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Zinc in PDB 7a9v: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635, PDB code: 7a9v 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) 91.29 / 2.17
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.199, 111.155, 159.684, 90, 90, 90
R / Rfree (%) 18.9 / 22.9

Other elements in 7a9v:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635 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-635 (pdb code 7a9v). 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-635, PDB code: 7a9v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7a9v

Go back to Zinc Binding Sites List in 7a9v
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635


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-635 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:36.4
occ:1.00
 OD2 A:ASP201 2.1 29.9 1.0
NE2 A:HIS164 2.2 32.2 1.0
O A:HOH625 2.2 30.0 1.0
NE2 A:HIS200 2.2 35.8 1.0
OD1 A:ASP318 2.2 40.6 1.0
O A:HOH655 2.3 37.9 1.0
CD2 A:HIS200 3.1 33.1 1.0
CG A:ASP318 3.1 38.0 1.0
CG A:ASP201 3.1 30.5 1.0
CD2 A:HIS164 3.1 30.8 1.0
CE1 A:HIS164 3.2 32.9 1.0
CE1 A:HIS200 3.2 34.3 1.0
OD2 A:ASP318 3.2 44.1 1.0
OD1 A:ASP201 3.5 29.8 1.0
O A:HOH707 3.7 59.2 1.0
MG A:MG502 3.8 27.0 1.0
O A:HOH696 3.9 33.5 1.0
O A:HOH656 3.9 43.2 1.0
CD2 A:HIS160 4.2 32.4 1.0
CG A:HIS200 4.2 33.7 1.0
ND1 A:HIS200 4.3 33.4 1.0
ND1 A:HIS164 4.3 32.5 1.0
CB A:ASP201 4.3 29.8 1.0
CG A:HIS164 4.3 32.2 1.0
NE2 A:HIS160 4.5 30.3 1.0
CB A:ASP318 4.5 34.4 1.0
CG2 A:VAL168 4.7 31.9 1.0
O A:HOH622 4.8 26.4 1.0

Zinc binding site 2 out of 4 in 7a9v

Go back to Zinc Binding Sites List in 7a9v
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635


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-635 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:43.3
occ:1.00
 O B:HOH612 1.9 33.6 1.0
NE2 B:HIS164 2.1 31.6 1.0
OD2 B:ASP201 2.2 40.3 1.0
NE2 B:HIS200 2.2 39.4 1.0
OD1 B:ASP318 2.2 38.8 1.0
O B:HOH667 2.5 32.9 1.0
CG B:ASP201 3.1 35.9 1.0
CG B:ASP318 3.1 43.8 1.0
CD2 B:HIS164 3.1 34.8 1.0
CD2 B:HIS200 3.1 36.1 1.0
CE1 B:HIS164 3.1 36.0 1.0
CE1 B:HIS200 3.2 36.2 1.0
OD2 B:ASP318 3.3 46.2 1.0
OD1 B:ASP201 3.5 36.7 1.0
O B:HOH670 3.7 39.1 1.0
MG B:MG502 3.8 34.3 1.0
O B:HOH702 3.9 50.2 1.0
O B:HOH628 4.0 40.6 1.0
CD2 B:HIS160 4.1 40.6 1.0
ND1 B:HIS164 4.2 33.0 1.0
CG B:HIS164 4.3 35.6 1.0
CB B:ASP201 4.3 39.9 1.0
CG B:HIS200 4.3 33.4 1.0
ND1 B:HIS200 4.3 36.7 1.0
NE2 B:HIS160 4.5 34.9 1.0
CB B:ASP318 4.5 44.6 1.0
CG2 B:VAL168 4.7 47.4 1.0
O B:HOH616 4.9 37.4 1.0

Zinc binding site 3 out of 4 in 7a9v

Go back to Zinc Binding Sites List in 7a9v
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635


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-635 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:41.3
occ:1.00
 OD2 C:ASP201 2.1 37.8 1.0
NE2 C:HIS200 2.2 33.9 1.0
NE2 C:HIS164 2.2 35.5 1.0
O C:HOH673 2.2 31.6 1.0
OD1 C:ASP318 2.2 40.7 1.0
O C:HOH619 2.3 34.9 1.0
CD2 C:HIS200 3.1 33.9 1.0
CG C:ASP201 3.1 34.2 1.0
CG C:ASP318 3.1 40.0 1.0
CD2 C:HIS164 3.2 36.6 1.0
CE1 C:HIS164 3.2 35.6 1.0
CE1 C:HIS200 3.2 34.1 1.0
OD2 C:ASP318 3.3 44.8 1.0
OD1 C:ASP201 3.5 33.0 1.0
MG C:MG502 3.7 28.2 1.0
O C:HOH682 3.9 31.5 1.0
O C:HOH644 4.1 46.4 1.0
CD2 C:HIS160 4.2 31.1 1.0
CG C:HIS200 4.2 34.2 1.0
CB C:ASP201 4.3 34.4 1.0
ND1 C:HIS200 4.3 34.0 1.0
ND1 C:HIS164 4.3 36.3 1.0
CG C:HIS164 4.3 32.5 1.0
CB C:ASP318 4.5 42.2 1.0
NE2 C:HIS160 4.5 29.8 1.0
O C:HOH617 4.7 29.8 1.0
CG2 C:VAL168 4.7 36.7 1.0
O C:HOH661 5.0 34.8 1.0

Zinc binding site 4 out of 4 in 7a9v

Go back to Zinc Binding Sites List in 7a9v
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635


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-635 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:35.7
occ:1.00
 OD2 D:ASP201 2.1 31.2 1.0
NE2 D:HIS200 2.1 30.5 1.0
NE2 D:HIS164 2.2 28.4 1.0
O D:HOH613 2.2 30.0 1.0
OD1 D:ASP318 2.2 34.1 1.0
O D:HOH698 2.3 35.1 1.0
CD2 D:HIS200 3.1 28.4 1.0
CG D:ASP201 3.1 31.9 1.0
CG D:ASP318 3.1 33.7 1.0
CD2 D:HIS164 3.2 29.0 1.0
CE1 D:HIS164 3.2 29.4 1.0
CE1 D:HIS200 3.2 32.9 1.0
OD2 D:ASP318 3.3 39.1 1.0
OD1 D:ASP201 3.5 31.9 1.0
O D:HOH699 3.6 41.2 1.0
MG D:MG502 3.7 30.9 1.0
O D:HOH669 4.1 41.5 1.0
CD2 D:HIS160 4.2 39.8 1.0
CG D:HIS200 4.2 27.9 1.0
CB D:ASP201 4.3 32.1 1.0
ND1 D:HIS200 4.3 29.0 1.0
ND1 D:HIS164 4.3 28.2 1.0
CG D:HIS164 4.3 28.6 1.0
CB D:ASP318 4.5 32.1 1.0
NE2 D:HIS160 4.5 41.8 1.0
O D:HOH743 4.6 69.0 1.0
O D:HOH648 4.6 29.7 1.0
CG2 D:VAL168 4.7 29.1 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-635 To Be Published.
Page generated: Thu Aug 21 22:13:10 2025

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