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Zinc in PDB 7abd: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768, PDB code: 7abd 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) 84.24 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.703, 110.935, 160.626, 90, 90, 90
R / Rfree (%) 17.3 / 22.7

Other elements in 7abd:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768 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-768 (pdb code 7abd). 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-768, PDB code: 7abd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7abd

Go back to Zinc Binding Sites List in 7abd
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768


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-768 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:40.9
occ:1.00
 OD2 A:ASP201 2.1 35.8 1.0
NE2 A:HIS164 2.1 34.7 1.0
NE2 A:HIS200 2.2 35.6 1.0
OD1 A:ASP318 2.2 42.9 1.0
O A:HOH609 2.4 47.2 1.0
O A:HOH603 2.4 34.5 1.0
CG A:ASP318 3.0 41.6 1.0
CG A:ASP201 3.1 34.6 1.0
CD2 A:HIS200 3.1 35.0 1.0
CE1 A:HIS164 3.1 31.7 1.0
CD2 A:HIS164 3.1 33.0 1.0
CE1 A:HIS200 3.2 35.5 1.0
OD2 A:ASP318 3.2 44.2 1.0
OD1 A:ASP201 3.5 32.1 1.0
O A:HOH661 3.6 38.5 1.0
MG A:MG502 3.7 26.7 1.0
O A:HOH632 3.8 42.2 1.0
CD2 A:HIS160 4.2 37.1 1.0
CG A:HIS200 4.2 34.6 1.0
ND1 A:HIS164 4.2 33.9 1.0
ND1 A:HIS200 4.2 32.3 1.0
CG A:HIS164 4.3 33.7 1.0
CB A:ASP201 4.3 32.3 1.0
CB A:ASP318 4.4 39.9 1.0
NE2 A:HIS160 4.4 34.7 1.0
O A:HOH619 4.6 27.2 1.0
CG2 A:VAL168 4.8 36.0 1.0
CA A:ASP318 5.0 41.7 1.0

Zinc binding site 2 out of 4 in 7abd

Go back to Zinc Binding Sites List in 7abd
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768


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-768 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:41.8
occ:1.00
 OD2 B:ASP201 2.1 38.5 1.0
NE2 B:HIS164 2.1 31.6 1.0
NE2 B:HIS200 2.2 40.3 1.0
OD1 B:ASP318 2.2 46.2 1.0
O B:HOH618 2.2 28.7 1.0
O B:HOH631 2.3 41.9 1.0
CE1 B:HIS164 3.0 34.2 1.0
CG B:ASP201 3.0 34.9 1.0
CG B:ASP318 3.1 41.3 1.0
CD2 B:HIS200 3.1 40.0 1.0
CD2 B:HIS164 3.1 29.6 1.0
CE1 B:HIS200 3.2 39.5 1.0
OD2 B:ASP318 3.3 56.8 1.0
O B:HOH659 3.5 35.9 1.0
OD1 B:ASP201 3.5 31.2 1.0
MG B:MG502 3.9 28.8 1.0
O B:HOH627 3.9 39.0 1.0
CD2 B:HIS160 4.1 38.0 1.0
ND1 B:HIS164 4.2 34.8 1.0
CG B:HIS164 4.2 33.9 1.0
CB B:ASP201 4.2 34.7 1.0
CG B:HIS200 4.3 37.5 1.0
ND1 B:HIS200 4.3 37.7 1.0
NE2 B:HIS160 4.4 38.8 1.0
CB B:ASP318 4.4 43.4 1.0
O B:HOH620 4.7 34.9 1.0
CG2 B:VAL168 4.7 42.0 1.0
CA B:ASP318 5.0 44.3 1.0

Zinc binding site 3 out of 4 in 7abd

Go back to Zinc Binding Sites List in 7abd
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768


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-768 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:42.3
occ:1.00
 OD2 C:ASP201 2.1 44.3 1.0
NE2 C:HIS164 2.1 39.2 1.0
NE2 C:HIS200 2.2 37.7 1.0
O C:HOH642 2.2 39.3 1.0
OD1 C:ASP318 2.2 36.5 1.0
O C:HOH604 2.3 29.9 1.0
CG C:ASP318 3.0 42.5 1.0
CG C:ASP201 3.1 35.7 1.0
CD2 C:HIS200 3.1 36.0 1.0
CE1 C:HIS164 3.1 36.5 1.0
CD2 C:HIS164 3.1 35.0 1.0
CE1 C:HIS200 3.2 43.6 1.0
OD2 C:ASP318 3.2 45.4 1.0
MG C:MG502 3.5 25.2 1.0
OD1 C:ASP201 3.5 33.8 1.0
O C:HOH641 3.8 39.5 1.0
O C:HOH633 4.0 40.4 1.0
CD2 C:HIS160 4.2 43.2 1.0
ND1 C:HIS164 4.2 35.7 1.0
CG C:HIS200 4.2 37.0 1.0
ND1 C:HIS200 4.3 36.2 1.0
CG C:HIS164 4.3 32.3 1.0
CB C:ASP201 4.3 32.2 1.0
CB C:ASP318 4.4 43.6 1.0
NE2 C:HIS160 4.4 40.5 1.0
O C:HOH601 4.5 24.7 1.0
CG2 C:VAL168 4.8 36.8 1.0
CA C:ASP318 5.0 44.4 1.0

Zinc binding site 4 out of 4 in 7abd

Go back to Zinc Binding Sites List in 7abd
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768


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-768 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:35.8
occ:1.00
 OD2 D:ASP201 2.1 39.4 1.0
NE2 D:HIS164 2.1 27.6 1.0
O D:HOH661 2.1 43.3 1.0
NE2 D:HIS200 2.2 33.0 1.0
OD1 D:ASP318 2.2 36.3 1.0
O D:HOH610 2.3 22.1 1.0
CG D:ASP201 3.0 35.6 1.0
CG D:ASP318 3.0 37.7 1.0
CE1 D:HIS164 3.1 27.2 1.0
CD2 D:HIS200 3.1 28.7 1.0
CD2 D:HIS164 3.1 25.6 1.0
CE1 D:HIS200 3.2 32.9 1.0
OD2 D:ASP318 3.2 39.1 1.0
OD1 D:ASP201 3.5 37.1 1.0
MG D:MG502 3.7 23.6 1.0
O D:HOH663 3.8 36.9 1.0
O D:HOH634 3.8 40.4 1.0
CD2 D:HIS160 4.2 40.2 1.0
ND1 D:HIS164 4.2 27.9 1.0
CG D:HIS164 4.2 28.0 1.0
CG D:HIS200 4.3 28.7 1.0
CB D:ASP201 4.3 36.9 1.0
ND1 D:HIS200 4.3 26.8 1.0
CB D:ASP318 4.4 31.5 1.0
NE2 D:HIS160 4.4 36.4 1.0
O D:HOH618 4.6 23.1 1.0
CG2 D:VAL168 4.7 33.8 1.0
CA D:ASP318 5.0 31.9 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-768 To Be Published.
Page generated: Tue Oct 29 16:32:56 2024

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