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:
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: Sun Oct 6 11:15:44 2024
|