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Zinc in PDB 6fta: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098, PDB code: 6fta 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) 80.67 / 2.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.990, 110.760, 161.340, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24

Other elements in 6fta:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098 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-3098 (pdb code 6fta). 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-3098, PDB code: 6fta:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6fta

Go back to Zinc Binding Sites List in 6fta
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:43.8
occ:1.00
OD2 A:ASP201 1.9 42.3 1.0
OD1 A:ASP318 2.1 42.0 1.0
NE2 A:HIS164 2.2 38.2 1.0
NE2 A:HIS200 2.3 41.5 1.0
O A:HOH654 2.3 41.6 1.0
O A:HOH629 2.4 37.0 1.0
CG A:ASP318 3.0 42.8 1.0
CG A:ASP201 3.0 39.8 1.0
CD2 A:HIS200 3.1 39.7 1.0
CE1 A:HIS164 3.1 36.7 1.0
CD2 A:HIS164 3.1 39.1 1.0
OD2 A:ASP318 3.2 46.1 1.0
CE1 A:HIS200 3.3 42.6 1.0
OD1 A:ASP201 3.6 37.4 1.0
MG A:MG502 3.7 29.2 1.0
O A:HOH659 3.8 43.4 1.0
O A:HOH651 4.0 38.1 1.0
CD2 A:HIS160 4.1 44.5 1.0
ND1 A:HIS164 4.2 40.1 1.0
CB A:ASP201 4.3 36.2 1.0
CG A:HIS200 4.3 38.2 1.0
CG A:HIS164 4.3 39.6 1.0
ND1 A:HIS200 4.3 34.5 1.0
NE2 A:HIS160 4.4 41.8 1.0
CB A:ASP318 4.4 41.9 1.0
C27 A:E6N510 4.6 63.3 1.0
O A:HOH605 4.8 30.0 1.0
CG2 A:VAL168 4.8 35.5 1.0
C28 A:E6N510 5.0 63.6 1.0

Zinc binding site 2 out of 4 in 6fta

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:44.1
occ:1.00
OD2 B:ASP201 2.0 46.1 1.0
NE2 B:HIS164 2.2 42.5 1.0
NE2 B:HIS200 2.2 32.8 1.0
OD1 B:ASP318 2.2 40.7 1.0
O B:HOH680 2.2 39.4 1.0
O B:HOH627 2.3 33.7 1.0
CG B:ASP201 3.1 40.5 1.0
CD2 B:HIS200 3.1 34.0 1.0
CD2 B:HIS164 3.1 40.0 1.0
CE1 B:HIS164 3.2 42.0 1.0
CG B:ASP318 3.2 42.6 1.0
CE1 B:HIS200 3.2 32.3 1.0
OD2 B:ASP318 3.5 37.6 1.0
OD1 B:ASP201 3.7 37.6 1.0
MG B:MG502 3.8 28.4 1.0
O B:HOH664 4.0 32.0 1.0
CD2 B:HIS160 4.1 43.9 1.0
CB B:ASP201 4.1 38.2 1.0
O B:HOH625 4.2 41.3 1.0
CG B:HIS200 4.3 34.2 1.0
CG B:HIS164 4.3 39.5 1.0
ND1 B:HIS164 4.3 40.9 1.0
ND1 B:HIS200 4.3 33.9 1.0
NE2 B:HIS160 4.5 39.4 1.0
CB B:ASP318 4.6 43.2 1.0
C27 B:E6N508 4.6 56.2 1.0
O B:HOH615 4.7 30.4 1.0
CG2 B:VAL168 4.8 37.4 1.0
C28 B:E6N508 4.9 61.6 1.0

Zinc binding site 3 out of 4 in 6fta

Go back to Zinc Binding Sites List in 6fta
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:42.8
occ:1.00
OD2 C:ASP201 2.0 43.1 1.0
OD1 C:ASP318 2.1 41.7 1.0
O C:HOH661 2.1 35.8 1.0
NE2 C:HIS200 2.2 34.2 1.0
NE2 C:HIS164 2.2 37.1 1.0
O C:HOH621 2.4 27.2 1.0
CD2 C:HIS200 3.0 34.4 1.0
CG C:ASP318 3.0 41.6 1.0
CG C:ASP201 3.1 36.9 1.0
CE1 C:HIS164 3.2 36.7 1.0
CD2 C:HIS164 3.2 35.8 1.0
CE1 C:HIS200 3.2 40.6 1.0
OD2 C:ASP318 3.2 39.1 1.0
OD1 C:ASP201 3.6 32.7 1.0
MG C:MG502 3.8 23.9 1.0
O C:HOH641 3.8 26.6 1.0
CG C:HIS200 4.1 33.3 1.0
CD2 C:HIS160 4.2 45.9 1.0
CB C:ASP201 4.2 35.5 1.0
ND1 C:HIS200 4.2 33.2 1.0
ND1 C:HIS164 4.3 39.7 1.0
CG C:HIS164 4.4 39.6 1.0
CB C:ASP318 4.4 39.0 1.0
O C:HOH629 4.4 39.4 1.0
NE2 C:HIS160 4.5 38.5 1.0
C27 C:E6N506 4.7 58.2 1.0
CG2 C:VAL168 4.8 40.1 1.0
O C:HOH609 4.8 31.0 1.0
CA C:ASP318 5.0 41.4 1.0

Zinc binding site 4 out of 4 in 6fta

Go back to Zinc Binding Sites List in 6fta
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:38.6
occ:1.00
OD1 D:ASP318 2.1 39.0 1.0
OD2 D:ASP201 2.1 35.0 1.0
NE2 D:HIS164 2.2 35.2 1.0
O D:HOH628 2.3 31.6 1.0
NE2 D:HIS200 2.3 31.8 1.0
O D:HOH669 2.4 35.0 1.0
CD2 D:HIS200 3.1 29.9 1.0
CG D:ASP318 3.1 40.9 1.0
CG D:ASP201 3.1 34.8 1.0
CD2 D:HIS164 3.2 36.7 1.0
CE1 D:HIS164 3.2 34.0 1.0
CE1 D:HIS200 3.3 30.8 1.0
OD2 D:ASP318 3.4 40.6 1.0
OD1 D:ASP201 3.6 32.4 1.0
MG D:MG503 3.7 22.0 1.0
O D:HOH699 3.9 30.6 1.0
O D:HOH666 4.1 34.6 1.0
CD2 D:HIS160 4.2 44.1 1.0
ND1 D:HIS164 4.3 34.9 1.0
CG D:HIS200 4.3 31.5 1.0
CG D:HIS164 4.3 33.6 1.0
CB D:ASP201 4.3 35.0 1.0
ND1 D:HIS200 4.4 28.2 1.0
NE2 D:HIS160 4.5 40.0 1.0
CB D:ASP318 4.5 35.8 1.0
C27 D:E6N514 4.6 60.5 1.0
O D:HOH606 4.7 24.7 1.0
CG2 D:VAL168 4.7 30.9 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-3098 To Be Published.
Page generated: Wed Dec 16 11:49:19 2020

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