List in 6c7i
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[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-Chloro-5- Methoxy-Phenyl)-N-Isobutyl-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:17.0
occ:1.00
 OD2 D:ASP697 2.1 14.8 1.0
NE2 D:HIS696 2.1 12.5 1.0
OD1 D:ASP808 2.1 15.5 1.0
NE2 D:HIS660 2.1 17.9 1.0
O D:HOH1184 2.2 13.2 1.0
O D:HOH1144 2.4 18.1 1.0
CD2 D:HIS696 3.0 11.9 1.0
CG D:ASP808 3.0 19.1 1.0
CE1 D:HIS696 3.1 12.9 1.0
CD2 D:HIS660 3.1 14.9 1.0
CG D:ASP697 3.1 13.4 1.0
CE1 D:HIS660 3.2 17.2 1.0
OD2 D:ASP808 3.3 20.0 1.0
OD1 D:ASP697 3.6 11.1 1.0
MG D:MG1003 3.9 12.4 1.0
O D:HOH1175 4.1 15.3 1.0
O D:HOH1251 4.1 12.6 1.0
CD2 D:HIS656 4.2 15.3 1.0
ND1 D:HIS696 4.2 13.5 1.0
CG D:HIS696 4.2 11.3 1.0
ND1 D:HIS660 4.3 14.4 1.0
CG D:HIS660 4.3 15.5 1.0
NE2 D:HIS656 4.3 14.4 1.0
CB D:ASP697 4.3 14.5 1.0
CB D:ASP808 4.5 14.0 1.0
O D:HOH1140 4.7 11.5 1.0
CG2 D:VAL664 4.8 17.8 1.0
CA D:ASP808 4.8 15.8 1.0
O D:ASP808 5.0 15.9 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 18:32:00 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