Atomistry » Zinc » PDB 6fju-6ful » 6ftw
Atomistry »
  Zinc »
    PDB 6fju-6ful »
      6ftw »

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

Go back to Zinc Binding Sites List in 6ftw
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

Go back to Zinc Binding Sites List in 6ftw
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy