Zinc in PDB 7me3: Yfea Oligomer Crystal 3, Form 2

The structure of Yfea Oligomer Crystal 3, Form 2, PDB code: 7me3 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)	45.45 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.09, 75.85, 106.55, 90, 90, 90
R / Rfree (%)	16.6 / 21.8

The structure of Yfea Oligomer Crystal 3, Form 2 also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Manganese	(Mn)	3 atoms

The binding sites of Zinc atom in the Yfea Oligomer Crystal 3, Form 2 (pdb code 7me3). 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 3, Form 2, PDB code: 7me3:
Jump to Zinc binding site number: 1; 2; 3;

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


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 3, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:3.7 occ:0.52 MN A:MN402 0.2 4.5 0.1 FE A:FE401 0.5 4.6 0.4 OE1 A:GLU207 1.9 5.8 1.0 OD2 A:ASP282 2.2 10.3 1.0 NE2 A:HIS141 2.3 6.1 1.0 NE2 A:HIS76 2.3 6.3 1.0 OD1 A:ASP282 2.4 6.6 1.0 CD A:GLU207 2.6 8.8 1.0 CG A:ASP282 2.6 8.2 1.0 OE2 A:GLU207 2.7 8.8 1.0 CE1 A:HIS76 3.2 6.3 1.0 CD2 A:HIS141 3.2 5.8 1.0 CE1 A:HIS141 3.2 6.3 1.0 CD2 A:HIS76 3.3 6.9 1.0 O A:HOH546 3.7 14.6 1.0 ND2 A:ASN228 3.9 11.5 1.0 CG A:GLU207 4.1 8.2 1.0 CB A:ASP282 4.1 7.7 1.0 CB A:ALA209 4.2 7.5 1.0 CG A:ASN228 4.3 9.6 1.0 ND1 A:HIS76 4.3 6.6 1.0 ND1 A:HIS141 4.3 6.2 1.0 O A:HOH513 4.3 15.9 1.0 CG A:HIS141 4.3 5.8 1.0 CG A:HIS76 4.4 7.4 1.0 OD1 A:ASN228 4.7 12.4 1.0 CB A:GLU207 4.7 9.2 1.0 CB A:ASN228 4.9 8.2 1.0 CA A:ASP282 5.0 6.2 1.0

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


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 3, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:6.4 occ:0.71 MN B:MN402 0.5 5.2 0.1 FE B:FE401 0.6 4.9 0.2 OE1 B:GLU207 2.0 9.1 1.0 OD2 B:ASP282 2.0 8.8 1.0 NE2 B:HIS141 2.3 6.3 1.0 NE2 B:HIS76 2.3 6.8 1.0 CD B:GLU207 2.5 13.5 1.0 OE2 B:GLU207 2.5 13.1 1.0 OD1 B:ASP282 2.6 8.0 1.0 CG B:ASP282 2.6 9.6 1.0 CE1 B:HIS141 3.2 7.1 1.0 CD2 B:HIS76 3.2 7.2 1.0 CD2 B:HIS141 3.2 5.9 1.0 CE1 B:HIS76 3.2 9.2 1.0 ND2 B:ASN228 3.6 16.5 1.0 O B:HOH514 3.9 10.9 1.0 CG B:GLU207 4.0 9.5 1.0 CB B:ALA209 4.1 7.1 1.0 CB B:ASP282 4.1 6.2 1.0 CG B:ASN228 4.2 16.9 1.0 ND1 B:HIS141 4.3 6.3 1.0 CG B:HIS141 4.3 9.5 1.0 ND1 B:HIS76 4.4 9.0 1.0 CG B:HIS76 4.4 10.1 1.0 O B:HOH518 4.4 14.7 1.0 OD1 B:ASN228 4.7 12.8 1.0 CB B:GLU207 4.8 10.8 1.0 CB B:ASN228 4.9 12.7 1.0

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


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 3, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:27.1 occ:0.84 MN B:MN404 0.4 27.2 0.2 ND1 B:HIS163 2.3 22.1 1.0 CE1 B:HIS163 3.2 26.4 1.0 CG B:HIS163 3.3 18.3 1.0 CB B:HIS163 3.6 10.2 1.0 CA B:HIS163 4.0 16.0 1.0 CG B:PRO116 4.2 19.5 1.0 NE2 B:HIS163 4.3 19.4 1.0 CD2 B:HIS163 4.4 12.3 1.0 O B:HIS163 4.6 23.2 1.0 C B:HIS163 4.9 14.1 1.0 CB B:PRO116 4.9 16.8 1.0 N B:HIS163 5.0 14.1 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.