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Zinc in PDB 6ibf: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417, PDB code: 6ibf 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) 80.11 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.476, 110.511, 160.298, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 26.2

Other elements in 6ibf:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417 also contains other interesting chemical elements:

Fluorine (F) 12 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-417 (pdb code 6ibf). 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-417, PDB code: 6ibf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ibf

Go back to Zinc Binding Sites List in 6ibf
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417


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-417 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:37.2
occ:1.00
OD2 A:ASP201 2.1 26.8 1.0
OD1 A:ASP318 2.2 28.2 1.0
O A:HOH611 2.2 33.0 1.0
NE2 A:HIS164 2.3 28.2 1.0
NE2 A:HIS200 2.3 33.3 1.0
O A:HOH639 2.4 39.6 1.0
CG A:ASP318 3.0 33.8 1.0
CD2 A:HIS200 3.1 31.1 1.0
CG A:ASP201 3.1 27.4 1.0
OD2 A:ASP318 3.1 34.7 1.0
CD2 A:HIS164 3.1 30.0 1.0
CE1 A:HIS164 3.3 29.6 1.0
CE1 A:HIS200 3.5 34.3 1.0
OD1 A:ASP201 3.5 31.1 1.0
MG A:MG502 3.7 23.9 1.0
O A:HOH646 3.7 34.4 1.0
O A:HOH631 4.0 40.7 1.0
CD2 A:HIS160 4.1 39.0 1.0
CB A:ASP201 4.3 28.4 1.0
CG A:HIS200 4.3 30.1 1.0
NE2 A:HIS160 4.3 39.4 1.0
CG A:HIS164 4.3 28.8 1.0
CB A:ASP318 4.4 31.8 1.0
ND1 A:HIS164 4.4 28.2 1.0
ND1 A:HIS200 4.5 30.5 1.0
CG2 A:VAL168 4.7 31.2 1.0
C31 A:4I7513 4.8 54.3 1.0
O A:HOH606 4.8 29.8 1.0
CA A:ASP318 5.0 33.2 1.0

Zinc binding site 2 out of 4 in 6ibf

Go back to Zinc Binding Sites List in 6ibf
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417


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-417 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:39.5
occ:1.00
O B:HOH603 2.1 21.9 1.0
OD2 B:ASP201 2.1 35.3 1.0
NE2 B:HIS200 2.2 27.3 1.0
NE2 B:HIS164 2.2 34.0 1.0
OD1 B:ASP318 2.2 33.6 1.0
O B:HOH673 2.4 31.6 1.0
CG B:ASP318 3.1 33.8 1.0
CG B:ASP201 3.1 32.4 1.0
CD2 B:HIS200 3.2 28.1 1.0
CD2 B:HIS164 3.2 34.8 1.0
CE1 B:HIS164 3.2 34.4 1.0
CE1 B:HIS200 3.2 28.3 1.0
OD2 B:ASP318 3.3 38.5 1.0
OD1 B:ASP201 3.6 30.5 1.0
O B:HOH653 3.8 22.8 1.0
MG B:MG502 3.9 21.6 1.0
CD2 B:HIS160 4.0 34.1 1.0
O B:HOH646 4.2 41.9 1.0
ND1 B:HIS164 4.3 34.3 1.0
CB B:ASP201 4.3 32.2 1.0
CG B:HIS164 4.3 35.9 1.0
CG B:HIS200 4.3 28.5 1.0
ND1 B:HIS200 4.3 28.9 1.0
NE2 B:HIS160 4.4 33.8 1.0
CB B:ASP318 4.5 34.4 1.0
CG2 B:VAL168 4.6 31.6 1.0
O B:HOH617 4.8 27.8 1.0
CA B:ASP318 4.9 33.9 1.0
C31 B:4I7513 4.9 53.5 1.0

Zinc binding site 3 out of 4 in 6ibf

Go back to Zinc Binding Sites List in 6ibf
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417


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-417 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:36.8
occ:1.00
OD1 C:ASP318 2.1 32.0 1.0
O C:HOH638 2.2 25.0 1.0
OD2 C:ASP201 2.2 32.2 1.0
NE2 C:HIS164 2.2 29.8 1.0
O C:HOH615 2.3 31.4 1.0
NE2 C:HIS200 2.3 25.6 1.0
CG C:ASP318 3.0 33.9 1.0
CD2 C:HIS200 3.1 28.4 1.0
CG C:ASP201 3.2 27.7 1.0
CD2 C:HIS164 3.2 30.9 1.0
CE1 C:HIS164 3.2 29.5 1.0
OD2 C:ASP318 3.3 38.1 1.0
CE1 C:HIS200 3.3 28.5 1.0
OD1 C:ASP201 3.6 25.9 1.0
MG C:MG502 3.7 19.0 1.0
O C:HOH678 3.9 19.7 1.0
CD2 C:HIS160 4.1 29.0 1.0
O C:HOH624 4.2 33.6 1.0
CG C:HIS200 4.3 28.9 1.0
ND1 C:HIS164 4.3 30.5 1.0
CG C:HIS164 4.3 32.6 1.0
CB C:ASP201 4.4 27.4 1.0
ND1 C:HIS200 4.4 30.0 1.0
NE2 C:HIS160 4.4 27.5 1.0
CB C:ASP318 4.4 34.0 1.0
O C:HOH630 4.7 23.2 1.0
CG2 C:VAL168 4.7 33.2 1.0
CA C:ASP318 5.0 35.2 1.0

Zinc binding site 4 out of 4 in 6ibf

Go back to Zinc Binding Sites List in 6ibf
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417


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-417 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:31.0
occ:1.00
OD2 D:ASP201 2.1 23.2 1.0
OD1 D:ASP318 2.1 28.1 1.0
NE2 D:HIS200 2.2 19.4 1.0
O D:HOH608 2.2 19.0 1.0
NE2 D:HIS164 2.2 26.6 1.0
O D:HOH669 2.3 25.9 1.0
CG D:ASP318 3.0 27.3 1.0
CG D:ASP201 3.0 23.0 1.0
CD2 D:HIS200 3.1 19.0 1.0
OD2 D:ASP318 3.2 25.8 1.0
CE1 D:HIS164 3.2 26.9 1.0
CE1 D:HIS200 3.2 20.9 1.0
CD2 D:HIS164 3.3 29.1 1.0
OD1 D:ASP201 3.5 22.8 1.0
MG D:MG502 3.8 16.4 1.0
O D:HOH673 3.9 24.7 1.0
CD2 D:HIS160 4.2 30.9 1.0
O D:HOH663 4.2 32.7 1.0
CG D:HIS200 4.2 18.0 1.0
CB D:ASP201 4.3 22.7 1.0
ND1 D:HIS200 4.3 19.6 1.0
ND1 D:HIS164 4.3 27.5 1.0
CG D:HIS164 4.4 26.8 1.0
NE2 D:HIS160 4.4 32.7 1.0
CB D:ASP318 4.4 24.8 1.0
O D:HOH641 4.5 18.7 1.0
CG2 D:VAL168 4.6 24.5 1.0
C31 D:4I7520 4.9 47.4 1.0
CA D:ASP318 5.0 25.6 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-417 To Be Published.
Page generated: Wed Dec 16 11:59:57 2020

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