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Zinc in PDB 6ft0: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425, PDB code: 6ft0 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) 91.28 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.939, 110.812, 160.983, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.2

Other elements in 6ft0:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425 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-425 (pdb code 6ft0). 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-425, PDB code: 6ft0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ft0

Go back to Zinc Binding Sites List in 6ft0
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425


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-425 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:35.8
occ:1.00
 NE2 A:HIS164 2.1 24.4 1.0
OD1 A:ASP318 2.2 34.0 1.0
O A:HOH611 2.2 25.8 1.0
OD2 A:ASP201 2.2 26.4 1.0
NE2 A:HIS200 2.3 27.5 1.0
O A:HOH680 2.5 37.6 1.0
CD2 A:HIS164 3.0 30.8 1.0
CE1 A:HIS164 3.1 29.6 1.0
CD2 A:HIS200 3.1 27.1 1.0
CG A:ASP318 3.1 34.6 1.0
CG A:ASP201 3.3 28.4 1.0
CE1 A:HIS200 3.3 29.4 1.0
OD2 A:ASP318 3.4 38.9 1.0
OD1 A:ASP201 3.7 29.5 1.0
O A:HOH649 3.8 36.1 1.0
MG A:MG502 3.9 18.4 1.0
O A:HOH697 4.0 29.0 1.0
CD2 A:HIS160 4.2 34.7 1.0
CG A:HIS164 4.2 28.4 1.0
ND1 A:HIS164 4.2 25.3 1.0
CG A:HIS200 4.3 28.5 1.0
ND1 A:HIS200 4.3 28.1 1.0
CB A:ASP201 4.4 28.0 1.0
CB A:ASP318 4.5 31.9 1.0
NE2 A:HIS160 4.5 39.7 1.0
CG2 A:VAL168 4.7 32.6 1.0
O A:HOH608 4.9 27.0 1.0
CA A:ASP318 5.0 30.3 1.0

Zinc binding site 2 out of 4 in 6ft0

Go back to Zinc Binding Sites List in 6ft0
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425


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-425 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:35.8
occ:1.00
 NE2 B:HIS164 2.2 27.2 1.0
OD2 B:ASP201 2.2 28.0 1.0
O B:HOH622 2.2 31.0 1.0
OD1 B:ASP318 2.2 34.1 1.0
NE2 B:HIS200 2.3 27.0 1.0
O B:HOH677 2.3 27.1 1.0
CD2 B:HIS200 3.0 26.5 1.0
CG B:ASP318 3.1 34.6 1.0
CG B:ASP201 3.2 27.7 1.0
CD2 B:HIS164 3.2 30.0 1.0
CE1 B:HIS164 3.2 30.7 1.0
OD2 B:ASP318 3.3 31.7 1.0
CE1 B:HIS200 3.4 28.5 1.0
OD1 B:ASP201 3.6 29.4 1.0
MG B:MG502 3.8 18.8 1.0
O B:HOH678 3.9 27.5 1.0
O B:HOH637 4.1 34.4 1.0
CD2 B:HIS160 4.2 31.5 1.0
CG B:HIS200 4.3 28.6 1.0
ND1 B:HIS164 4.3 29.8 1.0
CG B:HIS164 4.3 29.8 1.0
CB B:ASP201 4.3 29.3 1.0
ND1 B:HIS200 4.4 30.5 1.0
NE2 B:HIS160 4.4 31.4 1.0
CB B:ASP318 4.5 33.0 1.0
O B:HOH620 4.7 23.9 1.0
CG2 B:VAL168 4.7 33.7 1.0

Zinc binding site 3 out of 4 in 6ft0

Go back to Zinc Binding Sites List in 6ft0
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425


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-425 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:35.7
occ:1.00
 OD1 C:ASP318 2.1 34.1 1.0
OD2 C:ASP201 2.2 27.9 1.0
NE2 C:HIS164 2.2 27.4 1.0
O C:HOH666 2.3 32.5 1.0
NE2 C:HIS200 2.3 28.8 1.0
O C:HOH628 2.3 25.7 1.0
CG C:ASP318 3.0 34.6 1.0
CD2 C:HIS200 3.1 26.8 1.0
CG C:ASP201 3.2 27.9 1.0
CE1 C:HIS164 3.2 26.9 1.0
OD2 C:ASP318 3.2 35.5 1.0
CD2 C:HIS164 3.2 27.9 1.0
CE1 C:HIS200 3.4 28.4 1.0
OD1 C:ASP201 3.7 26.9 1.0
MG C:MG503 3.9 19.2 1.0
O C:HOH678 4.0 28.1 1.0
CD2 C:HIS160 4.2 35.4 1.0
O C:HOH619 4.3 36.9 1.0
CG C:HIS200 4.3 26.4 1.0
ND1 C:HIS164 4.3 24.3 1.0
CB C:ASP201 4.3 26.3 1.0
CG C:HIS164 4.4 26.9 1.0
ND1 C:HIS200 4.4 28.4 1.0
CB C:ASP318 4.4 33.6 1.0
NE2 C:HIS160 4.4 30.1 1.0
CG2 C:VAL168 4.7 31.7 1.0
O C:HOH633 4.7 25.1 1.0
CA C:ASP318 4.9 32.9 1.0
C28 C:E6E510 5.0 45.3 1.0

Zinc binding site 4 out of 4 in 6ft0

Go back to Zinc Binding Sites List in 6ft0
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425


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-425 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:31.0
occ:1.00
 OD2 D:ASP201 2.2 25.2 1.0
NE2 D:HIS164 2.2 21.5 1.0
OD1 D:ASP318 2.2 27.4 1.0
NE2 D:HIS200 2.3 22.2 1.0
O D:HOH648 2.3 23.9 1.0
O D:HOH697 2.4 30.8 1.0
CG D:ASP318 3.1 28.3 1.0
CD2 D:HIS200 3.1 20.5 1.0
CE1 D:HIS164 3.2 26.0 1.0
CG D:ASP201 3.2 28.7 1.0
CD2 D:HIS164 3.3 25.9 1.0
CE1 D:HIS200 3.3 23.1 1.0
OD2 D:ASP318 3.3 27.6 1.0
OD1 D:ASP201 3.7 24.0 1.0
MG D:MG503 3.9 16.9 1.0
O D:HOH727 3.9 26.5 1.0
O D:HOH690 4.1 29.2 1.0
CD2 D:HIS160 4.2 30.5 1.0
ND1 D:HIS164 4.3 23.5 1.0
CG D:HIS200 4.3 20.0 1.0
CB D:ASP201 4.3 27.3 1.0
ND1 D:HIS200 4.4 23.4 1.0
CG D:HIS164 4.4 27.0 1.0
NE2 D:HIS160 4.4 34.2 1.0
CB D:ASP318 4.5 28.6 1.0
CG2 D:VAL168 4.7 24.0 1.0
O D:HOH663 4.7 21.6 1.0
C27 D:E6E517 5.0 42.3 1.0
CA D:ASP318 5.0 27.2 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-425 To Be Published.
Page generated: Mon Oct 28 21:23:44 2024

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