Atomistry » Zinc » PDB 7a6u-7ae5 » 7abd
Atomistry »
  Zinc »
    PDB 7a6u-7ae5 »
      7abd »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy