Manganese 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:

Zinc	(Zn)	3 atoms
Iron	(Fe)	2 atoms

The binding sites of Manganese atom in the Yfea Oligomer Crystal 3, Form 2 (pdb code 7me3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Yfea Oligomer Crystal 3, Form 2, PDB code: 7me3:
Jump to Manganese binding site number: 1; 2; 3;

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Yfea Oligomer Crystal 3, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:4.5 occ:0.10 ZN A:ZN403 0.2 3.7 0.5 FE A:FE401 0.3 4.6 0.4 OE1 A:GLU207 1.9 5.8 1.0 NE2 A:HIS141 2.1 6.1 1.0 NE2 A:HIS76 2.2 6.3 1.0 OD2 A:ASP282 2.3 10.3 1.0 OD1 A:ASP282 2.5 6.6 1.0 OE2 A:GLU207 2.5 8.8 1.0 CD A:GLU207 2.5 8.8 1.0 CG A:ASP282 2.8 8.2 1.0 CE1 A:HIS76 3.0 6.3 1.0 CE1 A:HIS141 3.1 6.3 1.0 CD2 A:HIS141 3.1 5.8 1.0 CD2 A:HIS76 3.2 6.9 1.0 O A:HOH546 3.9 14.6 1.0 ND2 A:ASN228 3.9 11.5 1.0 CG A:GLU207 4.0 8.2 1.0 ND1 A:HIS76 4.2 6.6 1.0 ND1 A:HIS141 4.2 6.2 1.0 CB A:ALA209 4.2 7.5 1.0 CG A:HIS141 4.2 5.8 1.0 CB A:ASP282 4.3 7.7 1.0 CG A:HIS76 4.3 7.4 1.0 CG A:ASN228 4.3 9.6 1.0 O A:HOH513 4.4 15.9 1.0 OD1 A:ASN228 4.7 12.4 1.0 CB A:GLU207 4.8 9.2 1.0 CB A:ASN228 4.8 8.2 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Yfea Oligomer Crystal 3, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:5.2 occ:0.11 FE B:FE401 0.2 4.9 0.2 ZN B:ZN403 0.5 6.4 0.7 NE2 B:HIS76 1.9 6.8 1.0 NE2 B:HIS141 2.0 6.3 1.0 OD2 B:ASP282 2.3 8.8 1.0 OE1 B:GLU207 2.4 9.1 1.0 OE2 B:GLU207 2.6 13.1 1.0 OD1 B:ASP282 2.6 8.0 1.0 CG B:ASP282 2.8 9.6 1.0 CD B:GLU207 2.8 13.5 1.0 CE1 B:HIS76 2.8 9.2 1.0 CE1 B:HIS141 3.0 7.1 1.0 CD2 B:HIS76 3.0 7.2 1.0 CD2 B:HIS141 3.0 5.9 1.0 ND2 B:ASN228 3.8 16.5 1.0 ND1 B:HIS76 4.0 9.0 1.0 CG B:HIS76 4.1 10.1 1.0 ND1 B:HIS141 4.1 6.3 1.0 CG B:HIS141 4.2 9.5 1.0 CG B:GLU207 4.3 9.5 1.0 CB B:ASP282 4.3 6.2 1.0 CB B:ALA209 4.3 7.1 1.0 CG B:ASN228 4.4 16.9 1.0 O B:HOH514 4.4 10.9 1.0 O B:HOH518 4.6 14.7 1.0 CD1 B:LEU101 4.8 9.5 1.0 CB B:ASN228 4.9 12.7 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Yfea Oligomer Crystal 3, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn404 b:27.2 occ:0.16 ZN B:ZN405 0.4 27.1 0.8 ND1 B:HIS163 2.5 22.1 1.0 CG B:HIS163 3.5 18.3 1.0 CE1 B:HIS163 3.5 26.4 1.0 CB B:HIS163 3.6 10.2 1.0 CA B:HIS163 3.9 16.0 1.0 O B:HIS163 4.4 23.2 1.0 CG B:PRO116 4.4 19.5 1.0 NE2 B:HIS163 4.6 19.4 1.0 CD2 B:HIS163 4.6 12.3 1.0 C B:HIS163 4.7 14.1 1.0 O B:GLU162 5.0 20.1 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.