Zinc in PDB 7me2: Yfea Oligomer Crystal 2, Form 2

The structure of Yfea Oligomer Crystal 2, Form 2, PDB code: 7me2 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)	50.51 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.31, 76.43, 107.36, 90, 90, 90
R / Rfree (%)	15.2 / 18.4

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

Manganese	(Mn)	7 atoms
Iron	(Fe)	2 atoms

The binding sites of Zinc atom in the Yfea Oligomer Crystal 2, Form 2 (pdb code 7me2). 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 2, Form 2, PDB code: 7me2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Yfea Oligomer Crystal 2, 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 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:4.4 occ:0.27 MN A:MN403 0.6 3.5 0.5 FE A:FE401 0.6 4.1 0.3 OE1 A:GLU207 1.8 10.9 1.0 OD2 A:ASP282 2.0 17.9 1.0 NE2 A:HIS76 2.3 10.0 1.0 NE2 A:HIS141 2.3 10.6 1.0 CD A:GLU207 2.5 11.2 1.0 OE2 A:GLU207 2.6 10.1 1.0 CG A:ASP282 2.7 13.7 1.0 OD1 A:ASP282 2.7 11.7 1.0 CE1 A:HIS76 3.1 11.4 1.0 CE1 A:HIS141 3.2 8.0 1.0 CD2 A:HIS76 3.3 8.4 1.0 CD2 A:HIS141 3.3 8.1 1.0 ND2 A:ASN228 3.8 18.2 1.0 O A:HOH681 4.0 23.1 1.0 CG A:GLU207 4.0 8.3 1.0 CG A:ASN228 4.1 16.2 1.0 CB A:ASP282 4.2 10.0 1.0 CB A:ALA209 4.2 8.1 1.0 ND1 A:HIS76 4.3 10.2 1.0 ND1 A:HIS141 4.4 7.6 1.0 CG A:HIS76 4.4 8.7 1.0 CG A:HIS141 4.4 8.6 1.0 OD1 A:ASN228 4.4 15.1 1.0 O A:HOH555 4.5 12.2 1.0 CB A:GLU207 4.7 11.1 1.0 CB A:ASN228 4.7 10.6 1.0

Zinc binding site 2 out of 3 in the Yfea Oligomer Crystal 2, 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 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:6.3 occ:0.41 FE B:FE401 0.4 6.0 0.3 MN B:MN403 0.6 5.3 0.3 OD2 B:ASP282 1.9 15.3 1.0 OE1 B:GLU207 1.9 9.7 1.0 NE2 B:HIS76 2.2 10.2 1.0 NE2 B:HIS141 2.3 8.8 1.0 CG B:ASP282 2.6 14.9 1.0 CD B:GLU207 2.6 9.3 1.0 OD1 B:ASP282 2.6 12.5 1.0 OE2 B:GLU207 2.7 9.5 1.0 CD2 B:HIS76 3.2 10.0 1.0 CE1 B:HIS76 3.2 11.8 1.0 CE1 B:HIS141 3.2 8.6 1.0 CD2 B:HIS141 3.3 8.1 1.0 ND2 B:ASN228 3.8 18.2 1.0 CB B:ASP282 4.1 10.0 1.0 CG B:GLU207 4.1 11.4 1.0 O B:HOH647 4.2 23.2 1.0 CG B:ASN228 4.2 21.4 1.0 CB B:ALA209 4.2 9.6 1.0 ND1 B:HIS76 4.3 8.9 1.0 O B:HOH533 4.3 13.9 1.0 CG B:HIS76 4.3 9.1 1.0 ND1 B:HIS141 4.4 8.5 1.0 CG B:HIS141 4.4 9.2 1.0 OD1 B:ASN228 4.6 17.6 1.0 CB B:ASN228 4.8 15.2 1.0 CB B:GLU207 4.8 10.9 1.0

Zinc binding site 3 out of 3 in the Yfea Oligomer Crystal 2, 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 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:21.7 occ:0.45 MN B:MN405 0.4 21.5 0.6 ND1 B:HIS163 2.3 21.4 1.0 CE1 B:HIS163 3.0 28.2 1.0 CG B:HIS163 3.4 23.3 1.0 CB B:HIS163 3.9 20.7 1.0 CG B:PRO116 4.1 26.4 1.0 CA B:HIS163 4.2 19.3 1.0 NE2 B:HIS163 4.2 20.5 1.0 CD2 B:HIS163 4.4 20.4 1.0 CB B:PRO116 4.7 21.3 1.0 O B:HIS163 4.9 17.9 1.0 CD B:PRO116 4.9 18.6 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.