Manganese in PDB 7zz8: Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa and Cyclic Di-Amp

Enzymatic activity of Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa and Cyclic Di-Amp

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

Other elements in 7zz8:

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

Magnesium (Mg) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa and Cyclic Di-Amp (pdb code 7zz8). 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 and Cyclic Di-Amp, PDB code: 7zz8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7zz8

Go back to Manganese Binding Sites List in 7zz8
Manganese binding site 1 out of 4 in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa and Cyclic Di-Amp


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 and Cyclic Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1202

b:94.8
occ:1.00
 O A:HOH1301 2.2 59.0 1.0
OD2 A:ASP534 2.2 71.7 1.0
OQ2 A:KCX703 2.2 82.7 1.0
NE2 A:HIS732 2.3 64.5 1.0
NE2 A:HIS734 2.3 62.4 1.0
OQ1 A:KCX703 2.7 82.0 1.0
CX A:KCX703 2.9 81.9 1.0
CG A:ASP534 3.0 60.7 1.0
CE1 A:HIS734 3.1 61.5 1.0
OD1 A:ASP534 3.2 61.1 1.0
CE1 A:HIS732 3.2 63.5 1.0
NE2 A:GLN768 3.3 49.8 1.0
CD2 A:HIS732 3.3 61.4 1.0
CD2 A:HIS734 3.4 63.2 1.0
NH2 A:ARG533 4.0 55.0 1.0
NZ A:KCX703 4.2 79.9 1.0
ND1 A:HIS734 4.3 64.2 1.0
ND1 A:HIS732 4.3 59.9 1.0
CB A:ASP534 4.4 55.1 1.0
CG A:HIS732 4.4 62.9 1.0
CD A:GLN768 4.4 49.1 1.0
CG A:HIS734 4.5 63.9 1.0
OE1 A:GLN768 4.9 56.5 1.0
CE A:KCX703 4.9 79.2 1.0

Manganese binding site 2 out of 4 in 7zz8

Go back to Manganese Binding Sites List in 7zz8
Manganese binding site 2 out of 4 in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa and Cyclic Di-Amp


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 and Cyclic Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1202

b:72.0
occ:1.00
 O B:HOH1301 2.2 47.5 1.0
OD2 B:ASP534 2.2 57.3 1.0
OQ2 B:KCX703 2.2 58.3 1.0
NE2 B:HIS732 2.3 48.8 1.0
NE2 B:HIS734 2.3 49.2 1.0
CX B:KCX703 3.0 57.2 1.0
OQ1 B:KCX703 3.0 55.8 1.0
CE1 B:HIS732 3.1 46.2 1.0
CE1 B:HIS734 3.1 45.7 1.0
CG B:ASP534 3.2 49.6 1.0
CD2 B:HIS732 3.3 43.1 1.0
NE2 B:GLN768 3.4 40.1 1.0
CD2 B:HIS734 3.4 45.4 1.0
OD1 B:ASP534 3.5 54.4 1.0
NH2 B:ARG533 4.1 35.2 1.0
NZ B:KCX703 4.3 54.4 1.0
ND1 B:HIS732 4.3 33.3 1.0
ND1 B:HIS734 4.3 49.3 1.0
CG B:HIS732 4.4 38.4 1.0
CG B:HIS734 4.4 45.6 1.0
CB B:ASP534 4.5 30.3 1.0
CD B:GLN768 4.5 41.4 1.0
CE B:KCX703 4.9 52.2 1.0
OE1 B:GLN768 5.0 46.5 1.0

Manganese binding site 3 out of 4 in 7zz8

Go back to Manganese Binding Sites List in 7zz8
Manganese binding site 3 out of 4 in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa and Cyclic Di-Amp


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 and Cyclic Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1203

b:94.8
occ:1.00
 OQ1 C:KCX703 2.2 88.6 1.0
O C:HOH1301 2.2 57.1 1.0
NE2 C:HIS732 2.3 66.5 1.0
NE2 C:HIS734 2.3 61.9 1.0
CD2 C:HIS732 2.8 62.4 1.0
CD2 C:HIS734 2.8 61.9 1.0
CX C:KCX703 2.9 83.3 1.0
OQ2 C:KCX703 3.1 80.4 1.0
OD2 C:ASP534 3.3 66.7 1.0
CE1 C:HIS734 3.4 64.7 1.0
CE1 C:HIS732 3.5 65.0 1.0
NE2 C:GLN768 3.6 59.2 1.0
CG C:HIS734 4.0 65.1 1.0
NZ C:KCX703 4.0 80.7 1.0
O C:ASP704 4.0 84.2 1.0
CG C:HIS732 4.1 59.3 1.0
CG C:ASP534 4.2 66.2 1.0
CA C:MET705 4.2 84.1 1.0
ND1 C:HIS734 4.3 66.1 1.0
ND1 C:HIS732 4.4 56.8 1.0
OD1 C:ASP534 4.5 71.5 1.0
CE C:KCX703 4.5 80.3 1.0
C C:ASP704 4.7 78.9 1.0
NH2 C:ARG533 4.8 61.3 1.0
N C:MET705 4.9 83.7 1.0
O C:MET705 4.9 84.2 1.0
CG C:KCX703 4.9 78.9 1.0
CD C:GLN768 4.9 60.9 1.0
CB C:MET705 5.0 83.3 1.0
C C:MET705 5.0 85.5 1.0

Manganese binding site 4 out of 4 in 7zz8

Go back to Manganese Binding Sites List in 7zz8
Manganese binding site 4 out of 4 in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa and Cyclic Di-Amp


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 and Cyclic Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1202

b:65.3
occ:1.00
 O D:HOH1301 2.2 40.0 1.0
OD2 D:ASP534 2.2 57.0 1.0
OQ1 D:KCX703 2.2 61.7 1.0
NE2 D:HIS734 2.3 46.7 1.0
NE2 D:HIS732 2.3 47.6 1.0
OQ2 D:KCX703 2.8 60.8 1.0
CX D:KCX703 2.8 62.8 1.0
CE1 D:HIS732 3.0 45.5 1.0
CG D:ASP534 3.0 48.7 1.0
CE1 D:HIS734 3.1 46.5 1.0
OD1 D:ASP534 3.2 52.8 1.0
CD2 D:HIS734 3.4 44.9 1.0
CD2 D:HIS732 3.4 43.6 1.0
NE2 D:GLN768 3.5 34.9 1.0
NH2 D:ARG533 3.9 41.8 1.0
NZ D:KCX703 4.1 61.8 1.0
ND1 D:HIS732 4.2 34.4 1.0
ND1 D:HIS734 4.2 48.2 1.0
CB D:ASP534 4.4 36.7 1.0
CG D:HIS732 4.4 39.5 1.0
CG D:HIS734 4.4 45.6 1.0
CD D:GLN768 4.5 38.6 1.0
CE D:KCX703 4.9 56.3 1.0
OE1 D:GLN768 4.9 50.0 1.0

Reference:

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
Page generated: Fri Apr 7 13:12:00 2023

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