Manganese in PDB 3ki9: Crystal Structure of Staphylococcus Aureus Metallopeptidase (Sapep/Dape) in the MN2+ Bound Form

The structure of Crystal Structure of Staphylococcus Aureus Metallopeptidase (Sapep/Dape) in the MN2+ Bound Form, PDB code: 3ki9 was solved by T.S.Girish, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.88 / 2.90
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	158.150, 158.150, 158.150, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.3

The binding sites of Manganese atom in the Crystal Structure of Staphylococcus Aureus Metallopeptidase (Sapep/Dape) in the MN2+ Bound Form (pdb code 3ki9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Staphylococcus Aureus Metallopeptidase (Sapep/Dape) in the MN2+ Bound Form, PDB code: 3ki9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Staphylococcus Aureus Metallopeptidase (Sapep/Dape) in the MN2+ Bound Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Staphylococcus Aureus Metallopeptidase (Sapep/Dape) in the MN2+ Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn470 b:44.3 occ:1.00 O2 A:PO4472 1.9 20.3 1.0 OD1 A:ASP115 2.0 35.2 1.0 OE2 A:GLU150 2.0 39.2 1.0 NE2 A:HIS440 2.4 32.5 1.0 OE1 A:GLU150 2.6 39.8 1.0 CD A:GLU150 2.6 38.9 1.0 P A:PO4472 3.0 19.2 1.0 CG A:ASP115 3.1 35.6 1.0 CD2 A:HIS440 3.3 32.4 1.0 O3 A:PO4472 3.3 19.7 1.0 CE1 A:HIS440 3.4 32.4 1.0 O4 A:PO4472 3.4 19.6 1.0 MN A:MN471 3.5 34.6 1.0 OD2 A:ASP115 3.6 38.1 1.0 CG A:GLU150 4.1 37.9 1.0 NE2 A:HIS269 4.2 35.0 1.0 OE2 A:GLU149 4.3 39.6 1.0 CE A:MET439 4.3 33.7 1.0 CB A:ASP115 4.3 34.6 1.0 O1 A:PO4472 4.3 20.8 1.0 CD2 A:HIS269 4.4 34.9 1.0 CG A:HIS440 4.5 32.7 1.0 ND1 A:HIS440 4.5 32.6 1.0 CE1 A:HIS84 4.7 34.9 1.0 ND2 A:ASN216 4.7 39.2 1.0 NE2 A:HIS84 4.7 34.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Staphylococcus Aureus Metallopeptidase (Sapep/Dape) in the MN2+ Bound Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Staphylococcus Aureus Metallopeptidase (Sapep/Dape) in the MN2+ Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn471 b:34.6 occ:1.00 OD1 A:ASP173 2.0 36.3 1.0 OD2 A:ASP115 2.2 38.1 1.0 NE2 A:HIS84 2.4 34.8 1.0 CG A:ASP173 2.6 36.8 1.0 OD2 A:ASP173 2.7 37.6 1.0 CG A:ASP115 2.8 35.6 1.0 O4 A:PO4472 2.9 19.6 1.0 O3 A:PO4472 2.9 19.7 1.0 OD1 A:ASP115 3.1 35.2 1.0 CE1 A:HIS84 3.2 34.9 1.0 CD2 A:HIS84 3.4 34.1 1.0 P A:PO4472 3.4 19.2 1.0 MN A:MN470 3.5 44.3 1.0 OE2 A:GLU149 3.7 39.6 1.0 CB A:ASP115 3.9 34.6 1.0 OE1 A:GLU150 3.9 39.8 1.0 O2 A:PO4472 4.0 20.3 1.0 O A:ASP173 4.1 37.9 1.0 CB A:ASP173 4.1 37.3 1.0 CB A:ASP116 4.1 33.6 1.0 CD A:GLU149 4.3 38.4 1.0 ND1 A:HIS84 4.4 34.2 1.0 CG A:HIS84 4.4 34.0 1.0 CG A:ASP116 4.5 33.7 1.0 OE1 A:GLU149 4.5 38.2 1.0 CE A:MET439 4.7 33.7 1.0 CA A:ASP115 4.7 34.2 1.0 OD1 A:ASP116 4.8 34.4 1.0 CD A:GLU150 4.8 38.9 1.0 O1 A:PO4472 4.8 20.8 1.0 OE2 A:GLU150 4.8 39.2 1.0 CA A:ASP173 4.8 37.8 1.0 C A:ASP173 4.8 38.0 1.0 C A:ASP115 4.9 33.8 1.0 OD2 A:ASP116 4.9 33.3 1.0

T.S.Girish, B.Gopal. Crystal Structure of Staphylococcus Aureus Metallopeptidase (Sapep) Reveals Large Domain Motions Between the Manganese-Bound and Apo-States J.Biol.Chem. V. 285 29406 2010.
ISSN: ISSN 0021-9258
PubMed: 20610394
DOI: 10.1074/JBC.M110.147579