Manganese in PDB 5ks8: Crystal Structure of Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus

The structure of Crystal Structure of Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus, PDB code: 5ks8 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)	47.44 / 3.01
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	285.760, 285.760, 274.873, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 27.2

The binding sites of Manganese atom in the Crystal Structure of Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus (pdb code 5ks8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus, PDB code: 5ks8:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus


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 Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn2002 b:92.3 occ:1.00 OD2 C:ASP13 1.9 64.7 1.0 NE2 C:HIS203 2.4 68.0 1.0 NE2 C:HIS205 2.4 61.0 1.0 NZ C:LYS174 2.8 66.1 1.0 CG C:ASP13 3.0 66.8 1.0 CE1 C:HIS203 3.2 67.5 1.0 CE1 C:HIS205 3.3 64.7 1.0 OD1 C:ASP13 3.3 79.8 1.0 CD2 C:HIS205 3.4 61.5 1.0 CD2 C:HIS203 3.4 70.6 1.0 CE C:MET176 3.6 0.8 1.0 O3 C:PYR2001 3.9 97.2 1.0 NH2 C:ARG12 4.0 69.4 1.0 CE C:LYS174 4.2 69.6 1.0 CB C:ASP13 4.3 61.2 1.0 ND1 C:HIS203 4.3 72.7 1.0 ND1 C:HIS205 4.4 56.3 1.0 CG C:HIS203 4.5 63.0 1.0 CG C:HIS205 4.5 59.8 1.0 CZ C:ARG12 4.9 68.7 1.0 NH1 C:ARG12 5.0 66.3 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus


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 Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2002 b:64.5 occ:1.00 OD2 D:ASP13 1.9 78.1 1.0 NE2 D:HIS203 2.3 53.0 1.0 NE2 D:HIS205 2.4 56.9 1.0 NZ D:LYS174 2.8 57.1 1.0 CG D:ASP13 2.9 74.5 1.0 CE1 D:HIS203 3.0 61.1 1.0 OD1 D:ASP13 3.3 85.2 1.0 CE1 D:HIS205 3.4 65.4 1.0 CD2 D:HIS203 3.4 55.7 1.0 CD2 D:HIS205 3.4 54.4 1.0 NH2 D:ARG12 3.9 73.0 1.0 O3 D:PYR2001 3.9 70.0 1.0 CE D:LYS174 4.2 69.5 1.0 CB D:ASP13 4.2 62.4 1.0 ND1 D:HIS203 4.2 59.3 1.0 CG D:HIS203 4.4 52.4 1.0 ND1 D:HIS205 4.5 61.0 1.0 CG D:HIS205 4.6 51.7 1.0 CZ D:ARG12 4.8 58.8 1.0 NH1 D:ARG12 4.9 59.8 1.0 C2 D:PYR2001 4.9 72.3 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus


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 Two-Subunit Pyruvate Carboxylase From Methylobacillus Flagellatus within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn701 b:0.2 occ:1.00 NZ F:LYS174 2.4 0.7 1.0 OD2 F:ASP13 2.6 0.7 1.0 NE2 F:HIS205 2.9 0.7 1.0 NE2 F:HIS203 3.2 0.5 1.0 CG F:ASP13 3.4 0.4 1.0 OD1 F:ASP13 3.4 0.8 1.0 CE1 F:HIS205 3.6 0.5 1.0 CE F:LYS174 3.7 0.2 1.0 CG F:MET176 3.8 0.9 1.0 CD2 F:HIS205 3.9 1.0 1.0 CB F:MET176 3.9 0.8 1.0 NH2 F:ARG12 4.0 0.5 1.0 CE1 F:HIS203 4.1 0.8 1.0 CD2 F:HIS203 4.1 0.8 1.0 NH1 F:ARG12 4.6 0.4 1.0 ND1 F:HIS205 4.7 0.8 1.0 CB F:ASP13 4.8 0.9 1.0 CZ F:ARG12 4.8 0.0 1.0 CA F:MET176 4.8 0.9 1.0 CD F:LYS174 4.9 0.2 1.0 CG F:HIS205 4.9 0.8 1.0

P.H.Choi, J.Jo, Y.C.Lin, M.H.Lin, C.Y.Chou, L.E.Dietrich, L.Tong. A Distinct Holoenzyme Organization For Two-Subunit Pyruvate Carboxylase. Nat Commun V. 7 12713 2016.
ISSN: ESSN 2041-1723
PubMed: 27708276
DOI: 10.1038/NCOMMS12713