Zinc in PDB 6fe7: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356, PDB code: 6fe7 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) 54.30 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.220, 111.030, 160.960, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20

Other elements in 6fe7:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356 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-356 (pdb code 6fe7). 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-356, PDB code: 6fe7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6fe7

Go back to Zinc Binding Sites List in 6fe7
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356


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-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:33.4
occ:1.00
OD2 A:ASP201 1.4 26.7 1.0
OD1 A:ASP318 2.2 29.5 1.0
NE2 A:HIS164 2.2 25.7 1.0
O A:HOH629 2.3 25.6 1.0
NE2 A:HIS200 2.4 25.9 1.0
O A:HOH688 2.4 31.3 1.0
CG A:ASP201 2.7 28.1 1.0
CG A:ASP318 3.1 28.9 1.0
CD2 A:HIS200 3.1 26.7 1.0
CD2 A:HIS164 3.2 28.1 1.0
CE1 A:HIS164 3.2 26.6 1.0
OD2 A:ASP318 3.3 32.8 1.0
OD1 A:ASP201 3.3 29.2 1.0
CE1 A:HIS200 3.4 27.2 1.0
MG A:MG502 3.8 19.3 1.0
O A:HOH719 3.9 24.8 1.0
CB A:ASP201 4.0 25.2 1.0
CD2 A:HIS160 4.2 31.9 1.0
O A:HOH673 4.2 35.1 1.0
CG A:HIS200 4.3 25.6 1.0
ND1 A:HIS164 4.3 25.5 1.0
CG A:HIS164 4.4 24.9 1.0
NE2 A:HIS160 4.4 29.6 1.0
ND1 A:HIS200 4.4 26.2 1.0
CB A:ASP318 4.5 29.3 1.0
O A:HOH634 4.7 23.8 1.0
CG2 A:VAL168 4.7 28.4 1.0
C21 A:D62520 4.9 33.5 1.0
CA A:ASP318 5.0 28.1 1.0

Zinc binding site 2 out of 4 in 6fe7

Go back to Zinc Binding Sites List in 6fe7
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356


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-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:33.4
occ:1.00
O B:HOH616 2.0 25.9 1.0
OD2 B:ASP201 2.1 29.2 1.0
NE2 B:HIS164 2.2 25.7 1.0
OD1 B:ASP318 2.2 28.1 1.0
NE2 B:HIS200 2.3 26.6 1.0
O B:HOH688 2.3 24.7 1.0
CG B:ASP318 3.1 32.7 1.0
CD2 B:HIS200 3.1 30.4 1.0
CE1 B:HIS164 3.1 28.1 1.0
CG B:ASP201 3.1 26.9 1.0
CD2 B:HIS164 3.2 25.9 1.0
CE1 B:HIS200 3.3 30.6 1.0
OD2 B:ASP318 3.4 29.1 1.0
OD1 B:ASP201 3.6 28.8 1.0
MG B:MG502 3.8 22.4 1.0
O B:HOH724 4.0 27.0 1.0
CD2 B:HIS160 4.1 32.6 1.0
O B:HOH654 4.2 28.6 1.0
ND1 B:HIS164 4.3 27.4 1.0
CG B:HIS164 4.3 28.1 1.0
CG B:HIS200 4.3 28.2 1.0
CB B:ASP201 4.3 28.8 1.0
NE2 B:HIS160 4.4 34.0 1.0
ND1 B:HIS200 4.4 28.6 1.0
CB B:ASP318 4.5 31.9 1.0
CG2 B:VAL168 4.7 30.1 1.0
O B:HOH645 4.7 24.7 1.0
CA B:ASP318 5.0 31.0 1.0

Zinc binding site 3 out of 4 in 6fe7

Go back to Zinc Binding Sites List in 6fe7
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356


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-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:33.7
occ:1.00
OD1 C:ASP318 2.2 27.4 1.0
OD2 C:ASP201 2.2 25.8 1.0
O C:HOH611 2.2 24.7 1.0
NE2 C:HIS164 2.2 30.8 1.0
O C:HOH655 2.2 27.8 1.0
NE2 C:HIS200 2.3 29.0 1.0
CG C:ASP318 3.1 32.8 1.0
CD2 C:HIS200 3.1 25.3 1.0
CG C:ASP201 3.2 27.4 1.0
CE1 C:HIS164 3.2 27.4 1.0
CD2 C:HIS164 3.2 29.8 1.0
OD2 C:ASP318 3.3 31.9 1.0
CE1 C:HIS200 3.3 29.3 1.0
OD1 C:ASP201 3.6 27.0 1.0
MG C:MG506 3.8 21.5 1.0
O C:HOH681 4.0 26.9 1.0
CD2 C:HIS160 4.1 33.8 1.0
O C:HOH644 4.1 30.4 1.0
CG C:HIS200 4.3 25.5 1.0
ND1 C:HIS164 4.3 27.2 1.0
CG C:HIS164 4.4 25.5 1.0
NE2 C:HIS160 4.4 30.3 1.0
ND1 C:HIS200 4.4 27.4 1.0
CB C:ASP201 4.4 27.3 1.0
CB C:ASP318 4.5 30.6 1.0
O C:HOH627 4.7 27.0 1.0
CG2 C:VAL168 4.7 30.1 1.0
CA C:ASP318 5.0 30.8 1.0
C21 C:D62520 5.0 37.0 1.0

Zinc binding site 4 out of 4 in 6fe7

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356


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-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:30.5
occ:1.00
OD2 D:ASP201 2.2 22.6 1.0
OD1 D:ASP318 2.2 25.8 1.0
NE2 D:HIS164 2.2 22.2 1.0
NE2 D:HIS200 2.3 24.5 1.0
O D:HOH637 2.3 24.0 1.0
O D:HOH705 2.3 25.6 1.0
CG D:ASP318 3.1 26.6 1.0
CD2 D:HIS200 3.1 22.8 1.0
CG D:ASP201 3.1 25.6 1.0
CE1 D:HIS164 3.2 22.4 1.0
CD2 D:HIS164 3.2 23.9 1.0
CE1 D:HIS200 3.3 25.8 1.0
OD2 D:ASP318 3.4 28.4 1.0
OD1 D:ASP201 3.6 25.2 1.0
MG D:MG503 3.8 19.0 1.0
O D:HOH749 3.9 24.9 1.0
CD2 D:HIS160 4.1 31.4 1.0
O D:HOH676 4.2 26.0 1.0
ND1 D:HIS164 4.3 21.7 1.0
CG D:HIS200 4.3 23.8 1.0
CB D:ASP201 4.3 24.7 1.0
CG D:HIS164 4.3 23.8 1.0
NE2 D:HIS160 4.4 30.0 1.0
ND1 D:HIS200 4.4 22.4 1.0
CB D:ASP318 4.5 28.3 1.0
CG2 D:VAL168 4.7 22.5 1.0
O D:HOH638 4.7 22.4 1.0
C21 D:D62517 4.9 30.2 1.0
CA D:ASP318 4.9 25.0 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-356 To Be Published.
Page generated: Wed Dec 16 11:47:30 2020

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