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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5zkq:

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

Zinc Binding Sites:

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 5zkq

Go back to Zinc Binding Sites List in 5zkq
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 5zkq

Go back to Zinc Binding Sites List in 5zkq
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

Reference:

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
Page generated: Wed Dec 16 11:27:07 2020

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