Zinc in PDB 5uyv: Yfea Ancillary Sites That Do Not Co-Load with Site 2

The structure of Yfea Ancillary Sites That Do Not Co-Load with Site 2, PDB code: 5uyv was solved by C.D.Radka, L.J.Delucas, S.G.Aller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.96 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.516, 51.959, 112.751, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.6

The binding sites of Zinc atom in the Yfea Ancillary Sites That Do Not Co-Load with Site 2 (pdb code 5uyv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Yfea Ancillary Sites That Do Not Co-Load with Site 2, PDB code: 5uyv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yfea Ancillary Sites That Do Not Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yfea Ancillary Sites That Do Not Co-Load with Site 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:38.6 occ:1.00 OE1 A:GLU270 2.3 36.5 1.0 OE2 A:GLU270 2.6 40.6 1.0 CD A:GLU270 2.7 37.4 1.0 O A:HOH741 4.0 35.1 1.0 CG A:GLU270 4.1 31.7 1.0 O A:HOH752 4.4 40.8 1.0 CA A:GLU270 4.5 27.0 1.0 CB A:GLU270 4.6 28.4 1.0

Zinc binding site 2 out of 4 in the Yfea Ancillary Sites That Do Not Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yfea Ancillary Sites That Do Not Co-Load with Site 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:49.7 occ:1.00 OE1 A:GLN176 2.3 42.1 1.0 O A:HOH725 2.5 33.2 1.0 CD A:GLN176 3.0 43.7 1.0 NE2 A:GLN176 3.4 47.5 1.0 O A:HOH640 3.5 44.7 1.0 CG A:GLN176 4.2 24.9 1.0 CB A:GLN176 4.6 22.2 1.0 O A:HOH845 4.8 34.9 1.0

Zinc binding site 3 out of 4 in the Yfea Ancillary Sites That Do Not Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yfea Ancillary Sites That Do Not Co-Load with Site 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:15.8 occ:1.00 NE2 A:HIS76 2.0 7.6 1.0 NE2 A:HIS141 2.0 8.5 1.0 OE1 A:GLU207 2.1 8.0 1.0 OD2 A:ASP282 2.1 10.9 1.0 OD1 A:ASP282 2.7 11.0 1.0 OE2 A:GLU207 2.7 9.5 1.0 CD A:GLU207 2.7 9.6 1.0 CG A:ASP282 2.7 10.8 1.0 CE1 A:HIS76 2.9 9.2 1.0 CE1 A:HIS141 3.0 10.1 1.0 CD2 A:HIS141 3.1 10.1 1.0 CD2 A:HIS76 3.1 11.8 1.0 ND2 A:ASN228 3.9 10.4 1.0 ND1 A:HIS76 4.0 10.1 1.0 ND1 A:HIS141 4.1 8.7 1.0 CG A:HIS76 4.2 12.3 1.0 CG A:GLU207 4.2 8.7 1.0 CG A:HIS141 4.2 9.0 1.0 CB A:ASP282 4.2 10.7 1.0 CB A:ALA209 4.3 8.1 1.0 CG A:ASN228 4.3 13.9 1.0 O A:HOH661 4.3 11.9 1.0 O A:HOH538 4.4 12.2 1.0 OD1 A:ASN228 4.6 10.9 1.0 CB A:ASN228 4.9 15.6 1.0 CD1 A:LEU101 4.9 9.1 1.0 CB A:GLU207 5.0 8.5 1.0

Zinc binding site 4 out of 4 in the Yfea Ancillary Sites That Do Not Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yfea Ancillary Sites That Do Not Co-Load with Site 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:36.9 occ:1.00 OE2 A:GLU106 2.1 24.6 1.0 O A:HOH746 2.1 28.2 1.0 O A:HOH756 2.4 31.6 1.0 CD A:GLU106 2.8 24.2 1.0 OE1 A:GLU106 2.9 27.2 1.0 O A:HOH810 3.0 36.1 1.0 O A:HOH783 3.6 38.7 1.0 O A:HOH805 4.0 35.2 1.0 O A:HOH833 4.1 36.5 1.0 O A:HOH854 4.1 30.3 1.0 O A:HOH536 4.1 25.3 1.0 CG A:GLU106 4.2 18.1 1.0 O A:HOH755 4.3 29.4 1.0 O A:HOH853 4.3 37.2 1.0 O A:HOH688 4.6 22.9 1.0 O A:HOH679 4.7 32.3 1.0 CH2 A:TRP96 4.8 11.7 1.0

C.D.Radka, L.J.Delucas, L.S.Wilson, M.B.Lawrenz, R.D.Perry, S.G.Aller. Crystal Structure of Yersinia Pestis Virulence Factor Yfea Reveals Two Polyspecific Metal-Binding Sites. Acta Crystallogr D Struct V. 73 557 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28695856
DOI: 10.1107/S2059798317006349