Manganese in PDB 3bg5: Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase

The structure of Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase, PDB code: 3bg5 was solved by S.Xiang, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	96.428, 256.083, 126.010, 90.00, 109.47, 90.00
R / Rfree (%)	21.5 / 26.8

The binding sites of Manganese atom in the Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase (pdb code 3bg5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase, PDB code: 3bg5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase


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 Pyruvate Carboxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2002 b:0.5 occ:1.00 NE2 A:HIS771 2.6 40.5 1.0 NE2 A:HIS773 2.6 40.5 1.0 NZ A:LYS741 2.8 43.8 1.0 OD1 A:ASP572 2.9 43.6 1.0 O3 A:PYR2001 3.3 93.2 1.0 CD2 A:HIS771 3.4 38.9 1.0 CE1 A:HIS773 3.4 40.3 1.0 CE1 A:HIS771 3.5 39.8 1.0 CG A:ASP572 3.6 40.0 1.0 OD2 A:ASP572 3.7 40.9 1.0 CD2 A:HIS773 3.7 39.8 1.0 C3 A:PYR2001 3.8 93.7 1.0 C2 A:PYR2001 4.0 93.6 1.0 CE A:LYS741 4.3 43.8 1.0 ND1 A:HIS771 4.5 39.8 1.0 CG A:HIS771 4.5 39.6 1.0 ND1 A:HIS773 4.6 38.9 1.0 NH2 A:ARG571 4.6 33.3 1.0 OE1 A:GLN807 4.7 38.1 1.0 CG A:HIS773 4.8 38.0 1.0 CA A:MET743 4.9 39.5 1.0 CB A:ASP572 4.9 37.6 1.0 CG A:LYS741 4.9 41.6 1.0 CB A:MET743 5.0 40.0 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase


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 Pyruvate Carboxylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:94.8 occ:1.00 NE2 B:HIS773 2.3 51.5 1.0 NE2 B:HIS771 2.3 52.8 1.0 OD1 B:ASP572 2.4 48.0 1.0 CE1 B:HIS773 2.9 51.2 1.0 CE1 B:HIS771 3.3 52.4 1.0 CD2 B:HIS771 3.3 52.3 1.0 NZ B:LYS741 3.5 49.1 1.0 CG B:ASP572 3.5 46.2 1.0 CD2 B:HIS773 3.5 50.9 1.0 O3 B:PYR2001 3.6 89.7 1.0 OD2 B:ASP572 3.8 46.9 1.0 ND1 B:HIS773 4.2 51.1 1.0 C3 B:PYR2001 4.2 90.3 1.0 C2 B:PYR2001 4.2 90.5 1.0 ND1 B:HIS771 4.4 52.1 1.0 CG B:HIS771 4.4 52.0 1.0 CG B:HIS773 4.5 49.8 1.0 NH2 B:ARG571 4.7 40.5 1.0 CE B:LYS741 4.8 48.9 1.0 CB B:ASP572 4.8 45.2 1.0 CG B:LYS741 4.9 47.6 1.0 CA B:MET743 4.9 48.9 1.0 OE1 B:GLN807 5.0 48.9 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn2002 b:79.5 occ:1.00 NE2 C:HIS771 2.4 51.2 1.0 OD1 C:ASP572 2.6 44.6 1.0 NE2 C:HIS773 2.6 47.1 1.0 NZ C:LYS741 2.8 47.0 1.0 CE1 C:HIS771 3.1 50.5 1.0 CG C:ASP572 3.3 43.1 1.0 CE1 C:HIS773 3.4 46.3 1.0 OD2 C:ASP572 3.4 41.5 1.0 O3 C:PYR2001 3.4 85.0 1.0 CD2 C:HIS771 3.5 50.5 1.0 CD2 C:HIS773 3.7 47.8 1.0 CE C:LYS741 4.1 48.8 1.0 NH2 C:ARG571 4.1 43.0 1.0 ND1 C:HIS771 4.2 49.5 1.0 C2 C:PYR2001 4.3 85.2 1.0 CG C:HIS771 4.4 49.7 1.0 C3 C:PYR2001 4.5 85.3 1.0 ND1 C:HIS773 4.6 45.9 1.0 CB C:ASP572 4.6 42.8 1.0 NH1 C:ARG571 4.8 42.0 1.0 CG C:HIS773 4.8 46.7 1.0 OE1 C:GLN807 4.8 46.6 1.0 CZ C:ARG571 4.9 42.0 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2002 b:85.9 occ:1.00 OD1 D:ASP572 2.4 39.5 1.0 NE2 D:HIS771 2.6 36.1 1.0 NE2 D:HIS773 2.7 40.5 1.0 CE1 D:HIS773 3.2 39.9 1.0 CG D:ASP572 3.3 35.6 1.0 O3 D:PYR2001 3.3 85.9 1.0 CE1 D:HIS771 3.3 36.1 1.0 OD2 D:ASP572 3.4 37.2 1.0 NZ D:LYS741 3.5 38.8 1.0 CD2 D:HIS771 3.7 36.2 1.0 CD2 D:HIS773 3.9 39.5 1.0 NH2 D:ARG571 4.3 31.4 1.0 ND1 D:HIS773 4.5 38.8 1.0 ND1 D:HIS771 4.5 35.7 1.0 C2 D:PYR2001 4.5 85.6 1.0 CB D:ASP572 4.6 33.8 1.0 CG D:HIS771 4.7 36.2 1.0 CG D:HIS773 4.8 38.7 1.0 OE1 D:GLN807 4.8 33.7 1.0 CE D:LYS741 4.9 39.0 1.0 NH1 D:ARG571 4.9 32.3 1.0 C1 D:PYR2001 5.0 85.1 1.0

S.Xiang, L.Tong. Crystal Structures of Human and Staphylococcus Aureus Pyruvate Carboxylase and Molecular Insights Into the Carboxyltransfer Reaction. Nat.Struct.Mol.Biol. V. 15 295 2008.
ISSN: ISSN 1545-9993
PubMed: 18297087
DOI: 10.1038/NSMB.1393