Manganese in PDB 7zyy: Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa

All present enzymatic activity of Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa:
6.4.1.1;

The structure of Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Manganese atom in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa (pdb code 7zyy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa, PDB code: 7zyy:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1202 b:58.6 occ:1.00 O A:HOH1329 2.1 36.0 1.0 OQ1 A:KCX703 2.2 48.8 1.0 NE2 A:HIS734 2.2 33.1 1.0 NE2 A:HIS732 2.2 32.7 1.0 OD2 A:ASP534 2.6 41.5 1.0 OQ2 A:KCX703 2.7 48.3 1.0 CX A:KCX703 2.8 47.7 1.0 CE1 A:HIS732 2.9 28.6 1.0 CE1 A:HIS734 3.0 31.6 1.0 OD1 A:ASP534 3.1 47.7 1.0 CG A:ASP534 3.1 33.5 1.0 CD2 A:HIS734 3.3 32.8 1.0 CD2 A:HIS732 3.4 35.0 1.0 NE2 A:GLN768 3.8 30.3 1.0 O A:HOH1325 3.8 48.0 1.0 NZ A:KCX703 4.1 44.9 1.0 ND1 A:HIS732 4.1 25.9 1.0 ND1 A:HIS734 4.2 36.0 1.0 NH2 A:ARG533 4.2 32.4 1.0 CG A:HIS734 4.3 34.3 1.0 CG A:HIS732 4.4 28.2 1.0 CB A:ASP534 4.5 28.0 1.0 O A:HOH1326 4.6 40.4 1.0 O3 A:PYR1206 4.7 53.6 1.0 CD A:GLN768 4.7 30.9 1.0 OE1 A:GLN768 4.9 40.9 1.0 CA A:MET705 5.0 49.1 1.0

Manganese binding site 2 out of 4 in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1202 b:31.8 occ:1.00 O B:HOH1402 2.2 16.6 1.0 NE2 B:HIS734 2.2 20.2 1.0 NE2 B:HIS732 2.2 17.1 1.0 OD2 B:ASP534 2.3 32.5 1.0 OQ2 B:KCX703 2.4 29.2 1.0 OQ1 B:KCX703 2.4 28.5 1.0 CX B:KCX703 2.8 25.7 1.0 CE1 B:HIS732 3.1 12.0 1.0 CE1 B:HIS734 3.1 14.4 1.0 CD2 B:HIS734 3.2 15.6 1.0 CD2 B:HIS732 3.3 12.9 1.0 CG B:ASP534 3.3 12.6 1.0 OD1 B:ASP534 3.6 26.1 1.0 NE2 B:GLN768 3.7 20.8 1.0 O B:HOH1340 3.9 30.2 1.0 NZ B:KCX703 4.1 24.5 1.0 ND1 B:HIS732 4.2 12.0 1.0 ND1 B:HIS734 4.2 26.7 1.0 NH2 B:ARG533 4.3 17.3 1.0 CG B:HIS734 4.3 24.4 1.0 CG B:HIS732 4.3 13.6 1.0 O3 B:PYR1206 4.5 28.9 1.0 O B:HOH1326 4.6 26.3 1.0 CB B:ASP534 4.6 5.1 1.0 CD B:GLN768 4.7 21.0 1.0 CA B:MET705 4.8 23.3 1.0 CE B:KCX703 4.9 13.8 1.0 O B:MET705 5.0 30.5 1.0

Manganese binding site 3 out of 4 in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1202 b:56.3 occ:1.00 OQ2 C:KCX703 2.1 48.0 1.0 OD2 C:ASP534 2.2 47.0 1.0 O C:HOH1301 2.2 26.0 1.0 NE2 C:HIS734 2.2 37.0 1.0 NE2 C:HIS732 2.2 32.5 1.0 CG C:ASP534 2.8 30.7 1.0 CE1 C:HIS732 2.9 27.1 1.0 CX C:KCX703 2.9 44.5 1.0 OQ1 C:KCX703 2.9 38.6 1.0 OD1 C:ASP534 2.9 39.2 1.0 CE1 C:HIS734 3.0 32.0 1.0 CD2 C:HIS734 3.3 33.2 1.0 CD2 C:HIS732 3.5 31.6 1.0 NE2 C:GLN768 3.5 29.4 1.0 O C:HOH1334 3.9 40.1 1.0 CB C:ASP534 4.1 22.4 1.0 ND1 C:HIS732 4.1 23.9 1.0 NZ C:KCX703 4.1 44.1 1.0 ND1 C:HIS734 4.1 39.4 1.0 NH2 C:ARG533 4.1 30.0 1.0 CG C:HIS734 4.3 38.4 1.0 CD C:GLN768 4.4 34.3 1.0 CG C:HIS732 4.4 28.9 1.0 OE1 C:GLN768 4.5 37.5 1.0 O3 C:PYR1206 4.5 45.0 1.0 O C:HOH1340 4.6 33.8 1.0 CZ C:ARG533 5.0 28.8 1.0

Manganese binding site 4 out of 4 in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1202 b:46.6 occ:1.00 O D:HOH1341 2.1 25.5 1.0 NE2 D:HIS732 2.2 24.9 1.0 NE2 D:HIS734 2.2 31.6 1.0 OD2 D:ASP534 2.3 37.2 1.0 OQ1 D:KCX703 2.4 39.7 1.0 OQ2 D:KCX703 2.4 36.2 1.0 CX D:KCX703 2.7 35.9 1.0 CE1 D:HIS732 3.1 23.4 1.0 CE1 D:HIS734 3.2 28.2 1.0 CD2 D:HIS734 3.2 27.3 1.0 CD2 D:HIS732 3.2 21.6 1.0 CG D:ASP534 3.3 24.6 1.0 OD1 D:ASP534 3.6 37.1 1.0 O D:HOH1333 3.6 42.4 1.0 NE2 D:GLN768 3.8 27.4 1.0 NZ D:KCX703 4.1 34.9 1.0 ND1 D:HIS732 4.2 19.7 1.0 NH2 D:ARG533 4.3 31.5 1.0 ND1 D:HIS734 4.3 35.3 1.0 CG D:HIS732 4.3 19.1 1.0 CG D:HIS734 4.3 30.6 1.0 O3 D:PYR1206 4.5 41.3 1.0 O D:HOH1322 4.5 34.0 1.0 CB D:ASP534 4.6 23.7 1.0 CA D:MET705 4.7 31.7 1.0 CD D:GLN768 4.7 28.9 1.0 O D:MET705 4.9 42.8 1.0 CE D:KCX703 5.0 30.7 1.0 OE1 D:GLN768 5.0 35.9 1.0

J.P.Lopez-Alonso, M.Lazaro, D.Gil-Carton, P.H.Choi, L.Tong, M.Valle. Cryoem Structural Exploration of Catalytically Active Enzyme Pyruvate Carboxylase. Nat Commun V. 13 6185 2022.
ISSN: ESSN 2041-1723
PubMed: 36261450
DOI: 10.1038/S41467-022-33987-2