Zinc in PDB 7yqf: Crystal Structure of PDE4D Complexed with Glycyrrhisoflavone

All present enzymatic activity of Crystal Structure of PDE4D Complexed with Glycyrrhisoflavone:
3.1.4.53;

The structure of Crystal Structure of PDE4D Complexed with Glycyrrhisoflavone, PDB code: 7yqf was solved by J.Y.Liu, M.J.Li, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.39 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.57, 80.752, 163.143, 90, 90, 90
R / Rfree (%)	21.6 / 24.2

The structure of Crystal Structure of PDE4D Complexed with Glycyrrhisoflavone also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with Glycyrrhisoflavone (pdb code 7yqf). 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 Complexed with Glycyrrhisoflavone, PDB code: 7yqf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Complexed with Glycyrrhisoflavone


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 Complexed with Glycyrrhisoflavone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:8.4 occ:0.00 O A:HOH714 2.1 9.8 1.0 NE2 A:HIS164 2.2 9.0 1.0 OD2 A:ASP201 2.2 13.7 1.0 OD1 A:ASP318 2.2 11.1 1.0 O A:HOH753 2.2 14.9 1.0 NE2 A:HIS200 2.2 15.0 1.0 CG A:ASP318 3.1 18.0 1.0 CD2 A:HIS200 3.1 16.7 1.0 CG A:ASP201 3.1 15.9 1.0 CE1 A:HIS164 3.1 18.1 1.0 CD2 A:HIS164 3.1 17.7 1.0 CE1 A:HIS200 3.3 19.3 1.0 OD2 A:ASP318 3.3 24.0 1.0 OD1 A:ASP201 3.7 12.8 1.0 MG A:MG602 3.8 12.1 0.0 O A:HOH802 3.8 13.0 1.0 O A:HOH836 4.0 25.7 1.0 O A:HOH739 4.1 25.9 1.0 CD2 A:HIS160 4.1 19.1 1.0 ND1 A:HIS164 4.2 16.5 1.0 CG A:HIS200 4.3 16.5 1.0 CB A:ASP201 4.3 15.5 1.0 CG A:HIS164 4.3 17.4 1.0 NE2 A:HIS160 4.3 19.0 1.0 ND1 A:HIS200 4.3 17.1 1.0 CB A:ASP318 4.4 17.3 1.0 O A:HOH705 4.8 13.9 1.0 CG2 A:VAL168 4.8 17.8 1.0 CA A:ASP318 5.0 13.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Complexed with Glycyrrhisoflavone


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 Complexed with Glycyrrhisoflavone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:11.5 occ:0.00 O B:HOH702 2.1 11.0 1.0 OD1 B:ASP318 2.2 20.7 1.0 NE2 B:HIS164 2.2 18.0 1.0 OD2 B:ASP201 2.2 17.3 1.0 NE2 B:HIS200 2.2 18.5 1.0 O B:HOH752 2.2 16.6 1.0 CD2 B:HIS164 3.0 21.5 1.0 CG B:ASP318 3.0 22.8 1.0 CD2 B:HIS200 3.1 21.5 1.0 CG B:ASP201 3.1 16.3 1.0 OD2 B:ASP318 3.2 30.3 1.0 CE1 B:HIS200 3.3 21.1 1.0 CE1 B:HIS164 3.4 18.9 1.0 OD1 B:ASP201 3.6 18.1 1.0 MG B:MG602 3.8 13.4 0.0 O B:HOH768 3.8 14.9 1.0 O B:HOH781 3.9 49.7 1.0 O B:HOH743 4.0 27.6 1.0 CD2 B:HIS160 4.2 20.4 1.0 CG B:HIS164 4.2 21.9 1.0 CG B:HIS200 4.3 20.5 1.0 CB B:ASP201 4.3 19.6 1.0 ND1 B:HIS200 4.3 18.6 1.0 ND1 B:HIS164 4.3 25.4 1.0 CB B:ASP318 4.4 24.2 1.0 NE2 B:HIS160 4.5 22.2 1.0 O B:HOH719 4.8 16.7 1.0 CG2 B:VAL168 4.8 30.3 1.0 CA B:ASP318 5.0 24.5 1.0

H.Xu, S.Li, J.Liu, J.Cheng, L.Kang, W.Li, Y.Zhong, C.Wei, L.Fu, J.Qi, Y.Zhang, M.You, Z.Zhou, C.Zhang, H.Su, S.Yao, Z.Zhou, Y.Shi, R.Deng, Q.Lv, F.Li, F.Qi, J.Chen, S.Zhang, X.Ma, Z.Xu, S.Li, Y.Xu, K.Peng, Y.Shi, H.Jiang, G.F.Gao, L.Huang. Bioactive Compounds From Huashi Baidu Decoction Possess Both Antiviral and Anti-Inflammatory Effects Against Covid-19. Proc.Natl.Acad.Sci.Usa V. 120 75120 2023.
ISSN: ESSN 1091-6490
PubMed: 37094153
DOI: 10.1073/PNAS.2301775120