Atomistry » Zinc » PDB 6hqy-6hyh » 6hwo
Atomistry »
  Zinc »
    PDB 6hqy-6hyh »
      6hwo »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy