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Zinc 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:

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 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6c7d

Go back to Zinc Binding Sites List in 6c7d
Zinc 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 Zinc with other atoms in the Zn 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:Zn2002

b:19.9
occ:1.00
 OD2 A:ASP697 2.1 21.0 1.0
NE2 A:HIS696 2.1 13.4 1.0
OD1 A:ASP808 2.2 15.1 1.0
NE2 A:HIS660 2.2 17.8 1.0
O A:HOH2211 2.2 16.1 1.0
O A:HOH2125 2.5 16.1 1.0
CD2 A:HIS696 3.0 17.3 1.0
CD2 A:HIS660 3.1 21.4 1.0
CG A:ASP808 3.1 19.4 1.0
CG A:ASP697 3.2 15.2 1.0
CE1 A:HIS696 3.2 13.8 1.0
CE1 A:HIS660 3.2 14.9 1.0
OD2 A:ASP808 3.4 21.8 1.0
OD1 A:ASP697 3.8 15.5 1.0
O A:HOH2172 4.0 16.8 1.0
MG A:MG2003 4.0 15.2 1.0
CD2 A:HIS656 4.1 14.6 1.0
CG A:HIS696 4.2 10.2 1.0
O A:HOH2182 4.2 14.7 1.0
ND1 A:HIS696 4.2 10.4 1.0
CB A:ASP697 4.3 12.8 1.0
ND1 A:HIS660 4.3 17.7 1.0
CG A:HIS660 4.3 17.5 1.0
NE2 A:HIS656 4.4 19.8 1.0
CB A:ASP808 4.5 14.7 1.0
CG2 A:VAL664 4.7 12.8 1.0
O A:HOH2114 4.7 16.8 1.0
CA A:ASP808 4.8 16.8 1.0
O A:ASP808 4.9 15.7 1.0

Zinc binding site 2 out of 4 in 6c7d

Go back to Zinc Binding Sites List in 6c7d
Zinc 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 Zinc with other atoms in the Zn 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:Zn2002

b:19.5
occ:1.00
 NE2 B:HIS660 2.1 18.8 1.0
NE2 B:HIS696 2.1 11.1 1.0
OD2 B:ASP697 2.2 15.9 1.0
OD1 B:ASP808 2.2 16.0 1.0
O B:HOH2107 2.3 17.9 1.0
O B:HOH2180 2.3 15.2 1.0
CD2 B:HIS696 3.0 15.0 1.0
CG B:ASP808 3.1 17.9 1.0
CE1 B:HIS660 3.1 16.9 1.0
CD2 B:HIS660 3.1 14.9 1.0
CG B:ASP697 3.2 15.3 1.0
CE1 B:HIS696 3.2 13.5 1.0
OD2 B:ASP808 3.3 19.2 1.0
OD1 B:ASP697 3.6 15.4 1.0
MG B:MG2003 4.0 18.2 1.0
O B:HOH2154 4.0 17.2 1.0
CD2 B:HIS656 4.2 15.0 1.0
O B:HOH2161 4.2 14.3 1.0
CG B:HIS696 4.2 10.8 1.0
ND1 B:HIS660 4.2 13.6 1.0
ND1 B:HIS696 4.3 13.9 1.0
CG B:HIS660 4.3 14.8 1.0
NE2 B:HIS656 4.3 21.3 1.0
CB B:ASP697 4.4 15.6 1.0
CB B:ASP808 4.5 15.9 1.0
CG2 B:VAL664 4.8 10.3 1.0
O B:HOH2113 4.8 15.0 1.0
CA B:ASP808 4.9 15.8 1.0
O B:ASP808 5.0 19.4 1.0

Zinc binding site 3 out of 4 in 6c7d

Go back to Zinc Binding Sites List in 6c7d
Zinc 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 Zinc with other atoms in the Zn 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:Zn2002

b:24.1
occ:1.00
 OD2 C:ASP697 2.0 20.8 1.0
NE2 C:HIS696 2.1 17.5 1.0
OD1 C:ASP808 2.1 20.9 1.0
NE2 C:HIS660 2.1 15.9 1.0
O C:HOH2144 2.2 19.9 1.0
O C:HOH2118 2.4 25.0 1.0
CG C:ASP808 3.0 20.7 1.0
CD2 C:HIS660 3.0 16.3 1.0
CD2 C:HIS696 3.1 22.0 1.0
CG C:ASP697 3.1 24.7 1.0
CE1 C:HIS696 3.1 18.1 1.0
CE1 C:HIS660 3.2 20.2 1.0
OD2 C:ASP808 3.2 24.4 1.0
OD1 C:ASP697 3.7 18.5 1.0
MG C:MG2003 4.0 19.9 1.0
O C:HOH2119 4.1 21.1 1.0
CD2 C:HIS656 4.1 23.0 1.0
ND1 C:HIS696 4.2 17.9 1.0
CG C:HIS696 4.2 16.7 1.0
CG C:HIS660 4.2 21.1 1.0
CB C:ASP697 4.3 18.5 1.0
ND1 C:HIS660 4.3 19.5 1.0
NE2 C:HIS656 4.3 21.0 1.0
O C:HOH2156 4.3 16.6 1.0
CB C:ASP808 4.4 19.1 1.0
CA C:ASP808 4.8 21.0 1.0
CG2 C:VAL664 4.9 19.4 1.0
O C:HOH2123 4.9 17.0 1.0
O C:ASP808 5.0 22.8 1.0

Zinc binding site 4 out of 4 in 6c7d

Go back to Zinc Binding Sites List in 6c7d
Zinc 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 Zinc with other atoms in the Zn 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:Zn2002

b:23.1
occ:1.00
 OD2 D:ASP697 2.0 25.9 1.0
OD1 D:ASP808 2.0 21.3 1.0
NE2 D:HIS660 2.1 21.5 1.0
NE2 D:HIS696 2.2 19.2 1.0
O D:HOH2124 2.4 19.8 1.0
O D:HOH2119 2.5 18.6 1.0
CG D:ASP808 3.0 27.0 1.0
CD2 D:HIS696 3.1 22.0 1.0
CE1 D:HIS660 3.1 24.2 1.0
CG D:ASP697 3.1 22.7 1.0
CD2 D:HIS660 3.1 24.6 1.0
CE1 D:HIS696 3.2 21.1 1.0
OD2 D:ASP808 3.2 28.0 1.0
OD1 D:ASP697 3.7 17.9 1.0
MG D:MG2003 3.9 18.3 1.0
O D:HOH2157 4.1 18.8 1.0
CD2 D:HIS656 4.1 16.8 1.0
O D:HOH2193 4.2 17.7 1.0
ND1 D:HIS660 4.2 21.8 1.0
CG D:HIS696 4.2 20.2 1.0
ND1 D:HIS696 4.2 19.3 1.0
CB D:ASP697 4.3 19.4 1.0
CG D:HIS660 4.3 21.3 1.0
NE2 D:HIS656 4.3 18.8 1.0
CB D:ASP808 4.4 18.5 1.0
O D:HOH2115 4.7 16.0 1.0
CG2 D:VAL664 4.8 22.5 1.0
CA D:ASP808 4.8 18.3 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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