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Zinc in PDB 6fw3: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007, PDB code: 6fw3 was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.23 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.110, 110.717, 161.490, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.4

Other elements in 6fw3:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007 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-007 (pdb code 6fw3). 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-007, PDB code: 6fw3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6fw3

Go back to Zinc Binding Sites List in 6fw3
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007


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-007 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:20.5
occ:1.00
 OD2 A:ASP201 2.1 15.7 1.0
NE2 A:HIS200 2.2 16.8 1.0
NE2 A:HIS164 2.2 17.8 1.0
O A:HOH769 2.3 18.6 1.0
OD1 A:ASP318 2.3 20.2 1.0
O A:HOH617 2.3 16.0 1.0
CD2 A:HIS200 3.1 16.9 1.0
CD2 A:HIS164 3.1 18.2 1.0
CG A:ASP201 3.1 15.4 1.0
CG A:ASP318 3.1 20.3 1.0
CE1 A:HIS200 3.2 18.2 1.0
CE1 A:HIS164 3.2 19.9 1.0
OD2 A:ASP318 3.3 21.8 1.0
OD1 A:ASP201 3.6 15.5 1.0
MG A:MG502 3.9 13.0 1.0
O A:HOH779 4.1 19.1 1.0
O A:HOH728 4.1 19.0 1.0
CD2 A:HIS160 4.2 20.7 1.0
CG A:HIS200 4.2 16.0 1.0
ND1 A:HIS200 4.3 15.5 1.0
CG A:HIS164 4.3 19.1 1.0
CB A:ASP201 4.3 15.8 1.0
ND1 A:HIS164 4.3 18.3 1.0
NE2 A:HIS160 4.4 20.7 1.0
CB A:ASP318 4.5 18.5 1.0
CG2 A:VAL168 4.7 20.4 1.0
O A:HOH664 4.8 15.9 1.0
C24 A:E8H523 5.0 23.2 1.0

Zinc binding site 2 out of 4 in 6fw3

Go back to Zinc Binding Sites List in 6fw3
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007


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-007 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:22.5
occ:1.00
 NE2 B:HIS164 2.1 19.4 1.0
OD2 B:ASP201 2.2 16.4 1.0
O B:HOH610 2.2 17.4 1.0
OD1 B:ASP318 2.2 17.2 1.0
O B:HOH711 2.2 17.6 1.0
NE2 B:HIS200 2.2 17.0 1.0
CG B:ASP318 3.1 19.4 1.0
CE1 B:HIS164 3.1 18.3 1.0
CG B:ASP201 3.1 17.9 1.0
CD2 B:HIS164 3.1 19.0 1.0
CD2 B:HIS200 3.2 17.7 1.0
CE1 B:HIS200 3.2 19.3 1.0
OD2 B:ASP318 3.3 19.4 1.0
OD1 B:ASP201 3.6 19.3 1.0
MG B:MG502 3.9 13.8 1.0
O B:HOH745 4.0 17.1 1.0
CD2 B:HIS160 4.1 19.4 1.0
O B:HOH701 4.1 19.1 1.0
ND1 B:HIS164 4.2 18.1 1.0
CG B:HIS164 4.3 19.4 1.0
NE2 B:HIS160 4.3 20.4 1.0
CB B:ASP201 4.3 17.7 1.0
CG B:HIS200 4.3 17.0 1.0
ND1 B:HIS200 4.3 18.8 1.0
CB B:ASP318 4.5 18.3 1.0
CG2 B:VAL168 4.7 18.9 1.0
O B:HOH626 4.8 17.7 1.0
CA B:ASP318 4.9 19.7 1.0
C24 B:E8H517 5.0 22.1 1.0

Zinc binding site 3 out of 4 in 6fw3

Go back to Zinc Binding Sites List in 6fw3
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007


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-007 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:23.3
occ:1.00
 OD2 C:ASP201 2.1 16.7 1.0
NE2 C:HIS164 2.2 17.2 1.0
NE2 C:HIS200 2.2 18.2 1.0
OD1 C:ASP318 2.2 18.4 1.0
O C:HOH617 2.3 18.6 1.0
O C:HOH693 2.3 19.4 1.0
CG C:ASP318 3.1 24.4 1.0
CD2 C:HIS200 3.1 16.4 1.0
CE1 C:HIS164 3.1 18.8 1.0
CG C:ASP201 3.2 17.0 1.0
CD2 C:HIS164 3.2 19.2 1.0
CE1 C:HIS200 3.2 16.7 1.0
OD2 C:ASP318 3.3 21.0 1.0
OD1 C:ASP201 3.7 18.1 1.0
MG C:MG504 3.9 14.1 1.0
CD2 C:HIS160 4.1 18.8 1.0
O C:HOH723 4.1 16.1 1.0
O C:HOH679 4.2 19.6 1.0
ND1 C:HIS164 4.3 19.1 1.0
CG C:HIS200 4.3 15.7 1.0
CG C:HIS164 4.3 18.9 1.0
ND1 C:HIS200 4.3 16.9 1.0
NE2 C:HIS160 4.4 19.5 1.0
CB C:ASP201 4.4 16.3 1.0
CB C:ASP318 4.5 20.6 1.0
CG2 C:VAL168 4.7 20.1 1.0
O C:HOH621 4.8 18.7 1.0
CA C:ASP318 5.0 20.7 1.0

Zinc binding site 4 out of 4 in 6fw3

Go back to Zinc Binding Sites List in 6fw3
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007


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-007 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:19.4
occ:1.00
 NE2 D:HIS200 2.1 15.2 1.0
OD2 D:ASP201 2.1 16.0 1.0
NE2 D:HIS164 2.2 14.9 1.0
OD1 D:ASP318 2.2 14.1 1.0
O D:HOH610 2.2 14.2 1.0
O D:HOH734 2.2 19.0 1.0
CG D:ASP318 3.0 17.1 1.0
CD2 D:HIS200 3.1 14.2 1.0
CG D:ASP201 3.1 17.5 1.0
CE1 D:HIS164 3.1 15.9 1.0
CE1 D:HIS200 3.2 15.9 1.0
CD2 D:HIS164 3.2 15.5 1.0
OD2 D:ASP318 3.3 19.3 1.0
OD1 D:ASP201 3.6 16.3 1.0
MG D:MG504 3.9 11.7 1.0
O D:HOH788 4.0 18.6 1.0
CD2 D:HIS160 4.2 20.2 1.0
O D:HOH737 4.2 17.8 1.0
CG D:HIS200 4.2 14.2 1.0
ND1 D:HIS200 4.3 13.5 1.0
ND1 D:HIS164 4.3 14.9 1.0
NE2 D:HIS160 4.3 21.0 1.0
CG D:HIS164 4.3 15.4 1.0
CB D:ASP201 4.3 16.3 1.0
CB D:ASP318 4.4 16.3 1.0
CG2 D:VAL168 4.7 16.8 1.0
O D:HOH657 4.8 14.6 1.0
CA D:ASP318 4.9 16.1 1.0

Reference:

I.G.Salado, C.Moreno, G.Sakaine, A.K.Singh, A.R.Blaazer, M.Siderius, A.Matheeussen, S.Gul, L.Maes, R.Leurs, D.G.Brown, K.Augustyns. HPDE4D2 Structure with Inhibitor Npd-007 To Be Published.
Page generated: Mon Oct 28 21:28:56 2024

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