Magnesium in PDB 5wqa: Crystal Structure of PDE4D Catalytic Domain Complexed with Selaginpulvilins K

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with Selaginpulvilins K:
3.1.4.53;

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Selaginpulvilins K, PDB code: 5wqa was solved by Y.Huang, T.Zhang, X.Zheng, S.Yin, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.79 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.992, 80.784, 163.575, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.2

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Selaginpulvilins K also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE4D Catalytic Domain Complexed with Selaginpulvilins K (pdb code 5wqa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of PDE4D Catalytic Domain Complexed with Selaginpulvilins K, PDB code: 5wqa:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Selaginpulvilins K


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 Catalytic Domain Complexed with Selaginpulvilins K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:7.2 occ:1.00 O A:HOH648 2.0 5.7 1.0 O A:HOH641 2.1 9.7 1.0 O A:HOH628 2.1 11.6 1.0 O A:HOH638 2.1 5.7 1.0 OD1 A:ASP201 2.2 8.6 1.0 O A:HOH668 2.2 8.7 1.0 CG A:ASP201 3.2 9.4 1.0 OD2 A:ASP201 3.5 9.9 1.0 ZN A:ZN502 3.9 13.5 1.0 OE2 A:GLU230 3.9 12.4 1.0 CD2 A:HIS200 4.1 10.7 1.0 NE2 A:HIS233 4.2 12.2 1.0 O A:HIS200 4.2 9.8 1.0 OG1 A:THR271 4.3 12.0 1.0 O A:HOH620 4.3 7.5 1.0 O39 A:J20501 4.4 19.2 1.0 CD2 A:HIS233 4.4 11.9 1.0 OD2 A:ASP318 4.5 11.0 1.0 NE2 A:HIS200 4.5 11.0 1.0 O A:THR271 4.5 12.9 1.0 CB A:ASP201 4.5 9.4 1.0 CD2 A:HIS204 4.6 11.1 1.0 O A:HOH653 4.7 14.8 1.0 CB A:THR271 4.8 12.2 1.0 CD A:GLU230 4.8 11.9 1.0 CA A:ASP201 4.8 9.7 1.0 CG A:GLU230 4.9 11.8 1.0 NE2 A:HIS204 4.9 11.0 1.0 CD2 A:HIS160 4.9 11.9 1.0 NE2 A:HIS160 5.0 11.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Selaginpulvilins K


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 Catalytic Domain Complexed with Selaginpulvilins K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:10.1 occ:1.00 O B:HOH634 2.0 9.7 1.0 O B:HOH614 2.1 12.0 1.0 O B:HOH628 2.1 9.8 1.0 OD1 B:ASP201 2.2 11.7 1.0 O B:HOH609 2.2 10.9 1.0 O B:HOH647 2.3 14.7 1.0 CG B:ASP201 3.1 12.9 1.0 OD2 B:ASP201 3.3 14.0 1.0 ZN B:ZN503 3.7 18.7 1.0 CD2 B:HIS200 4.0 15.2 1.0 O B:HIS200 4.1 13.0 1.0 NE2 B:HIS233 4.1 12.9 1.0 OE2 B:GLU230 4.2 12.5 1.0 O B:HOH610 4.2 11.4 1.0 OG1 B:THR271 4.3 14.6 1.0 O39 B:J20501 4.3 22.0 1.0 NE2 B:HIS200 4.3 15.8 1.0 CD2 B:HIS233 4.4 12.9 1.0 OD2 B:ASP318 4.4 17.6 1.0 CB B:ASP201 4.5 13.1 1.0 O B:HOH631 4.5 15.9 1.0 CD2 B:HIS204 4.7 13.4 1.0 O B:THR271 4.8 15.4 1.0 CA B:ASP201 4.8 13.3 1.0 CD2 B:HIS160 4.9 13.6 1.0 NE2 B:HIS204 4.9 13.2 1.0 NE2 B:HIS160 4.9 13.7 1.0 CB B:THR271 4.9 14.9 1.0 O B:HOH665 4.9 17.7 1.0 C B:HIS200 5.0 13.6 1.0 OD1 B:ASP318 5.0 16.8 1.0

Y.Huang, X.Liu, D.Wu, G.Tang, Z.Lai, X.Zheng, S.Yin, H.B.Luo. The Discovery, Complex Crystal Structure, and Recognition Mechanism of A Novel Natural PDE4 Inhibitor From Selaginella Pulvinata Biochem. Pharmacol. V. 130 51 2017.
ISSN: ISSN 1873-2968
PubMed: 28159622
DOI: 10.1016/J.BCP.2017.01.016