Zinc in PDB 5zkq: Crystal Structure of the Human Platelet-Activating Factor Receptor in Complex with Abt-491

All present enzymatic activity of Crystal Structure of the Human Platelet-Activating Factor Receptor in Complex with Abt-491:
3.2.1.17;

The structure of Crystal Structure of the Human Platelet-Activating Factor Receptor in Complex with Abt-491, PDB code: 5zkq was solved by C.Cao, Q.Zhao, X.C.Zhang, B.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.39 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.220, 166.540, 100.310, 90.00, 100.00, 90.00
R / Rfree (%)	20.3 / 23.5

The structure of Crystal Structure of the Human Platelet-Activating Factor Receptor in Complex with Abt-491 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Human Platelet-Activating Factor Receptor in Complex with Abt-491 (pdb code 5zkq). 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 the Human Platelet-Activating Factor Receptor in Complex with Abt-491, PDB code: 5zkq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Human Platelet-Activating Factor Receptor in Complex with Abt-491


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 the Human Platelet-Activating Factor Receptor in Complex with Abt-491 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:0.4 occ:1.00 NE2 A:HIS268 2.0 0.5 1.0 OE2 A:GLU259 2.2 96.2 1.0 NE2 A:HIS4 2.4 0.3 1.0 CE1 A:HIS268 2.7 0.2 1.0 CD A:GLU259 2.9 0.8 1.0 OE1 A:GLU259 3.1 98.8 1.0 CD2 A:HIS268 3.2 0.6 1.0 CE1 A:HIS4 3.3 0.0 1.0 NE2 A:HIS8 3.3 0.7 1.0 CD2 A:HIS4 3.3 0.6 1.0 ND2 A:ASN272 3.7 0.9 1.0 CE1 A:HIS8 3.7 0.3 1.0 ND1 A:HIS268 4.0 0.8 1.0 CD2 A:HIS8 4.0 0.8 1.0 CG A:HIS268 4.2 0.6 1.0 CG A:ASN272 4.3 0.7 1.0 OD1 A:ASN272 4.3 0.5 1.0 ND1 A:HIS4 4.3 0.7 1.0 CG A:GLU259 4.3 87.6 1.0 CG A:HIS4 4.4 0.1 1.0 CB A:SER7 4.6 0.3 1.0 ND1 A:HIS8 4.6 0.9 1.0 CA A:GLU259 4.7 70.7 1.0 CG A:HIS8 4.7 0.1 1.0 O A:HIS4 4.7 1.0 1.0 O A:ALA258 5.0 73.5 1.0 CB A:GLU259 5.0 72.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Human Platelet-Activating Factor Receptor in Complex with Abt-491


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 the Human Platelet-Activating Factor Receptor in Complex with Abt-491 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1205 b:0.1 occ:1.00 OE2 B:GLU259 1.9 1.0 1.0 NE2 B:HIS268 2.4 0.9 1.0 CE1 B:HIS268 2.6 0.6 1.0 CD B:GLU259 3.0 0.8 1.0 ND2 B:ASN272 3.3 0.8 1.0 NE2 B:HIS8 3.6 1.0 1.0 OE1 B:GLU259 3.6 0.4 1.0 CD2 B:HIS268 3.7 0.9 1.0 CD2 B:HIS8 3.7 0.2 1.0 ND1 B:HIS268 3.8 0.9 1.0 CE1 B:HIS8 4.1 0.7 1.0 CG B:ASN272 4.2 0.9 1.0 CG B:GLU259 4.2 88.1 1.0 N B:MET9 4.3 0.8 1.0 CG B:HIS8 4.3 0.3 1.0 CG B:HIS268 4.4 0.5 1.0 CB B:MET9 4.4 0.7 1.0 OD1 B:ASN272 4.4 0.5 1.0 ND1 B:HIS8 4.6 0.2 1.0

C.Cao, Q.Tan, C.Xu, L.He, L.Yang, Y.Zhou, Y.Zhou, A.Qiao, M.Lu, C.Yi, G.W.Han, X.Wang, X.Li, H.Yang, Z.Rao, H.Jiang, Y.Zhao, J.Liu, R.C.Stevens, Q.Zhao, X.C.Zhang, B.Wu. Structural Basis For Signal Recognition and Transduction By Platelet-Activating-Factor Receptor. Nat. Struct. Mol. Biol. V. 25 488 2018.
ISSN: ESSN 1545-9985
PubMed: 29808000
DOI: 10.1038/S41594-018-0068-Y