Zinc in PDB 6ftw: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048, PDB code: 6ftw 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) 65.00 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.140, 111.430, 160.060, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.3

Other elements in 6ftw:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048 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-048 (pdb code 6ftw). 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-048, PDB code: 6ftw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ftw

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048


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-048 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:36.7
occ:1.00
 O A:HOH626 2.0 32.5 1.0
OD2 A:ASP201 2.1 28.1 1.0
NE2 A:HIS164 2.2 27.7 1.0
NE2 A:HIS200 2.2 33.7 1.0
OD1 A:ASP318 2.2 35.5 1.0
O A:HOH649 2.4 36.2 1.0
CD2 A:HIS200 3.0 30.1 1.0
CG A:ASP318 3.1 32.4 1.0
CG A:ASP201 3.1 29.0 1.0
OD2 A:ASP318 3.2 37.5 1.0
CD2 A:HIS164 3.2 29.8 1.0
CE1 A:HIS164 3.2 27.4 1.0
CE1 A:HIS200 3.3 34.5 1.0
OD1 A:ASP201 3.6 32.3 1.0
MG A:MG502 3.7 26.9 1.0
O A:HOH717 4.0 31.7 1.0
O A:HOH668 4.1 38.1 1.0
CD2 A:HIS160 4.1 30.0 1.0
CG A:HIS200 4.2 31.6 1.0
CB A:ASP201 4.3 30.0 1.0
ND1 A:HIS164 4.3 29.7 1.0
ND1 A:HIS200 4.3 37.3 1.0
CG A:HIS164 4.3 31.1 1.0
NE2 A:HIS160 4.4 27.6 1.0
CB A:ASP318 4.5 32.3 1.0
CG2 A:VAL168 4.7 32.4 1.0
C22 A:E6Z517 4.8 49.2 1.0
O A:HOH613 4.9 29.9 1.0

Zinc binding site 2 out of 4 in 6ftw

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048


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-048 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:44.2
occ:1.00
 O B:HOH626 2.0 39.5 1.0
NE2 B:HIS164 2.2 29.3 1.0
O B:HOH673 2.2 36.4 1.0
OD2 B:ASP201 2.2 39.2 1.0
OD1 B:ASP318 2.3 34.3 1.0
NE2 B:HIS200 2.3 40.6 1.0
CG B:ASP201 3.1 34.6 1.0
CG B:ASP318 3.1 42.8 1.0
CE1 B:HIS164 3.1 31.9 1.0
CD2 B:HIS164 3.2 35.7 1.0
CD2 B:HIS200 3.2 34.2 1.0
CE1 B:HIS200 3.3 41.0 1.0
OD2 B:ASP318 3.4 41.3 1.0
OD1 B:ASP201 3.4 32.1 1.0
O B:HOH658 3.7 38.0 1.0
MG B:MG502 3.7 33.0 1.0
CD2 B:HIS160 4.1 36.6 1.0
O B:HOH651 4.3 40.7 1.0
ND1 B:HIS164 4.3 29.8 1.0
CG B:HIS164 4.3 30.7 1.0
CB B:ASP201 4.3 40.2 1.0
CG B:HIS200 4.4 35.7 1.0
ND1 B:HIS200 4.4 38.9 1.0
CB B:ASP318 4.5 45.2 1.0
NE2 B:HIS160 4.5 33.3 1.0
C22 B:E6Z509 4.6 60.2 1.0
CG2 B:VAL168 4.7 41.1 1.0
O B:HOH614 4.7 33.4 1.0
C23 B:E6Z509 5.0 63.3 1.0
O B:HOH654 5.0 31.6 1.0

Zinc binding site 3 out of 4 in 6ftw

Go back to Zinc Binding Sites List in 6ftw
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048


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-048 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:41.6
occ:1.00
 O C:HOH625 2.2 33.8 1.0
O C:HOH658 2.2 27.7 1.0
OD1 C:ASP318 2.2 36.0 1.0
NE2 C:HIS200 2.3 34.6 1.0
NE2 C:HIS164 2.3 30.2 1.0
OD2 C:ASP201 2.3 35.9 1.0
CD2 C:HIS200 3.0 28.5 1.0
CG C:ASP318 3.1 38.3 1.0
CG C:ASP201 3.2 35.4 1.0
CE1 C:HIS164 3.2 29.6 1.0
CD2 C:HIS164 3.3 33.0 1.0
OD2 C:ASP318 3.3 45.8 1.0
CE1 C:HIS200 3.4 34.4 1.0
OD1 C:ASP201 3.6 32.1 1.0
MG C:MG502 3.7 28.0 1.0
O C:HOH675 3.8 30.8 1.0
CD2 C:HIS160 4.2 33.0 1.0
CG C:HIS200 4.2 33.0 1.0
O C:HOH644 4.3 43.4 1.0
ND1 C:HIS164 4.4 34.2 1.0
CB C:ASP201 4.4 37.0 1.0
CB C:ASP318 4.4 39.9 1.0
CG C:HIS164 4.4 32.7 1.0
ND1 C:HIS200 4.4 31.6 1.0
NE2 C:HIS160 4.6 30.8 1.0
CG2 C:VAL168 4.7 33.0 1.0
O C:HOH607 4.7 26.4 1.0
C22 C:E6Z512 4.9 54.4 1.0
CA C:ASP318 4.9 40.5 1.0

Zinc binding site 4 out of 4 in 6ftw

Go back to Zinc Binding Sites List in 6ftw
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-048


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-048 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:38.2
occ:1.00
 OD2 D:ASP201 2.1 29.6 1.0
NE2 D:HIS200 2.2 30.4 1.0
OD1 D:ASP318 2.2 35.1 1.0
NE2 D:HIS164 2.3 29.6 1.0
O D:HOH617 2.4 35.3 1.0
O D:HOH654 2.4 33.4 1.0
CG D:ASP318 3.1 36.6 1.0
CD2 D:HIS200 3.1 27.4 1.0
CG D:ASP201 3.1 33.5 1.0
CE1 D:HIS200 3.2 30.1 1.0
CE1 D:HIS164 3.2 30.3 1.0
OD2 D:ASP318 3.3 39.1 1.0
CD2 D:HIS164 3.3 29.8 1.0
OD1 D:ASP201 3.6 32.6 1.0
O D:HOH709 3.7 37.3 1.0
MG D:MG502 3.8 29.1 1.0
CD2 D:HIS160 4.1 36.9 1.0
CG D:HIS200 4.2 28.3 1.0
ND1 D:HIS200 4.3 28.5 1.0
NE2 D:HIS160 4.3 36.0 1.0
O D:HOH648 4.3 38.4 1.0
CB D:ASP201 4.3 32.4 1.0
ND1 D:HIS164 4.4 28.9 1.0
CB D:ASP318 4.4 36.7 1.0
CG D:HIS164 4.4 27.6 1.0
O D:HOH652 4.7 31.5 1.0
CG2 D:VAL168 4.8 25.1 1.0
C22 D:E6Z516 5.0 57.7 1.0
CA D:ASP318 5.0 31.2 1.0

Reference:

E.De Heuvel, A.K.Singh, E.Edink, T.Van Der Meer, M.Van Der Woude, P.Sadek, M.P.Krell-Jorgensen, T.Van Den Bergh, J.Veerman, G.Caljon, T.D.Kalejaiye, M.Wijtmans, L.Maes, H.P.De Koning, G.Jan Sterk, M.Siderius, I.J.P.De Esch, D.G.Brown, R.Leurs. Alkynamide Phthalazinones As A New Class of TBRPDEB1 Inhibitors. Bioorg.Med.Chem. V. 27 3998 2019.
ISSN: ESSN 1464-3391
PubMed: 31327675
DOI: 10.1016/J.BMC.2019.06.027
Page generated: Wed Dec 16 11:49:21 2020

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