Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE4D Catalytic Domain Complexed with Selaginpulvilins K, PDB code: 5wqa:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn502 b:13.5 occ:1.00 OD2 A:ASP201 2.0 9.9 1.0 OD1 A:ASP318 2.0 11.3 1.0 O A:HOH638 2.0 5.7 1.0 O A:HOH620 2.1 7.5 1.0 NE2 A:HIS200 2.1 11.0 1.0 NE2 A:HIS164 2.1 11.1 1.0 CG A:ASP318 3.0 11.2 1.0 CG A:ASP201 3.0 9.4 1.0 CE1 A:HIS164 3.1 10.9 1.0 CD2 A:HIS200 3.1 10.7 1.0 CE1 A:HIS200 3.1 10.6 1.0 CD2 A:HIS164 3.1 10.8 1.0 OD2 A:ASP318 3.3 11.0 1.0 OD1 A:ASP201 3.6 8.6 1.0 MG A:MG503 3.9 7.2 1.0 O A:HOH628 4.0 11.6 1.0 O A:HOH623 4.1 9.7 1.0 ND1 A:HIS200 4.2 10.6 1.0 ND1 A:HIS164 4.2 10.8 1.0 CG A:HIS200 4.2 10.5 1.0 CB A:ASP201 4.2 9.4 1.0 CD2 A:HIS160 4.2 11.9 1.0 CG A:HIS164 4.2 10.7 1.0 O39 A:J20501 4.4 19.2 1.0 CB A:ASP318 4.4 11.2 1.0 NE2 A:HIS160 4.6 11.9 1.0 O A:HOH648 4.6 5.7 1.0 CG2 A:VAL168 4.8 9.4 1.0 CA A:ASP318 4.9 11.2 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn503 b:18.7 occ:1.00 OD2 B:ASP201 2.0 14.0 1.0 OD1 B:ASP318 2.0 16.8 1.0 O B:HOH634 2.1 9.7 1.0 NE2 B:HIS200 2.1 15.8 1.0 NE2 B:HIS164 2.1 15.8 1.0 O B:HOH610 2.2 11.4 1.0 CG B:ASP318 3.0 17.1 1.0 CE1 B:HIS200 3.0 15.3 1.0 CE1 B:HIS164 3.1 15.5 1.0 CD2 B:HIS164 3.1 15.6 1.0 CG B:ASP201 3.1 12.9 1.0 CD2 B:HIS200 3.1 15.2 1.0 OD2 B:ASP318 3.3 17.6 1.0 OD1 B:ASP201 3.7 11.7 1.0 MG B:MG502 3.7 10.1 1.0 O B:HOH620 4.1 18.4 1.0 O B:HOH628 4.1 9.8 1.0 ND1 B:HIS200 4.1 15.0 1.0 CD2 B:HIS160 4.2 13.6 1.0 ND1 B:HIS164 4.2 15.5 1.0 CG B:HIS200 4.2 14.9 1.0 CG B:HIS164 4.2 15.4 1.0 CB B:ASP201 4.3 13.1 1.0 CB B:ASP318 4.4 16.9 1.0 O39 B:J20501 4.4 22.0 1.0 NE2 B:HIS160 4.5 13.7 1.0 O B:HOH614 4.7 12.0 1.0 CG2 B:VAL168 4.8 18.1 1.0 CA B:ASP318 4.9 16.9 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