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Zinc in PDB 6hwo: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335, PDB code: 6hwo 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) 80.19 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.465, 110.848, 160.461, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.5

Other elements in 6hwo:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335 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-1335 (pdb code 6hwo). 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-1335, PDB code: 6hwo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hwo

Go back to Zinc Binding Sites List in 6hwo
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:34.1
occ:1.00
 O A:HOH631 2.1 28.3 1.0
OD2 A:ASP201 2.1 25.4 1.0
NE2 A:HIS164 2.2 24.4 1.0
NE2 A:HIS200 2.2 28.3 1.0
OD1 A:ASP318 2.2 28.5 1.0
O A:HOH683 2.4 40.0 1.0
CG A:ASP318 3.0 36.3 1.0
CD2 A:HIS200 3.1 27.5 1.0
CD2 A:HIS164 3.1 26.4 1.0
CG A:ASP201 3.1 28.8 1.0
OD2 A:ASP318 3.2 39.4 1.0
CE1 A:HIS164 3.2 27.4 1.0
CE1 A:HIS200 3.2 27.0 1.0
OD1 A:ASP201 3.7 28.0 1.0
MG A:MG514 3.7 21.7 1.0
O A:HOH690 3.8 34.8 1.0
O A:HOH659 4.0 35.5 1.0
CD2 A:HIS160 4.2 36.8 1.0
CG A:HIS164 4.3 26.2 1.0
CG A:HIS200 4.3 27.4 1.0
ND1 A:HIS164 4.3 23.6 1.0
CB A:ASP201 4.3 28.8 1.0
ND1 A:HIS200 4.3 26.8 1.0
CB A:ASP318 4.4 31.4 1.0
NE2 A:HIS160 4.5 34.6 1.0
CG2 A:VAL168 4.7 29.0 1.0
O A:HOH610 4.8 27.7 1.0
C25 A:FFZ513 4.9 69.7 1.0
CA A:ASP318 4.9 30.0 1.0

Zinc binding site 2 out of 4 in 6hwo

Go back to Zinc Binding Sites List in 6hwo
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn508

b:34.6
occ:1.00
 O B:HOH612 1.9 28.4 1.0
OD2 B:ASP201 2.1 29.5 1.0
NE2 B:HIS164 2.2 28.1 1.0
OD1 B:ASP318 2.2 29.3 1.0
O B:HOH691 2.2 25.4 1.0
NE2 B:HIS200 2.3 29.7 1.0
CG B:ASP201 3.1 29.3 1.0
CG B:ASP318 3.1 33.0 1.0
CD2 B:HIS200 3.1 32.5 1.0
CD2 B:HIS164 3.1 30.0 1.0
CE1 B:HIS164 3.2 32.6 1.0
CE1 B:HIS200 3.3 32.3 1.0
OD2 B:ASP318 3.4 33.5 1.0
OD1 B:ASP201 3.5 29.5 1.0
MG B:MG513 3.8 18.3 1.0
O B:HOH701 3.9 28.0 1.0
O B:HOH652 4.2 33.0 1.0
CD2 B:HIS160 4.2 33.8 1.0
CB B:ASP201 4.3 32.4 1.0
ND1 B:HIS164 4.3 32.1 1.0
CG B:HIS200 4.3 30.4 1.0
CG B:HIS164 4.3 30.8 1.0
ND1 B:HIS200 4.3 32.5 1.0
NE2 B:HIS160 4.5 27.4 1.0
CB B:ASP318 4.5 30.9 1.0
CG2 B:VAL168 4.7 30.5 1.0
O B:HOH625 4.8 26.5 1.0
CA B:ASP318 5.0 31.3 1.0
C25 B:FFZ512 5.0 51.2 1.0

Zinc binding site 3 out of 4 in 6hwo

Go back to Zinc Binding Sites List in 6hwo
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn509

b:32.5
occ:1.00
 O C:HOH617 2.0 28.8 1.0
OD2 C:ASP201 2.1 23.4 1.0
OD1 C:ASP318 2.2 34.0 1.0
NE2 C:HIS164 2.2 25.6 1.0
O C:HOH680 2.2 27.6 1.0
NE2 C:HIS200 2.2 28.7 1.0
CG C:ASP318 3.1 36.5 1.0
CD2 C:HIS200 3.2 27.7 1.0
CG C:ASP201 3.2 27.8 1.0
CE1 C:HIS164 3.2 26.5 1.0
CD2 C:HIS164 3.2 25.9 1.0
CE1 C:HIS200 3.2 29.0 1.0
OD2 C:ASP318 3.4 36.1 1.0
OD1 C:ASP201 3.7 26.1 1.0
MG C:MG512 3.8 18.4 1.0
O C:HOH701 3.9 28.4 1.0
CD2 C:HIS160 4.1 27.1 1.0
ND1 C:HIS164 4.3 24.6 1.0
ND1 C:HIS200 4.3 29.7 1.0
CB C:ASP201 4.3 25.8 1.0
CG C:HIS200 4.3 27.0 1.0
O C:HOH631 4.3 34.6 1.0
CG C:HIS164 4.3 29.2 1.0
NE2 C:HIS160 4.4 22.5 1.0
CB C:ASP318 4.5 33.7 1.0
CG2 C:VAL168 4.7 28.6 1.0
O C:HOH618 4.8 26.7 1.0

Zinc binding site 4 out of 4 in 6hwo

Go back to Zinc Binding Sites List in 6hwo
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn512

b:29.3
occ:1.00
 OD2 D:ASP201 2.1 23.6 1.0
NE2 D:HIS200 2.1 21.5 1.0
NE2 D:HIS164 2.2 22.8 1.0
O D:HOH638 2.2 27.5 1.0
OD1 D:ASP318 2.2 23.6 1.0
O D:HOH706 2.3 27.7 1.0
CG D:ASP201 3.1 24.1 1.0
CD2 D:HIS200 3.1 21.0 1.0
CE1 D:HIS164 3.1 22.6 1.0
CG D:ASP318 3.1 25.7 1.0
CE1 D:HIS200 3.2 22.1 1.0
CD2 D:HIS164 3.2 22.4 1.0
OD2 D:ASP318 3.3 29.2 1.0
OD1 D:ASP201 3.5 22.0 1.0
MG D:MG516 3.9 18.0 1.0
O D:HOH680 3.9 27.6 1.0
CD2 D:HIS160 4.1 28.6 1.0
O D:HOH666 4.2 27.8 1.0
CG D:HIS200 4.2 20.9 1.0
ND1 D:HIS200 4.3 20.0 1.0
ND1 D:HIS164 4.3 20.8 1.0
CB D:ASP201 4.3 23.0 1.0
CG D:HIS164 4.4 21.5 1.0
NE2 D:HIS160 4.4 30.6 1.0
CB D:ASP318 4.5 24.6 1.0
O D:HOH658 4.7 23.4 1.0
CG2 D:VAL168 4.7 23.2 1.0
C25 D:FFZ515 4.9 42.2 1.0
CA D:ASP318 5.0 23.3 1.0

Reference:

E.De Heuvel, A.K.Singh, P.Boronat, A.J.Kooistra, T.Van Der Meer, P.Sadek, A.R.Blaazer, N.C.Shaner, D.S.Bindels, G.Caljon, L.Maes, G.J.Sterk, M.Siderius, M.Oberholzer, I.J.P.De Esch, D.G.Brown, R.Leurs. Alkynamide Phthalazinones As A New Class of TBRPDEB1 Inhibitors (Part 2). Bioorg.Med.Chem. V. 27 4013 2019.
ISSN: ESSN 1464-3391
PubMed: 31378593
DOI: 10.1016/J.BMC.2019.06.026
Page generated: Mon Oct 28 23:25:02 2024

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