Zinc in PDB 5cio: Crystal Structure of Pqqf

The structure of Crystal Structure of Pqqf, PDB code: 5cio was solved by Q.Wei, D.Xu, T.Ran, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.51 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	175.090, 133.370, 92.110, 90.00, 119.40, 90.00
R / Rfree (%)	19.9 / 25.5

The binding sites of Zinc atom in the Crystal Structure of Pqqf (pdb code 5cio). 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 Pqqf, PDB code: 5cio:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Pqqf


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 Pqqf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:53.3 occ:1.00 NE2 A:HIS48 2.0 48.7 1.0 NE2 A:HIS52 2.1 52.4 1.0 ND1 B:HIS-13 2.1 51.1 1.0 OE1 A:GLU129 2.1 56.4 1.0 N B:HIS-13 2.1 53.0 1.0 CD2 A:HIS48 3.0 45.8 1.0 CG B:HIS-13 3.0 48.6 1.0 CE1 A:HIS52 3.0 54.5 1.0 CD2 A:HIS52 3.0 50.6 1.0 CE1 A:HIS48 3.0 44.2 1.0 CE1 B:HIS-13 3.1 50.0 1.0 CA B:HIS-13 3.1 52.6 1.0 CD A:GLU129 3.1 52.8 1.0 CB B:HIS-13 3.3 53.5 1.0 OE2 A:GLU129 3.5 52.0 1.0 ND1 A:HIS52 4.1 48.5 1.0 ND1 A:HIS48 4.1 46.1 1.0 CG A:HIS52 4.1 47.8 1.0 CG A:HIS48 4.1 44.3 1.0 CD2 B:HIS-13 4.2 42.6 1.0 NE2 B:HIS-13 4.2 45.0 1.0 C B:HIS-13 4.4 57.3 1.0 CG A:GLU129 4.4 51.8 1.0 O B:HOH962 4.6 50.8 1.0 CG1 A:ILE126 4.7 47.0 1.0 O B:HIS-13 4.8 64.7 1.0 CB A:GLU129 4.9 48.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Pqqf


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 Pqqf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:54.5 occ:1.00 NE2 B:HIS48 2.0 41.8 1.0 N A:HIS-13 2.0 56.6 1.0 ND1 A:HIS-13 2.1 48.4 1.0 NE2 B:HIS52 2.1 53.8 1.0 OE1 B:GLU129 2.2 63.3 1.0 CE1 B:HIS48 2.9 43.6 1.0 CE1 B:HIS52 3.0 52.9 1.0 CA A:HIS-13 3.0 57.2 1.0 CG A:HIS-13 3.0 49.6 1.0 CD2 B:HIS48 3.1 43.9 1.0 CE1 A:HIS-13 3.1 41.8 1.0 CD2 B:HIS52 3.2 46.1 1.0 CB A:HIS-13 3.3 54.0 1.0 CD B:GLU129 3.4 59.7 1.0 OE2 B:GLU129 4.0 64.9 1.0 ND1 B:HIS48 4.1 45.5 1.0 ND1 B:HIS52 4.1 47.9 1.0 CG B:HIS48 4.1 40.2 1.0 CD2 A:HIS-13 4.2 49.3 1.0 NE2 A:HIS-13 4.2 46.5 1.0 CG B:HIS52 4.3 48.6 1.0 C A:HIS-13 4.4 57.5 1.0 O A:HOH960 4.5 54.1 1.0 CG B:GLU129 4.5 54.5 1.0 CG1 B:ILE126 4.6 49.6 1.0 O A:HIS-13 4.7 64.2 1.0 CB B:GLU129 4.9 53.5 1.0

Q.Wei, T.Ran, C.Ma, J.He, D.Xu, W.Wang. Crystal Structure and Function of Pqqf Protein in the Pyrroloquinoline Quinone Biosynthetic Pathway J.Biol.Chem. V. 291 15575 2016.
ISSN: ESSN 1083-351X
PubMed: 27231346
DOI: 10.1074/JBC.M115.711226