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Zinc in PDB 7a8q: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654, PDB code: 7a8q 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) 91.49 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.349, 111.441, 160.227, 90, 90, 90
R / Rfree (%) 18.7 / 22.9

Other elements in 7a8q:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654 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-654 (pdb code 7a8q). 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-654, PDB code: 7a8q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7a8q

Go back to Zinc Binding Sites List in 7a8q
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654


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-654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:44.1
occ:1.00
 OD2 A:ASP201 2.1 35.2 1.0
OD1 A:ASP318 2.2 43.9 1.0
NE2 A:HIS200 2.2 40.3 1.0
NE2 A:HIS164 2.2 38.1 1.0
O A:HOH613 2.3 34.9 1.0
O A:HOH627 2.4 42.0 1.0
CG A:ASP318 3.0 41.9 1.0
CD2 A:HIS200 3.1 38.3 1.0
CG A:ASP201 3.1 40.5 1.0
OD2 A:ASP318 3.2 45.0 1.0
CD2 A:HIS164 3.2 36.7 1.0
CE1 A:HIS164 3.2 37.5 1.0
CE1 A:HIS200 3.2 42.8 1.0
OD1 A:ASP201 3.6 40.0 1.0
O A:HOH688 3.6 48.0 1.0
O A:HOH662 3.7 43.0 1.0
MG A:MG502 3.9 32.8 1.0
CD2 A:HIS160 4.2 38.8 1.0
CG A:HIS200 4.2 39.8 1.0
ND1 A:HIS200 4.3 38.5 1.0
ND1 A:HIS164 4.3 35.0 1.0
O A:HOH718 4.3 59.9 1.0
CG A:HIS164 4.3 39.9 1.0
CB A:ASP201 4.4 39.4 1.0
CB A:ASP318 4.4 41.2 1.0
NE2 A:HIS160 4.4 42.3 1.0
CG2 A:VAL168 4.7 37.7 1.0
O A:HOH625 4.8 37.5 1.0
CA A:ASP318 5.0 41.9 1.0

Zinc binding site 2 out of 4 in 7a8q

Go back to Zinc Binding Sites List in 7a8q
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654


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-654 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:53.0
occ:1.00
 O B:HOH607 2.0 32.6 1.0
OD2 B:ASP201 2.1 49.7 1.0
NE2 B:HIS164 2.1 38.2 1.0
OD1 B:ASP318 2.2 46.7 1.0
NE2 B:HIS200 2.2 49.9 1.0
O B:HOH655 2.3 39.6 1.0
CG B:ASP318 3.1 48.0 1.0
CG B:ASP201 3.1 42.1 1.0
CD2 B:HIS164 3.1 39.7 1.0
CE1 B:HIS164 3.1 39.8 1.0
CD2 B:HIS200 3.2 42.9 1.0
CE1 B:HIS200 3.2 42.8 1.0
OD2 B:ASP318 3.3 57.0 1.0
OD1 B:ASP201 3.6 39.7 1.0
O B:HOH660 3.7 40.1 1.0
O B:HOH682 3.7 60.1 1.0
MG B:MG502 3.8 33.7 1.0
O B:HOH632 3.9 49.2 1.0
CD2 B:HIS160 4.1 42.9 1.0
ND1 B:HIS164 4.2 40.5 1.0
CG B:HIS164 4.2 40.7 1.0
CB B:ASP201 4.3 44.9 1.0
ND1 B:HIS200 4.3 49.1 1.0
CG B:HIS200 4.3 43.8 1.0
NE2 B:HIS160 4.4 43.7 1.0
CB B:ASP318 4.4 50.0 1.0
CG2 B:VAL168 4.7 51.7 1.0
O B:HOH612 4.9 41.2 1.0
CA B:ASP318 5.0 53.7 1.0

Zinc binding site 3 out of 4 in 7a8q

Go back to Zinc Binding Sites List in 7a8q
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654


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-654 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:48.9
occ:1.00
 OD2 C:ASP201 2.1 47.0 1.0
OD1 C:ASP318 2.2 45.2 1.0
NE2 C:HIS200 2.2 39.2 1.0
NE2 C:HIS164 2.2 40.5 1.0
O C:HOH612 2.3 38.1 1.0
O C:HOH631 2.3 40.9 1.0
CG C:ASP318 3.0 43.8 1.0
CG C:ASP201 3.1 40.8 1.0
CD2 C:HIS200 3.1 40.1 1.0
OD2 C:ASP318 3.2 51.3 1.0
CD2 C:HIS164 3.2 39.8 1.0
CE1 C:HIS164 3.2 38.8 1.0
CE1 C:HIS200 3.2 39.4 1.0
O C:HOH673 3.5 30.0 1.0
OD1 C:ASP201 3.5 36.5 1.0
MG C:MG502 3.7 32.8 1.0
O C:HOH655 3.8 34.1 1.0
O C:HOH633 4.1 55.8 1.0
CD2 C:HIS160 4.1 39.4 1.0
CG C:HIS200 4.3 39.6 1.0
ND1 C:HIS200 4.3 37.5 1.0
CB C:ASP201 4.3 38.0 1.0
ND1 C:HIS164 4.3 38.6 1.0
CG C:HIS164 4.3 36.2 1.0
NE2 C:HIS160 4.4 36.7 1.0
CB C:ASP318 4.4 50.6 1.0
O C:HOH616 4.7 33.8 1.0
CG2 C:VAL168 4.8 42.6 1.0
CA C:ASP318 5.0 47.8 1.0

Zinc binding site 4 out of 4 in 7a8q

Go back to Zinc Binding Sites List in 7a8q
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654


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-654 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:42.3
occ:1.00
 OD2 D:ASP201 2.1 36.4 1.0
OD1 D:ASP318 2.2 37.6 1.0
NE2 D:HIS200 2.2 40.6 1.0
NE2 D:HIS164 2.2 30.1 1.0
O D:HOH620 2.3 33.1 1.0
O D:HOH603 2.8 43.5 1.0
CG D:ASP318 3.0 41.0 1.0
CG D:ASP201 3.1 36.2 1.0
CD2 D:HIS200 3.1 38.9 1.0
CD2 D:HIS164 3.2 31.3 1.0
CE1 D:HIS164 3.2 30.3 1.0
O D:HOH685 3.2 30.0 1.0
OD2 D:ASP318 3.2 42.3 1.0
CE1 D:HIS200 3.2 39.1 1.0
OD1 D:ASP201 3.6 34.4 1.0
O D:HOH686 3.7 40.6 1.0
MG D:MG502 3.9 33.2 1.0
O D:HOH670 4.0 52.8 1.0
CD2 D:HIS160 4.2 44.7 1.0
CG D:HIS200 4.3 34.6 1.0
ND1 D:HIS164 4.3 31.0 1.0
ND1 D:HIS200 4.3 36.0 1.0
CG D:HIS164 4.3 29.2 1.0
CB D:ASP201 4.3 36.3 1.0
CB D:ASP318 4.4 36.6 1.0
NE2 D:HIS160 4.4 47.4 1.0
O D:HOH628 4.7 30.6 1.0
CG2 D:VAL168 4.7 35.5 1.0
CA D:ASP318 5.0 33.8 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-654 To Be Published.
Page generated: Tue Oct 29 16:22:44 2024

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