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Zinc in PDB 6rcw: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053, PDB code: 6rcw 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) 91.22 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.894, 110.505, 160.694, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.1

Other elements in 6rcw:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053 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-053 (pdb code 6rcw). 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-053, PDB code: 6rcw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6rcw

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053


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-053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:35.8
occ:1.00
 OD2 A:ASP201 2.1 31.0 1.0
OD1 A:ASP318 2.2 32.8 1.0
NE2 A:HIS200 2.2 31.0 1.0
NE2 A:HIS164 2.2 30.3 1.0
O A:HOH711 2.3 35.6 1.0
O A:HOH650 2.3 32.9 1.0
CD2 A:HIS200 3.0 28.7 1.0
CG A:ASP318 3.0 35.3 1.0
CG A:ASP201 3.1 31.1 1.0
CD2 A:HIS164 3.2 28.9 1.0
OD2 A:ASP318 3.2 42.0 1.0
CE1 A:HIS164 3.3 32.9 1.0
CE1 A:HIS200 3.3 29.7 1.0
OD1 A:ASP201 3.6 31.0 1.0
MG A:MG502 3.8 26.4 1.0
O A:HOH677 3.8 40.2 1.0
O A:HOH730 3.8 33.0 1.0
O A:HOH747 4.2 54.2 1.0
CD2 A:HIS160 4.2 35.5 1.0
CG A:HIS200 4.2 29.1 1.0
CB A:ASP201 4.3 31.4 1.0
CG A:HIS164 4.3 31.5 1.0
ND1 A:HIS200 4.4 30.4 1.0
ND1 A:HIS164 4.4 28.7 1.0
CB A:ASP318 4.4 32.7 1.0
NE2 A:HIS160 4.6 35.0 1.0
O A:HOH629 4.8 28.8 1.0
CG2 A:VAL168 4.8 32.2 1.0
CA A:ASP318 5.0 32.1 1.0

Zinc binding site 2 out of 4 in 6rcw

Go back to Zinc Binding Sites List in 6rcw
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053


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-053 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:41.2
occ:1.00
 O B:HOH612 2.0 35.0 1.0
OD2 B:ASP201 2.0 34.1 1.0
NE2 B:HIS164 2.1 32.8 1.0
O B:HOH703 2.2 35.7 1.0
OD1 B:ASP318 2.2 37.1 1.0
NE2 B:HIS200 2.3 34.1 1.0
CE1 B:HIS164 3.0 32.9 1.0
CG B:ASP318 3.1 38.0 1.0
CD2 B:HIS164 3.2 35.7 1.0
CD2 B:HIS200 3.2 30.6 1.0
CG B:ASP201 3.2 32.4 1.0
OD2 B:ASP318 3.3 38.3 1.0
CE1 B:HIS200 3.4 32.7 1.0
O B:HOH667 3.7 34.9 1.0
MG B:MG502 3.8 28.7 1.0
OD1 B:ASP201 3.9 32.2 1.0
O B:HOH680 4.0 41.8 1.0
CD2 B:HIS160 4.1 39.4 1.0
ND1 B:HIS164 4.2 33.2 1.0
CB B:ASP201 4.2 34.6 1.0
CG B:HIS164 4.3 33.9 1.0
CG B:HIS200 4.4 33.3 1.0
C27 B:JX2514 4.4 73.9 1.0
ND1 B:HIS200 4.4 35.5 1.0
NE2 B:HIS160 4.4 36.7 1.0
CB B:ASP318 4.5 39.1 1.0
CG2 B:VAL168 4.7 37.8 1.0
C28 B:JX2514 4.7 77.2 1.0
O B:HOH601 4.8 31.2 1.0
CA B:ASP318 5.0 39.6 1.0

Zinc binding site 3 out of 4 in 6rcw

Go back to Zinc Binding Sites List in 6rcw
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053


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-053 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:38.7
occ:1.00
 OD2 C:ASP201 2.1 34.3 1.0
O C:HOH604 2.2 30.1 1.0
NE2 C:HIS164 2.2 34.0 1.0
O C:HOH710 2.3 36.8 1.0
NE2 C:HIS200 2.3 34.7 1.0
OD1 C:ASP318 2.3 38.5 1.0
CG C:ASP318 3.0 37.3 1.0
OD2 C:ASP318 3.0 37.7 1.0
CG C:ASP201 3.0 29.9 1.0
CD2 C:HIS200 3.1 29.2 1.0
CD2 C:HIS164 3.2 29.5 1.0
CE1 C:HIS164 3.2 33.3 1.0
CE1 C:HIS200 3.3 33.4 1.0
OD1 C:ASP201 3.5 32.9 1.0
MG C:MG502 3.7 28.6 1.0
O C:HOH706 3.8 31.6 1.0
O C:HOH663 4.2 43.5 1.0
CD2 C:HIS160 4.2 31.7 1.0
CG C:HIS200 4.3 29.2 1.0
CB C:ASP201 4.3 30.8 1.0
ND1 C:HIS200 4.3 30.7 1.0
ND1 C:HIS164 4.3 30.7 1.0
CG C:HIS164 4.4 30.5 1.0
CB C:ASP318 4.4 37.2 1.0
NE2 C:HIS160 4.6 32.5 1.0
C27 C:JX2510 4.7 67.8 1.0
O C:HOH622 4.7 27.3 1.0
CG2 C:VAL168 4.8 34.4 1.0

Zinc binding site 4 out of 4 in 6rcw

Go back to Zinc Binding Sites List in 6rcw
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-053


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-053 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:34.8
occ:1.00
 OD1 D:ASP318 2.2 30.6 1.0
NE2 D:HIS164 2.2 28.2 1.0
NE2 D:HIS200 2.2 26.8 1.0
OD2 D:ASP201 2.2 31.5 1.0
O D:HOH619 2.3 30.2 1.0
O D:HOH736 2.3 35.3 1.0
CG D:ASP318 3.0 32.1 1.0
CG D:ASP201 3.1 32.7 1.0
CD2 D:HIS200 3.2 27.0 1.0
CE1 D:HIS164 3.2 27.6 1.0
CD2 D:HIS164 3.2 27.4 1.0
CE1 D:HIS200 3.2 29.7 1.0
OD2 D:ASP318 3.3 35.6 1.0
OD1 D:ASP201 3.5 31.9 1.0
MG D:MG503 3.8 26.9 1.0
O D:HOH744 3.9 35.6 1.0
O D:HOH711 4.1 37.4 1.0
CD2 D:HIS160 4.3 39.5 1.0
ND1 D:HIS164 4.3 27.7 1.0
CG D:HIS200 4.3 29.1 1.0
CG D:HIS164 4.3 29.8 1.0
ND1 D:HIS200 4.3 27.9 1.0
CB D:ASP201 4.3 30.1 1.0
CB D:ASP318 4.4 31.3 1.0
NE2 D:HIS160 4.6 38.4 1.0
C27 D:JX2515 4.6 68.4 1.0
O D:HOH630 4.6 26.3 1.0
CG2 D:VAL168 4.8 30.9 1.0
CA D:ASP318 5.0 28.4 1.0
C28 D:JX2515 5.0 67.4 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: Tue Oct 29 06:10:57 2024

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