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Zinc in PDB 6fdi: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226, PDB code: 6fdi 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) 67.10 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.804, 111.042, 161.089, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20

Other elements in 6fdi:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226 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-226 (pdb code 6fdi). 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-226, PDB code: 6fdi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6fdi

Go back to Zinc Binding Sites List in 6fdi
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:23.4
occ:1.00
 OD2 A:ASP201 2.1 17.7 1.0
OD1 A:ASP318 2.2 20.9 1.0
NE2 A:HIS164 2.2 16.5 1.0
NE2 A:HIS200 2.2 17.8 1.0
O A:HOH634 2.3 18.6 1.0
O A:HOH707 2.4 20.2 1.0
CD2 A:HIS200 3.1 17.3 1.0
CG A:ASP318 3.1 20.6 1.0
CG A:ASP201 3.1 19.6 1.0
CE1 A:HIS164 3.2 17.2 1.0
CD2 A:HIS164 3.2 16.6 1.0
CE1 A:HIS200 3.3 17.6 1.0
OD2 A:ASP318 3.3 22.6 1.0
OD1 A:ASP201 3.6 20.4 1.0
MG A:MG502 3.8 17.1 1.0
O A:HOH755 4.0 18.6 1.0
CD2 A:HIS160 4.1 20.8 1.0
O A:HOH715 4.2 21.0 1.0
CG A:HIS200 4.3 16.6 1.0
NE2 A:HIS160 4.3 19.3 1.0
ND1 A:HIS164 4.3 17.1 1.0
CB A:ASP201 4.3 18.3 1.0
ND1 A:HIS200 4.3 17.7 1.0
CG A:HIS164 4.4 17.1 1.0
CB A:ASP318 4.5 18.9 1.0
O A:HOH636 4.7 18.1 1.0
CG2 A:VAL168 4.8 18.5 1.0
C24 A:D5T514 5.0 21.8 1.0
CA A:ASP318 5.0 19.4 1.0

Zinc binding site 2 out of 4 in 6fdi

Go back to Zinc Binding Sites List in 6fdi
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:26.2
occ:1.00
 O B:HOH621 2.0 20.4 1.0
NE2 B:HIS164 2.1 19.2 1.0
OD2 B:ASP201 2.2 21.3 1.0
OD1 B:ASP318 2.2 20.6 1.0
O B:HOH705 2.2 19.6 1.0
NE2 B:HIS200 2.3 19.8 1.0
CE1 B:HIS164 3.1 20.1 1.0
CG B:ASP318 3.1 21.7 1.0
CG B:ASP201 3.1 20.5 1.0
CD2 B:HIS200 3.1 21.5 1.0
CD2 B:HIS164 3.2 19.2 1.0
CE1 B:HIS200 3.3 23.2 1.0
OD2 B:ASP318 3.4 21.6 1.0
OD1 B:ASP201 3.6 21.6 1.0
MG B:MG502 3.9 20.3 1.0
O B:HOH738 4.0 20.2 1.0
CD2 B:HIS160 4.1 23.6 1.0
O B:HOH678 4.1 19.3 1.0
ND1 B:HIS164 4.2 20.2 1.0
CG B:HIS164 4.3 21.9 1.0
NE2 B:HIS160 4.3 23.6 1.0
CB B:ASP201 4.3 21.7 1.0
CG B:HIS200 4.3 20.5 1.0
ND1 B:HIS200 4.4 20.1 1.0
CB B:ASP318 4.5 22.3 1.0
CG2 B:VAL168 4.7 21.8 1.0
O B:HOH632 4.7 22.4 1.0
C24 B:D5T512 4.9 21.4 1.0
CA B:ASP318 5.0 22.9 1.0

Zinc binding site 3 out of 4 in 6fdi

Go back to Zinc Binding Sites List in 6fdi
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn504

b:26.4
occ:1.00
 O C:HOH615 2.1 19.1 1.0
OD2 C:ASP201 2.2 21.8 1.0
OD1 C:ASP318 2.2 24.0 1.0
NE2 C:HIS200 2.2 20.7 1.0
NE2 C:HIS164 2.2 18.5 1.0
O C:HOH680 2.2 20.2 1.0
CD2 C:HIS200 3.1 18.3 1.0
CG C:ASP318 3.1 25.1 1.0
CG C:ASP201 3.2 20.2 1.0
CE1 C:HIS164 3.2 19.2 1.0
CD2 C:HIS164 3.2 20.1 1.0
CE1 C:HIS200 3.3 18.9 1.0
OD2 C:ASP318 3.3 24.4 1.0
OD1 C:ASP201 3.6 20.4 1.0
MG C:MG505 3.8 20.1 1.0
O C:HOH718 4.0 20.2 1.0
CD2 C:HIS160 4.1 21.8 1.0
O C:HOH669 4.2 20.0 1.0
CG C:HIS200 4.3 18.3 1.0
NE2 C:HIS160 4.3 23.4 1.0
ND1 C:HIS164 4.3 19.2 1.0
ND1 C:HIS200 4.3 19.5 1.0
CB C:ASP201 4.3 20.5 1.0
CG C:HIS164 4.4 19.8 1.0
CB C:ASP318 4.5 23.7 1.0
O C:HOH643 4.7 19.7 1.0
CG2 C:VAL168 4.7 22.6 1.0
C24 C:D5T513 5.0 25.6 1.0
CA C:ASP318 5.0 22.9 1.0

Zinc binding site 4 out of 4 in 6fdi

Go back to Zinc Binding Sites List in 6fdi
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:21.8
occ:1.00
 OD2 D:ASP201 2.1 15.9 1.0
NE2 D:HIS164 2.2 15.5 1.0
O D:HOH625 2.2 19.7 1.0
OD1 D:ASP318 2.3 16.4 1.0
NE2 D:HIS200 2.3 15.5 1.0
O D:HOH762 2.3 18.3 1.0
CG D:ASP318 3.1 18.7 1.0
CG D:ASP201 3.1 18.2 1.0
CE1 D:HIS164 3.1 15.8 1.0
CD2 D:HIS200 3.2 14.3 1.0
CD2 D:HIS164 3.2 16.1 1.0
OD2 D:ASP318 3.3 21.4 1.0
CE1 D:HIS200 3.3 17.0 1.0
OD1 D:ASP201 3.6 18.7 1.0
MG D:MG504 3.9 15.8 1.0
O D:HOH776 4.0 18.4 1.0
CD2 D:HIS160 4.2 20.5 1.0
O D:HOH727 4.3 18.3 1.0
ND1 D:HIS164 4.3 16.1 1.0
CB D:ASP201 4.3 17.1 1.0
CG D:HIS164 4.3 17.1 1.0
CG D:HIS200 4.3 13.8 1.0
ND1 D:HIS200 4.4 15.5 1.0
NE2 D:HIS160 4.4 20.3 1.0
CB D:ASP318 4.5 18.0 1.0
CG2 D:VAL168 4.7 17.9 1.0
O D:HOH677 4.7 16.4 1.0
C24 D:D5T512 4.9 20.9 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-226 To Be Published.
Page generated: Mon Oct 28 20:51:35 2024

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