Manganese in PDB 5vyw: Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase

All present enzymatic activity of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase:
6.4.1.1;

The structure of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase, PDB code: 5vyw was solved by P.H.Choi, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 3.10
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	139.664, 139.664, 610.490, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 24.8

The binding sites of Manganese atom in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase (pdb code 5vyw). 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 Lactococcus Lactis Pyruvate Carboxylase, PDB code: 5vyw:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Lactococcus Lactis 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 Lactococcus Lactis Pyruvate Carboxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1201 b:98.5 occ:1.00 OD2 A:ASP534 2.6 41.4 1.0 NE2 A:HIS734 2.9 53.4 1.0 NE2 A:HIS732 3.0 59.8 1.0 NZ A:LYS703 3.2 60.4 1.0 CG A:ASP534 3.3 46.6 1.0 OD1 A:ASP534 3.4 51.0 1.0 CE1 A:HIS734 3.4 55.5 1.0 CE1 A:HIS732 3.7 63.4 1.0 CE A:LYS703 3.8 54.7 1.0 CD2 A:HIS732 4.0 55.7 1.0 CD2 A:HIS734 4.1 51.0 1.0 NH2 A:ARG533 4.3 63.9 1.0 CB A:ASP534 4.6 47.5 1.0 ND1 A:HIS734 4.7 58.7 1.0 ND1 A:HIS732 4.8 64.4 1.0 CA A:MET705 4.8 55.0 1.0 O A:MET705 4.9 46.1 1.0 CG A:HIS732 5.0 54.1 1.0 NE2 A:GLN768 5.0 42.3 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Lactococcus Lactis 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 Lactococcus Lactis Pyruvate Carboxylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2000 b:90.8 occ:1.00 OD2 B:ASP534 2.4 60.1 1.0 NE2 B:HIS734 2.7 37.2 1.0 NE2 B:HIS732 2.7 71.0 1.0 CG B:ASP534 3.2 63.8 1.0 NZ B:LYS703 3.2 62.1 1.0 CE1 B:HIS734 3.2 42.4 1.0 OD1 B:ASP534 3.3 77.1 1.0 CE1 B:HIS732 3.5 78.0 1.0 CD2 B:HIS732 3.8 57.1 1.0 CD2 B:HIS734 3.9 40.8 1.0 CE B:LYS703 4.0 56.1 1.0 NH2 B:ARG533 4.3 70.2 1.0 ND1 B:HIS734 4.5 40.9 1.0 CB B:ASP534 4.5 55.7 1.0 ND1 B:HIS732 4.6 72.7 1.0 NE2 B:GLN768 4.8 53.9 1.0 CG B:HIS732 4.8 60.0 1.0 CA B:MET705 4.8 49.6 1.0 O B:MET705 4.8 49.2 1.0 CG B:HIS734 4.9 39.0 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Lactococcus Lactis 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 Lactococcus Lactis Pyruvate Carboxylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn2000 b:99.2 occ:1.00 NE2 C:HIS732 2.7 57.1 1.0 OD2 C:ASP534 2.7 46.3 1.0 NE2 C:HIS734 2.8 55.8 1.0 NZ C:LYS703 2.9 68.7 1.0 CG C:ASP534 3.5 50.8 1.0 CE1 C:HIS732 3.5 60.0 1.0 CE1 C:HIS734 3.5 60.8 1.0 CD2 C:HIS732 3.6 53.1 1.0 CE C:LYS703 3.6 70.2 1.0 OD1 C:ASP534 3.7 49.1 1.0 CD2 C:HIS734 4.0 61.7 1.0 NH2 C:ARG533 4.4 72.4 1.0 ND1 C:HIS732 4.5 51.9 1.0 CA C:MET705 4.6 66.5 1.0 CG C:HIS732 4.6 51.5 1.0 ND1 C:HIS734 4.7 59.6 1.0 O C:MET705 4.8 60.3 1.0 CB C:ASP534 4.8 49.4 1.0 CD C:LYS703 4.8 79.4 1.0 CG C:LYS703 4.8 80.2 1.0 CG C:HIS734 5.0 59.2 1.0 NE2 C:GLN768 5.0 48.5 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Lactococcus Lactis 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 Lactococcus Lactis Pyruvate Carboxylase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2000 b:88.1 occ:1.00 OD2 D:ASP534 2.7 49.5 1.0 NE2 D:HIS734 2.7 45.0 1.0 NE2 D:HIS732 2.7 64.2 1.0 NZ D:LYS703 3.1 46.9 1.0 CE1 D:HIS734 3.4 43.9 1.0 CG D:ASP534 3.4 58.8 1.0 CE1 D:HIS732 3.5 71.5 1.0 OD1 D:ASP534 3.6 64.8 1.0 CD2 D:HIS732 3.7 62.8 1.0 CE D:LYS703 3.8 41.7 1.0 CD2 D:HIS734 3.9 44.1 1.0 NH2 D:ARG533 4.4 70.3 1.0 ND1 D:HIS732 4.6 72.4 1.0 CA D:MET705 4.6 50.1 1.0 ND1 D:HIS734 4.7 38.8 1.0 CG D:HIS732 4.7 60.0 1.0 O D:MET705 4.7 50.3 1.0 CB D:ASP534 4.7 57.6 1.0 NE2 D:GLN768 4.9 54.0 1.0 CG D:HIS734 4.9 39.2 1.0

P.H.Choi, T.M.N.Vu, H.T.Pham, J.J.Woodward, M.S.Turner, L.Tong. Structural and Functional Studies of Pyruvate Carboxylase Regulation By Cyclic Di-Amp in Lactic Acid Bacteria. Proc. Natl. Acad. Sci. V. 114 E7226 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28808024
DOI: 10.1073/PNAS.1704756114