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Zinc in PDB 7aag: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617, PDB code: 7aag was solved by A.K.Singh, A.R.Blaazer, L.Zara, I.J.P.De Esch, R.Leurs, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.94 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.44, 110.82, 161.03, 90, 90, 90
R / Rfree (%) 16.7 / 19.7

Other elements in 7aag:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617 also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617 (pdb code 7aag). 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 4D2 Catalytic Domain with Inhibitor Npd-617, PDB code: 7aag:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7aag

Go back to Zinc Binding Sites List in 7aag
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617


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 4D2 Catalytic Domain with Inhibitor Npd-617 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.9
occ:1.00
 OD2 A:ASP201 2.1 17.1 1.0
O A:HOH675 2.2 19.6 1.0
NE2 A:HIS164 2.2 17.6 1.0
NE2 A:HIS200 2.2 18.8 1.0
OD1 A:ASP318 2.2 21.5 1.0
O A:HOH716 2.3 23.1 1.0
CD2 A:HIS200 3.1 20.4 1.0
CG A:ASP318 3.1 22.6 1.0
CG A:ASP201 3.1 19.0 1.0
CD2 A:HIS164 3.2 18.9 1.0
CE1 A:HIS164 3.2 18.7 1.0
CE1 A:HIS200 3.2 19.2 1.0
OD2 A:ASP318 3.3 28.4 1.0
OD1 A:ASP201 3.6 19.8 1.0
MG A:MG502 3.7 13.8 1.0
O A:HOH770 4.0 21.5 1.0
CD2 A:HIS160 4.1 23.7 1.0
O A:HOH655 4.2 22.4 1.0
CG A:HIS200 4.3 18.9 1.0
CB A:ASP201 4.3 18.8 1.0
ND1 A:HIS164 4.3 17.7 1.0
CG A:HIS164 4.3 18.7 1.0
ND1 A:HIS200 4.3 20.2 1.0
NE2 A:HIS160 4.3 21.5 1.0
CB A:ASP318 4.5 20.8 1.0
O A:HOH673 4.7 16.9 1.0
CG2 A:VAL168 4.7 19.8 1.0
CA A:ASP318 5.0 21.0 1.0

Zinc binding site 2 out of 4 in 7aag

Go back to Zinc Binding Sites List in 7aag
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617


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 4D2 Catalytic Domain with Inhibitor Npd-617 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:23.6
occ:1.00
 O B:HOH635 2.1 19.4 1.0
NE2 B:HIS164 2.1 20.6 1.0
OD2 B:ASP201 2.1 18.8 1.0
NE2 B:HIS200 2.2 17.6 1.0
OD1 B:ASP318 2.2 20.9 1.0
O B:HOH738 2.2 20.2 1.0
CD2 B:HIS200 3.1 19.1 1.0
CG B:ASP318 3.1 20.0 1.0
CG B:ASP201 3.1 18.8 1.0
CE1 B:HIS164 3.2 19.8 1.0
CD2 B:HIS164 3.2 20.9 1.0
CE1 B:HIS200 3.2 18.2 1.0
OD2 B:ASP318 3.4 25.3 1.0
OD1 B:ASP201 3.6 19.1 1.0
MG B:MG503 3.8 13.4 1.0
O B:HOH764 4.0 20.2 1.0
O B:HOH698 4.1 20.8 1.0
CD2 B:HIS160 4.1 21.2 1.0
CG B:HIS200 4.2 18.2 1.0
ND1 B:HIS164 4.3 19.5 1.0
ND1 B:HIS200 4.3 17.6 1.0
CG B:HIS164 4.3 19.6 1.0
CB B:ASP201 4.3 20.0 1.0
NE2 B:HIS160 4.3 22.0 1.0
CB B:ASP318 4.5 22.1 1.0
O B:HOH675 4.7 20.9 1.0
CG2 B:VAL168 4.7 20.6 1.0
CA B:ASP318 5.0 22.9 1.0

Zinc binding site 3 out of 4 in 7aag

Go back to Zinc Binding Sites List in 7aag
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617


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 4D2 Catalytic Domain with Inhibitor Npd-617 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn504

b:25.1
occ:1.00
 OD2 C:ASP201 2.1 20.7 1.0
NE2 C:HIS164 2.2 18.3 1.0
NE2 C:HIS200 2.2 22.9 1.0
OD1 C:ASP318 2.2 22.2 1.0
O C:HOH631 2.2 21.0 1.0
O C:HOH702 2.3 21.7 1.0
CD2 C:HIS200 3.1 20.1 1.0
CG C:ASP318 3.1 24.2 1.0
CG C:ASP201 3.1 19.6 1.0
CE1 C:HIS164 3.2 21.3 1.0
CD2 C:HIS164 3.2 22.2 1.0
CE1 C:HIS200 3.2 19.9 1.0
OD2 C:ASP318 3.3 25.9 1.0
OD1 C:ASP201 3.6 21.6 1.0
MG C:MG505 3.8 14.4 1.0
O C:HOH733 3.9 21.4 1.0
CD2 C:HIS160 4.1 24.7 1.0
O C:HOH678 4.1 25.1 1.0
CG C:HIS200 4.2 19.6 1.0
ND1 C:HIS164 4.3 19.4 1.0
ND1 C:HIS200 4.3 20.6 1.0
CB C:ASP201 4.3 20.1 1.0
CG C:HIS164 4.3 19.3 1.0
NE2 C:HIS160 4.3 23.1 1.0
CB C:ASP318 4.5 23.5 1.0
O C:HOH632 4.7 20.2 1.0
CG2 C:VAL168 4.7 21.7 1.0
CA C:ASP318 5.0 23.1 1.0

Zinc binding site 4 out of 4 in 7aag

Go back to Zinc Binding Sites List in 7aag
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617


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 4D2 Catalytic Domain with Inhibitor Npd-617 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:22.2
occ:1.00
 OD2 D:ASP201 2.1 17.3 1.0
O D:HOH639 2.2 18.7 1.0
NE2 D:HIS164 2.2 15.9 1.0
NE2 D:HIS200 2.2 15.7 1.0
OD1 D:ASP318 2.2 18.2 1.0
O D:HOH691 2.3 21.5 1.0
CG D:ASP318 3.1 20.6 1.0
CD2 D:HIS200 3.1 14.6 1.0
CG D:ASP201 3.1 20.0 1.0
CE1 D:HIS164 3.1 16.9 1.0
CD2 D:HIS164 3.2 17.6 1.0
CE1 D:HIS200 3.2 17.3 1.0
OD2 D:ASP318 3.3 24.6 1.0
OD1 D:ASP201 3.6 18.4 1.0
MG D:MG504 3.8 11.6 1.0
O D:HOH777 3.9 20.2 1.0
CD2 D:HIS160 4.1 22.2 1.0
O D:HOH694 4.2 20.6 1.0
CG D:HIS200 4.2 15.3 1.0
ND1 D:HIS164 4.3 15.9 1.0
ND1 D:HIS200 4.3 16.3 1.0
CG D:HIS164 4.3 16.9 1.0
CB D:ASP201 4.3 18.6 1.0
NE2 D:HIS160 4.3 22.1 1.0
CB D:ASP318 4.4 19.0 1.0
O D:HOH796 4.5 50.4 1.0
O D:HOH687 4.7 15.8 1.0
CG2 D:VAL168 4.7 18.9 1.0
CA D:ASP318 4.9 18.9 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-617 To Be Published.
Page generated: Tue Oct 29 16:30:07 2024

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