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Zinc in PDB 6fet: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439, PDB code: 6fet 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) 55.35 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.190, 110.710, 161.480, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.9

Other elements in 6fet:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Nickel (Ni) 2 atoms
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-1439 (pdb code 6fet). 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-1439, PDB code: 6fet:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6fet

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


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-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:33.3
occ:1.00
 OD2 A:ASP201 2.2 26.6 1.0
O A:HOH618 2.2 27.2 1.0
NE2 A:HIS164 2.2 23.3 1.0
OD1 A:ASP318 2.2 28.4 1.0
NE2 A:HIS200 2.3 26.1 1.0
O A:HOH674 2.3 28.7 1.0
CD2 A:HIS200 3.1 27.0 1.0
CG A:ASP318 3.1 29.6 1.0
CG A:ASP201 3.1 27.8 1.0
CE1 A:HIS164 3.2 28.3 1.0
CD2 A:HIS164 3.2 28.4 1.0
CE1 A:HIS200 3.3 28.7 1.0
OD2 A:ASP318 3.3 33.0 1.0
OD1 A:ASP201 3.5 30.9 1.0
MG A:MG502 3.7 23.1 1.0
O A:HOH725 3.9 28.4 1.0
CD2 A:HIS160 4.1 29.7 1.0
O A:HOH662 4.2 34.0 1.0
CG A:HIS200 4.3 26.7 1.0
NE2 A:HIS160 4.3 28.9 1.0
ND1 A:HIS164 4.3 25.5 1.0
CB A:ASP201 4.3 26.9 1.0
CG A:HIS164 4.4 26.4 1.0
ND1 A:HIS200 4.4 24.1 1.0
CB A:ASP318 4.5 29.8 1.0
O A:HOH624 4.7 25.8 1.0
CG2 A:VAL168 4.8 29.9 1.0
C23 A:D68517 4.9 39.0 1.0

Zinc binding site 2 out of 4 in 6fet

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


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-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:32.4
occ:1.00
 O B:HOH613 2.0 27.2 1.0
NE2 B:HIS164 2.1 27.6 1.0
O B:HOH698 2.2 25.9 1.0
OD2 B:ASP201 2.2 25.0 1.0
OD1 B:ASP318 2.2 26.4 1.0
NE2 B:HIS200 2.2 24.7 1.0
CE1 B:HIS164 3.1 29.6 1.0
CG B:ASP318 3.1 32.5 1.0
CD2 B:HIS200 3.1 26.1 1.0
CG B:ASP201 3.1 26.2 1.0
CD2 B:HIS164 3.2 26.6 1.0
CE1 B:HIS200 3.3 24.3 1.0
OD2 B:ASP318 3.4 32.5 1.0
OD1 B:ASP201 3.6 26.7 1.0
MG B:MG502 3.8 22.4 1.0
O B:HOH709 4.0 26.9 1.0
CD2 B:HIS160 4.1 30.9 1.0
ND1 B:HIS164 4.2 29.4 1.0
O B:HOH650 4.3 29.3 1.0
CG B:HIS164 4.3 26.9 1.0
CG B:HIS200 4.3 24.9 1.0
CB B:ASP201 4.3 24.6 1.0
ND1 B:HIS200 4.3 28.1 1.0
NE2 B:HIS160 4.3 29.9 1.0
CB B:ASP318 4.5 30.9 1.0
CG2 B:VAL168 4.7 30.9 1.0
O B:HOH631 4.7 24.9 1.0
C23 B:D68514 5.0 34.5 1.0
CA B:ASP318 5.0 32.8 1.0

Zinc binding site 3 out of 4 in 6fet

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


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-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn504

b:34.1
occ:1.00
 O C:HOH676 2.2 27.6 1.0
OD1 C:ASP318 2.2 30.8 1.0
O C:HOH607 2.2 25.9 1.0
NE2 C:HIS164 2.2 29.7 1.0
NE2 C:HIS200 2.2 25.6 1.0
OD2 C:ASP201 2.2 27.9 1.0
CD2 C:HIS200 3.1 24.8 1.0
CG C:ASP318 3.1 31.9 1.0
CE1 C:HIS164 3.2 28.0 1.0
CG C:ASP201 3.2 27.2 1.0
CD2 C:HIS164 3.2 29.0 1.0
CE1 C:HIS200 3.3 27.1 1.0
OD2 C:ASP318 3.3 33.7 1.0
OD1 C:ASP201 3.6 31.0 1.0
MG C:MG505 3.8 23.8 1.0
O C:HOH683 4.0 25.9 1.0
CD2 C:HIS160 4.1 31.3 1.0
CG C:HIS200 4.2 27.8 1.0
O C:HOH642 4.2 31.1 1.0
ND1 C:HIS164 4.3 27.6 1.0
ND1 C:HIS200 4.3 26.3 1.0
NE2 C:HIS160 4.3 29.6 1.0
CG C:HIS164 4.3 27.1 1.0
CB C:ASP201 4.4 28.1 1.0
CB C:ASP318 4.5 34.0 1.0
CG2 C:VAL168 4.7 30.6 1.0
O C:HOH628 4.7 27.0 1.0
C23 C:D68515 4.8 35.3 1.0
CA C:ASP318 5.0 30.9 1.0

Zinc binding site 4 out of 4 in 6fet

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


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-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn504

b:29.2
occ:1.00
 OD2 D:ASP201 2.2 21.7 1.0
OD1 D:ASP318 2.2 23.9 1.0
NE2 D:HIS164 2.2 23.5 1.0
O D:HOH617 2.2 22.3 1.0
NE2 D:HIS200 2.2 25.2 1.0
O D:HOH715 2.4 27.2 1.0
CG D:ASP318 3.1 23.0 1.0
CD2 D:HIS200 3.1 23.2 1.0
CG D:ASP201 3.1 23.5 1.0
CE1 D:HIS164 3.2 23.1 1.0
CD2 D:HIS164 3.2 23.6 1.0
CE1 D:HIS200 3.3 25.0 1.0
OD2 D:ASP318 3.3 27.2 1.0
OD1 D:ASP201 3.6 23.1 1.0
MG D:MG505 3.8 20.8 1.0
O D:HOH716 4.0 25.8 1.0
CD2 D:HIS160 4.1 29.7 1.0
O D:HOH651 4.2 26.3 1.0
CG D:HIS200 4.3 22.9 1.0
ND1 D:HIS164 4.3 21.4 1.0
CB D:ASP201 4.3 23.1 1.0
NE2 D:HIS160 4.3 28.5 1.0
ND1 D:HIS200 4.3 22.3 1.0
CG D:HIS164 4.3 21.8 1.0
CB D:ASP318 4.5 26.2 1.0
CG2 D:VAL168 4.7 24.9 1.0
O D:HOH634 4.7 22.9 1.0
C23 D:D68520 4.9 33.4 1.0
CA D:ASP318 5.0 24.3 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-1439 To Be Published.
Page generated: Mon Oct 28 20:56:20 2024

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