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Zinc in PDB 7ab9: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656, PDB code: 7ab9 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) 91.69 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.168, 111.797, 160.261, 90, 90, 90
R / Rfree (%) 18.5 / 22.3

Other elements in 7ab9:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656 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-656 (pdb code 7ab9). 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-656, PDB code: 7ab9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7ab9

Go back to Zinc Binding Sites List in 7ab9
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656


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-656 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:37.5
occ:1.00
 OD2 A:ASP201 2.1 30.6 1.0
NE2 A:HIS200 2.1 36.9 1.0
NE2 A:HIS164 2.2 30.1 1.0
OD1 A:ASP318 2.2 35.8 1.0
O A:HOH613 2.3 33.3 1.0
O A:HOH659 2.4 40.0 1.0
CG A:ASP318 3.0 36.5 1.0
CD2 A:HIS200 3.0 33.5 1.0
CG A:ASP201 3.1 30.6 1.0
CE1 A:HIS164 3.2 33.3 1.0
OD2 A:ASP318 3.2 43.5 1.0
CD2 A:HIS164 3.2 29.6 1.0
CE1 A:HIS200 3.2 38.4 1.0
OD1 A:ASP201 3.5 28.9 1.0
MG A:MG502 3.8 24.4 1.0
O A:HOH693 3.9 34.2 1.0
O A:HOH663 4.1 46.5 1.0
CD2 A:HIS160 4.1 33.1 1.0
CG A:HIS200 4.2 33.7 1.0
ND1 A:HIS200 4.2 37.2 1.0
CB A:ASP201 4.3 31.9 1.0
ND1 A:HIS164 4.3 31.1 1.0
CG A:HIS164 4.3 31.9 1.0
NE2 A:HIS160 4.4 35.0 1.0
CB A:ASP318 4.4 35.7 1.0
O A:HOH705 4.4 62.5 1.0
CG2 A:VAL168 4.7 31.1 1.0
O A:HOH615 4.7 27.4 1.0
CA A:ASP318 5.0 36.5 1.0

Zinc binding site 2 out of 4 in 7ab9

Go back to Zinc Binding Sites List in 7ab9
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656


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-656 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:43.5
occ:1.00
 O B:HOH622 2.0 33.2 1.0
NE2 B:HIS164 2.1 29.0 1.0
OD2 B:ASP201 2.1 41.8 1.0
OD1 B:ASP318 2.2 40.2 1.0
NE2 B:HIS200 2.2 38.1 1.0
O B:HOH680 2.3 32.5 1.0
CG B:ASP318 3.1 41.1 1.0
CG B:ASP201 3.1 34.1 1.0
CE1 B:HIS164 3.1 32.6 1.0
CD2 B:HIS200 3.1 32.4 1.0
CD2 B:HIS164 3.1 31.4 1.0
OD2 B:ASP318 3.2 47.0 1.0
CE1 B:HIS200 3.3 33.9 1.0
OD1 B:ASP201 3.5 32.8 1.0
MG B:MG502 3.8 29.2 1.0
O B:HOH659 3.8 37.6 1.0
O B:HOH646 4.0 35.9 1.0
CD2 B:HIS160 4.1 37.0 1.0
ND1 B:HIS164 4.2 33.2 1.0
CG B:HIS164 4.3 35.9 1.0
CB B:ASP201 4.3 38.1 1.0
CG B:HIS200 4.3 34.5 1.0
ND1 B:HIS200 4.3 35.4 1.0
NE2 B:HIS160 4.4 34.8 1.0
CB B:ASP318 4.5 43.0 1.0
CG2 B:VAL168 4.7 39.2 1.0
O B:HOH616 4.8 38.0 1.0
CA B:ASP318 5.0 44.5 1.0

Zinc binding site 3 out of 4 in 7ab9

Go back to Zinc Binding Sites List in 7ab9
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656


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-656 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:42.6
occ:1.00
 OD2 C:ASP201 2.1 38.1 1.0
OD1 C:ASP318 2.2 43.1 1.0
NE2 C:HIS200 2.2 34.2 1.0
NE2 C:HIS164 2.2 37.2 1.0
O C:HOH662 2.2 34.2 1.0
O C:HOH621 2.3 32.8 1.0
CG C:ASP318 3.0 39.9 1.0
CD2 C:HIS200 3.1 33.0 1.0
CG C:ASP201 3.1 35.1 1.0
CE1 C:HIS164 3.2 33.5 1.0
OD2 C:ASP318 3.2 41.1 1.0
CD2 C:HIS164 3.2 36.8 1.0
CE1 C:HIS200 3.3 37.9 1.0
OD1 C:ASP201 3.5 34.0 1.0
MG C:MG502 3.7 27.1 1.0
O C:HOH664 3.9 32.7 1.0
CD2 C:HIS160 4.2 35.2 1.0
O C:HOH637 4.2 44.7 1.0
CG C:HIS200 4.2 35.2 1.0
ND1 C:HIS164 4.3 35.5 1.0
CB C:ASP201 4.3 35.3 1.0
ND1 C:HIS200 4.3 32.9 1.0
CG C:HIS164 4.3 32.6 1.0
CB C:ASP318 4.4 42.8 1.0
NE2 C:HIS160 4.5 34.8 1.0
O C:HOH611 4.6 29.9 1.0
CG2 C:VAL168 4.8 42.6 1.0
CA C:ASP318 5.0 41.9 1.0

Zinc binding site 4 out of 4 in 7ab9

Go back to Zinc Binding Sites List in 7ab9
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656


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-656 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:37.4
occ:1.00
 OD2 D:ASP201 2.1 30.9 1.0
NE2 D:HIS200 2.1 29.5 1.0
O D:HOH610 2.2 32.6 1.0
NE2 D:HIS164 2.2 28.4 1.0
OD1 D:ASP318 2.2 35.3 1.0
O D:HOH688 2.3 37.3 1.0
CG D:ASP318 3.0 33.8 1.0
CE1 D:HIS200 3.0 29.4 1.0
CG D:ASP201 3.1 33.1 1.0
CD2 D:HIS200 3.1 27.7 1.0
CE1 D:HIS164 3.1 29.5 1.0
CD2 D:HIS164 3.2 30.6 1.0
OD2 D:ASP318 3.2 39.5 1.0
OD1 D:ASP201 3.5 30.5 1.0
MG D:MG502 3.8 26.8 1.0
O D:HOH687 3.9 33.1 1.0
O D:HOH675 4.1 37.9 1.0
ND1 D:HIS200 4.1 27.8 1.0
CG D:HIS200 4.2 26.7 1.0
CD2 D:HIS160 4.2 43.0 1.0
ND1 D:HIS164 4.3 27.6 1.0
CB D:ASP201 4.3 33.3 1.0
CG D:HIS164 4.3 29.6 1.0
CB D:ASP318 4.4 32.7 1.0
NE2 D:HIS160 4.5 42.4 1.0
CG2 D:VAL168 4.7 34.0 1.0
O D:HOH645 4.8 30.4 1.0
CA D:ASP318 5.0 32.6 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-656 To Be Published.
Page generated: Tue Oct 29 16:32:57 2024

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