Magnesium in PDB 6imb: Crystal Structure of PDE4D Complexed with A Novel Inhibitor

Enzymatic activity of Crystal Structure of PDE4D Complexed with A Novel Inhibitor

All present enzymatic activity of Crystal Structure of PDE4D Complexed with A Novel Inhibitor:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of PDE4D Complexed with A Novel Inhibitor, PDB code: 6imb was solved by X.Zhang, H.Su, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.45 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.497, 80.432, 163.532, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 21.9

Other elements in 6imb:

The structure of Crystal Structure of PDE4D Complexed with A Novel Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor (pdb code 6imb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor, PDB code: 6imb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6imb

Go back to Magnesium Binding Sites List in 6imb
Magnesium binding site 1 out of 4 in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of PDE4D Complexed with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:7.2
occ:1.00
O A:HOH753 2.1 8.0 1.0
OD1 A:ASP201 2.1 5.6 1.0
O A:HOH611 2.1 7.0 1.0
O A:HOH661 2.1 6.5 1.0
O A:HOH669 2.1 7.6 1.0
O A:HOH686 2.1 8.3 1.0
CG A:ASP201 3.1 4.8 1.0
OD2 A:ASP201 3.4 5.4 1.0
ZN A:ZN501 3.7 11.3 1.0
O A:HOH804 3.8 18.1 1.0
O A:HOH725 4.0 8.2 1.0
OE2 A:GLU230 4.1 10.6 1.0
CD2 A:HIS200 4.1 4.8 1.0
NE2 A:HIS233 4.1 6.4 1.0
O A:HIS200 4.2 5.7 1.0
O A:HOH724 4.2 12.9 1.0
OG1 A:THR271 4.2 7.4 1.0
CD2 A:HIS233 4.4 5.9 1.0
OD2 A:ASP318 4.4 12.8 1.0
CB A:ASP201 4.4 5.7 1.0
NE2 A:HIS200 4.5 4.3 1.0
CD2 A:HIS204 4.5 6.6 1.0
O A:HOH696 4.6 23.5 1.0
O A:THR271 4.7 11.0 1.0
CB A:THR271 4.7 8.9 1.0
CD2 A:HIS160 4.8 8.2 1.0
NE2 A:HIS160 4.8 11.1 1.0
CA A:ASP201 4.8 5.4 1.0
NE2 A:HIS204 4.8 7.0 1.0
CG A:GLU230 4.8 8.9 1.0
CD A:GLU230 4.9 9.1 1.0

Magnesium binding site 2 out of 4 in 6imb

Go back to Magnesium Binding Sites List in 6imb
Magnesium binding site 2 out of 4 in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of PDE4D Complexed with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:15.9
occ:1.00
O B:HOH700 2.1 14.4 1.0
OD1 B:ASP301 2.1 14.5 1.0
O B:HOH611 2.1 15.8 1.0
O B:HOH634 2.2 15.4 1.0
CG B:ASP301 3.0 13.9 1.0
OD2 B:ASP301 3.4 16.4 1.0
O B:HOH769 3.7 42.7 1.0
O B:ASP301 4.0 24.2 1.0
CB B:ASP301 4.3 17.9 1.0
CA B:ASP301 4.6 21.1 1.0
C B:ASP301 4.7 22.6 1.0

Magnesium binding site 3 out of 4 in 6imb

Go back to Magnesium Binding Sites List in 6imb
Magnesium binding site 3 out of 4 in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of PDE4D Complexed with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:7.3
occ:1.00
OD1 B:ASP201 2.0 7.5 1.0
O B:HOH625 2.1 9.0 1.0
O B:HOH738 2.1 9.0 1.0
O B:HOH661 2.1 9.5 1.0
O B:HOH685 2.1 8.8 1.0
O B:HOH640 2.1 8.6 1.0
CG B:ASP201 3.0 7.2 1.0
OD2 B:ASP201 3.4 7.5 1.0
ZN B:ZN501 3.7 13.7 1.0
O B:HOH759 3.8 22.7 1.0
OE2 B:GLU230 4.0 11.8 1.0
O B:HOH696 4.1 10.6 1.0
CD2 B:HIS200 4.1 9.1 1.0
O B:HIS200 4.1 7.7 1.0
NE2 B:HIS233 4.1 8.5 1.0
O B:HOH739 4.2 13.4 1.0
OG1 B:THR271 4.2 9.2 1.0
CD2 B:HIS233 4.3 8.8 1.0
CB B:ASP201 4.4 8.0 1.0
OD2 B:ASP318 4.5 15.0 1.0
NE2 B:HIS200 4.5 7.4 1.0
CD2 B:HIS204 4.6 8.4 1.0
O B:HOH665 4.6 22.0 1.0
O B:THR271 4.7 12.6 1.0
CD2 B:HIS160 4.7 8.8 1.0
CB B:THR271 4.8 11.4 1.0
CA B:ASP201 4.8 7.3 1.0
NE2 B:HIS160 4.8 11.8 1.0
CG B:GLU230 4.8 8.7 1.0
NE2 B:HIS204 4.8 9.5 1.0
CD B:GLU230 4.8 12.4 1.0
O B:HOH695 4.9 37.8 1.0
C B:HIS200 5.0 8.3 1.0

Magnesium binding site 4 out of 4 in 6imb

Go back to Magnesium Binding Sites List in 6imb
Magnesium binding site 4 out of 4 in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of PDE4D Complexed with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:22.6
occ:1.00
O B:HOH603 2.0 40.0 1.0
O B:HOH720 2.2 29.6 1.0
O B:HOH728 2.4 29.8 1.0
OD2 B:ASP401 4.2 19.6 1.0
O B:HOH704 4.3 21.0 1.0
O B:HOH646 4.4 30.4 1.0
CB B:ASP397 4.5 22.0 1.0
OD2 B:ASP397 4.6 24.9 1.0
CG B:ASP397 4.9 23.4 1.0

Reference:

X.Zhang, G.Dong, H.Li, W.Chen, J.Li, C.Feng, Z.Gu, F.Zhu, R.Zhang, M.Li, W.Tang, H.Liu, Y.Xu. Structure-Aided Identification and Optimization of Tetrahydro-Isoquinolines As Novel PDE4 Inhibitors Leading to Discovery of An Effective Antipsoriasis Agent. J.Med.Chem. V. 62 5579 2019.
ISSN: ISSN 0022-2623
PubMed: 31099559
DOI: 10.1021/ACS.JMEDCHEM.9B00518
Page generated: Mon Dec 14 22:58:11 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy