Zinc in PDB 7me1: Yfea Oligomer Crystal 1, Form 1

The structure of Yfea Oligomer Crystal 1, Form 1, PDB code: 7me1 was solved by C.D.Radka, S.G.Aller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.10 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.52, 76.91, 110.29, 90, 90, 90
R / Rfree (%)	16.6 / 19.5

The structure of Yfea Oligomer Crystal 1, Form 1 also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Manganese	(Mn)	1 atom

The binding sites of Zinc atom in the Yfea Oligomer Crystal 1, Form 1 (pdb code 7me1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Yfea Oligomer Crystal 1, Form 1, PDB code: 7me1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Yfea Oligomer Crystal 1, Form 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yfea Oligomer Crystal 1, Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:15.5 occ:0.59 FE A:FE401 0.4 15.1 0.4 OD2 A:ASP282 2.0 17.6 1.0 OE1 A:GLU207 2.0 17.8 1.0 NE2 A:HIS76 2.3 17.4 1.0 NE2 A:HIS141 2.3 16.7 1.0 OE2 A:GLU207 2.6 16.9 1.0 OD1 A:ASP282 2.6 16.0 1.0 CG A:ASP282 2.6 17.2 1.0 CD A:GLU207 2.6 18.7 1.0 CD2 A:HIS76 3.2 17.4 1.0 CD2 A:HIS141 3.2 16.9 1.0 CE1 A:HIS76 3.2 19.1 1.0 CE1 A:HIS141 3.3 16.8 1.0 ND2 A:ASN228 3.7 20.1 1.0 O A:HOH560 4.1 17.0 1.0 CG A:ASN228 4.1 20.8 1.0 CB A:ASP282 4.1 12.8 1.0 CG A:GLU207 4.1 17.3 1.0 CB A:ALA209 4.1 18.3 1.0 CG A:HIS76 4.3 21.3 1.0 ND1 A:HIS76 4.3 20.0 1.0 ND1 A:HIS141 4.4 16.3 1.0 CG A:HIS141 4.4 16.9 1.0 O A:HOH524 4.5 15.4 1.0 OD1 A:ASN228 4.6 18.6 1.0 CB A:ASN228 4.7 20.3 1.0 CB A:GLU207 4.9 18.8 1.0

Zinc binding site 2 out of 3 in the Yfea Oligomer Crystal 1, Form 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yfea Oligomer Crystal 1, Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:10.1 occ:0.60 FE B:FE401 0.9 13.2 0.4 OE1 B:GLU207 1.9 18.2 1.0 OD2 B:ASP282 2.1 15.7 1.0 NE2 B:HIS141 2.3 12.1 1.0 NE2 B:HIS76 2.3 11.8 1.0 OE2 B:GLU207 2.4 14.5 1.0 CD B:GLU207 2.4 14.8 1.0 OD1 B:ASP282 2.8 13.2 1.0 CG B:ASP282 2.8 15.4 1.0 CE1 B:HIS141 3.1 14.0 1.0 CE1 B:HIS76 3.1 13.8 1.0 CD2 B:HIS76 3.3 15.4 1.0 CD2 B:HIS141 3.3 11.2 1.0 ND2 B:ASN228 3.5 16.5 1.0 CG B:GLU207 3.9 16.1 1.0 CG B:ASN228 4.0 17.1 1.0 CB B:ALA209 4.0 11.6 1.0 O B:HOH591 4.1 13.9 1.0 ND1 B:HIS76 4.2 14.6 1.0 ND1 B:HIS141 4.3 13.3 1.0 CB B:ASP282 4.3 13.6 1.0 CG B:HIS76 4.3 16.1 1.0 OD1 B:ASN228 4.3 18.5 1.0 CG B:HIS141 4.4 12.4 1.0 O B:HOH554 4.5 15.8 1.0 CB B:ASN228 4.7 16.3 1.0 CB B:GLU207 4.7 11.5 1.0 N B:ASN228 5.0 19.5 1.0

Zinc binding site 3 out of 3 in the Yfea Oligomer Crystal 1, Form 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yfea Oligomer Crystal 1, Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:49.7 occ:0.52 MN B:MN403 0.4 48.0 0.5 OD1 B:ASP114 3.2 53.4 1.0 CG B:ASP114 4.4 43.6 1.0

C.D.Radka, S.G.Aller. Yersinia Pestis Substrate-Binding Protein Yfea Site 2 Is A Dynamic and Polyspecific Surface Metal Binding Site To Be Published.