Manganese 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:

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

The binding sites of Manganese atom in the Yfea Oligomer Crystal 2, Form 2 (pdb code 7me2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Yfea Oligomer Crystal 2, Form 2, PDB code: 7me2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in the Yfea Oligomer Crystal 2, 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 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:3.5 occ:0.46 FE A:FE401 0.5 4.1 0.3 ZN A:ZN402 0.6 4.4 0.3 NE2 A:HIS76 1.8 10.0 1.0 NE2 A:HIS141 2.1 10.6 1.0 OD2 A:ASP282 2.2 17.9 1.0 OE1 A:GLU207 2.3 10.9 1.0 CE1 A:HIS76 2.7 11.4 1.0 OD1 A:ASP282 2.7 11.7 1.0 OE2 A:GLU207 2.7 10.1 1.0 CG A:ASP282 2.8 13.7 1.0 CD A:GLU207 2.8 11.2 1.0 CD2 A:HIS76 3.0 8.4 1.0 CE1 A:HIS141 3.0 8.0 1.0 CD2 A:HIS141 3.1 8.1 1.0 ND1 A:HIS76 3.8 10.2 1.0 CG A:HIS76 4.0 8.7 1.0 ND2 A:ASN228 4.0 18.2 1.0 ND1 A:HIS141 4.2 7.6 1.0 CG A:HIS141 4.2 8.6 1.0 CB A:ASP282 4.3 10.0 1.0 CG A:ASN228 4.3 16.2 1.0 CG A:GLU207 4.4 8.3 1.0 CB A:ALA209 4.5 8.1 1.0 O A:HOH681 4.6 23.1 1.0 O A:HOH555 4.6 12.2 1.0 OD1 A:ASN228 4.7 15.1 1.0 CB A:ASN228 4.8 10.6 1.0 CD1 A:LEU101 4.9 13.1 1.0

Manganese binding site 2 out of 7 in the Yfea Oligomer Crystal 2, 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 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:36.9 occ:0.45 O A:HOH718 1.9 44.1 1.0 O A:HOH730 2.1 39.6 1.0 O A:HOH556 2.3 38.0 1.0 OE2 A:GLU287 2.6 79.6 1.0 CD A:GLU287 3.4 82.4 1.0 CG A:GLU287 3.6 58.4 1.0 O A:HOH676 3.9 41.3 1.0 O A:HOH777 4.2 42.4 1.0 OD1 A:ASP53 4.3 18.4 1.0 OE1 A:GLN52 4.4 17.1 1.0 O A:HOH797 4.5 39.7 1.0 OE1 A:GLU287 4.5 72.9 1.0 O A:HOH587 4.6 35.8 1.0 O A:PRO292 4.6 15.6 1.0 NE2 A:GLN52 4.7 22.8 1.0 CD A:GLN52 5.0 21.3 1.0

Manganese binding site 3 out of 7 in the Yfea Oligomer Crystal 2, 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 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:5.3 occ:0.30 FE B:FE401 0.4 6.0 0.3 ZN B:ZN402 0.6 6.3 0.4 NE2 B:HIS76 1.9 10.2 1.0 NE2 B:HIS141 2.0 8.8 1.0 OD2 B:ASP282 2.1 15.3 1.0 OE1 B:GLU207 2.4 9.7 1.0 OD1 B:ASP282 2.6 12.5 1.0 CG B:ASP282 2.7 14.9 1.0 CE1 B:HIS76 2.8 11.8 1.0 OE2 B:GLU207 2.9 9.5 1.0 CD2 B:HIS141 3.0 8.1 1.0 CD2 B:HIS76 3.0 10.0 1.0 CE1 B:HIS141 3.0 8.6 1.0 CD B:GLU207 3.0 9.3 1.0 ND1 B:HIS76 4.0 8.9 1.0 CG B:HIS76 4.1 9.1 1.0 ND1 B:HIS141 4.1 8.5 1.0 ND2 B:ASN228 4.1 18.2 1.0 CG B:HIS141 4.1 9.2 1.0 CB B:ASP282 4.2 10.0 1.0 CB B:ALA209 4.5 9.6 1.0 O B:HOH533 4.5 13.9 1.0 CG B:ASN228 4.5 21.4 1.0 CG B:GLU207 4.5 11.4 1.0 CD1 B:LEU101 4.7 13.9 1.0 O B:HOH647 4.7 23.2 1.0 CB B:ASN228 5.0 15.2 1.0 CD1 B:ILE75 5.0 10.3 1.0 OD1 B:ASN228 5.0 17.6 1.0

Manganese binding site 4 out of 7 in the Yfea Oligomer Crystal 2, Form 2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn404 b:98.8 occ:0.91 OE2 B:GLU287 2.9 75.2 1.0 O B:HOH664 3.6 30.0 1.0 CG B:GLU287 3.7 57.6 1.0 CD B:GLU287 3.7 79.8 1.0 OE1 B:GLN52 3.8 18.9 1.0 NE2 B:GLN52 4.1 18.9 1.0 OD1 B:ASP53 4.3 18.6 1.0 CD B:GLN52 4.4 23.1 1.0 O B:PRO292 4.7 16.4 1.0 O B:HOH553 4.9 30.7 1.0 OE1 B:GLU287 4.9 76.7 1.0 O B:HOH721 5.0 41.9 1.0

Manganese binding site 5 out of 7 in the Yfea Oligomer Crystal 2, Form 2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn405 b:21.5 occ:0.55 ZN B:ZN406 0.4 21.7 0.5 ND1 B:HIS163 2.1 21.4 1.0 CE1 B:HIS163 3.0 28.2 1.0 CG B:HIS163 3.2 23.3 1.0 CB B:HIS163 3.6 20.7 1.0 CA B:HIS163 3.8 19.3 1.0 NE2 B:HIS163 4.2 20.5 1.0 CD2 B:HIS163 4.3 20.4 1.0 CG B:PRO116 4.3 26.4 1.0 O B:HIS163 4.5 17.9 1.0 O B:GLU162 4.7 24.8 1.0 C B:HIS163 4.7 19.2 1.0 N B:HIS163 4.8 14.6 1.0 CB B:PRO116 4.9 21.3 1.0

Manganese binding site 6 out of 7 in the Yfea Oligomer Crystal 2, Form 2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn407 b:103.2 occ:0.59 O B:HOH653 2.8 42.2 1.0 OD2 B:ASP114 2.8 48.9 1.0 CG B:ASP114 3.3 47.4 1.0 OD1 B:ASP114 3.4 48.0 1.0 O B:HOH707 3.9 33.5 1.0 CB B:ASP114 4.4 27.2 1.0

Manganese binding site 7 out of 7 in the Yfea Oligomer Crystal 2, Form 2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn408 b:112.3 occ:0.96 OD1 B:ASP92 2.8 25.7 1.0 O B:HOH639 3.6 32.2 1.0 CG B:ASP92 3.8 29.8 1.0 O B:HOH620 4.1 37.0 1.0 OD2 B:ASP92 4.1 20.7 1.0 O B:SER90 4.2 25.5 1.0 O B:ALA91 4.6 14.6 1.0 O B:HOH563 4.8 47.1 1.0 C B:ALA91 4.9 17.5 1.0 C B:SER90 5.0 21.1 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.