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Zinc in PDB 7abj: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361, PDB code: 7abj 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) 84.41 / 2.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.999, 111.037, 160.565, 90, 90, 90
R / Rfree (%) 18.1 / 21.8

Other elements in 7abj:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361 (pdb code 7abj). 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-1361, PDB code: 7abj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7abj

Go back to Zinc Binding Sites List in 7abj
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361


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-1361 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:40.4
occ:1.00
 OD2 A:ASP201 2.0 31.6 1.0
OD1 A:ASP318 2.2 38.8 1.0
NE2 A:HIS164 2.2 30.8 1.0
NE2 A:HIS200 2.2 39.0 1.0
O A:HOH668 2.4 33.9 1.0
O A:HOH655 2.5 44.4 1.0
CG A:ASP318 3.0 37.3 1.0
CD2 A:HIS200 3.0 36.0 1.0
CG A:ASP201 3.1 34.2 1.0
CE1 A:HIS164 3.2 33.0 1.0
CD2 A:HIS164 3.2 34.6 1.0
OD2 A:ASP318 3.3 48.8 1.0
CE1 A:HIS200 3.3 36.0 1.0
OD1 A:ASP201 3.6 32.3 1.0
O A:HOH695 3.8 36.8 1.0
O A:HOH697 3.8 47.2 1.0
MG A:MG502 3.8 29.3 1.0
CG A:HIS200 4.2 35.5 1.0
CD2 A:HIS160 4.3 40.8 1.0
ND1 A:HIS164 4.3 30.0 1.0
CB A:ASP201 4.3 33.2 1.0
CG A:HIS164 4.3 31.5 1.0
ND1 A:HIS200 4.3 37.2 1.0
CB A:ASP318 4.4 37.2 1.0
NE2 A:HIS160 4.5 38.0 1.0
O A:HOH703 4.5 66.7 1.0
O A:HOH623 4.7 32.5 1.0
CG2 A:VAL168 4.7 38.1 1.0
CA A:ASP318 4.9 38.1 1.0

Zinc binding site 2 out of 4 in 7abj

Go back to Zinc Binding Sites List in 7abj
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361


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-1361 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:44.6
occ:1.00
 O B:HOH623 1.9 33.2 1.0
OD2 B:ASP201 2.1 39.2 1.0
NE2 B:HIS164 2.1 33.1 1.0
OD1 B:ASP318 2.2 41.3 1.0
O B:HOH699 2.2 38.1 1.0
NE2 B:HIS200 2.3 39.1 1.0
CG B:ASP201 3.1 33.8 1.0
CG B:ASP318 3.1 43.6 1.0
CE1 B:HIS164 3.1 35.5 1.0
CD2 B:HIS200 3.1 35.5 1.0
CD2 B:HIS164 3.2 36.0 1.0
CE1 B:HIS200 3.3 38.7 1.0
OD2 B:ASP318 3.4 48.2 1.0
OD1 B:ASP201 3.5 36.7 1.0
MG B:MG502 3.8 31.8 1.0
O B:HOH684 3.9 36.4 1.0
O B:HOH626 4.0 45.8 1.0
CD2 B:HIS160 4.2 41.2 1.0
ND1 B:HIS164 4.2 36.8 1.0
CB B:ASP201 4.3 37.1 1.0
CG B:HIS164 4.3 35.4 1.0
CG B:HIS200 4.3 37.8 1.0
ND1 B:HIS200 4.4 39.5 1.0
CB B:ASP318 4.4 44.1 1.0
NE2 B:HIS160 4.5 37.0 1.0
CG2 B:VAL168 4.7 46.3 1.0
O B:HOH613 4.7 37.2 1.0
CA B:ASP318 5.0 44.2 1.0

Zinc binding site 3 out of 4 in 7abj

Go back to Zinc Binding Sites List in 7abj
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361


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-1361 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:41.8
occ:1.00
 OD2 C:ASP201 2.1 36.6 1.0
OD1 C:ASP318 2.2 39.8 1.0
NE2 C:HIS164 2.2 32.6 1.0
O C:HOH616 2.3 34.5 1.0
O C:HOH658 2.3 39.1 1.0
NE2 C:HIS200 2.3 37.7 1.0
CG C:ASP318 3.1 39.5 1.0
CG C:ASP201 3.1 34.9 1.0
CD2 C:HIS200 3.1 34.5 1.0
CE1 C:HIS164 3.2 30.4 1.0
CD2 C:HIS164 3.2 30.7 1.0
OD2 C:ASP318 3.3 43.3 1.0
CE1 C:HIS200 3.4 35.7 1.0
OD1 C:ASP201 3.5 33.0 1.0
MG C:MG504 3.7 27.9 1.0
O C:HOH646 3.8 31.6 1.0
O C:HOH647 4.1 43.2 1.0
CD2 C:HIS160 4.2 34.4 1.0
CG C:HIS200 4.3 34.5 1.0
ND1 C:HIS164 4.3 31.0 1.0
CB C:ASP201 4.3 32.9 1.0
CG C:HIS164 4.4 31.1 1.0
ND1 C:HIS200 4.4 34.8 1.0
NE2 C:HIS160 4.4 32.6 1.0
CB C:ASP318 4.4 45.2 1.0
O C:HOH613 4.7 32.3 1.0
CG2 C:VAL168 4.8 41.7 1.0
CA C:ASP318 5.0 39.2 1.0

Zinc binding site 4 out of 4 in 7abj

Go back to Zinc Binding Sites List in 7abj
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361


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-1361 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:36.9
occ:1.00
 OD2 D:ASP201 2.1 32.5 1.0
OD1 D:ASP318 2.2 34.3 1.0
NE2 D:HIS164 2.2 26.4 1.0
O D:HOH660 2.2 28.9 1.0
NE2 D:HIS200 2.3 32.2 1.0
O D:HOH722 2.3 36.7 1.0
CG D:ASP318 3.1 35.4 1.0
CG D:ASP201 3.1 33.9 1.0
CD2 D:HIS200 3.1 29.7 1.0
CE1 D:HIS164 3.2 28.3 1.0
CD2 D:HIS164 3.2 31.8 1.0
OD2 D:ASP318 3.3 42.5 1.0
CE1 D:HIS200 3.3 31.0 1.0
OD1 D:ASP201 3.5 29.6 1.0
O D:HOH689 3.7 36.5 1.0
MG D:MG502 3.8 26.3 1.0
CD2 D:HIS160 4.2 39.2 1.0
O D:HOH668 4.3 41.8 1.0
CG D:HIS200 4.3 29.7 1.0
CB D:ASP201 4.3 33.0 1.0
ND1 D:HIS164 4.3 29.7 1.0
CG D:HIS164 4.3 28.2 1.0
ND1 D:HIS200 4.4 31.2 1.0
CB D:ASP318 4.4 33.6 1.0
NE2 D:HIS160 4.5 41.0 1.0
O D:HOH744 4.5 67.6 1.0
O D:HOH658 4.7 27.1 1.0
CG2 D:VAL168 4.7 33.2 1.0
CA D:ASP318 5.0 30.5 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-1361 To Be Published.
Page generated: Thu Aug 21 22:17:51 2025

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