Manganese in PDB 7zyy: Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
Enzymatic activity of 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;
Other elements in 7zyy:
The structure of Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa 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
(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 7zyy
Go back to
Manganese Binding Sites List in 7zyy
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 7zyy
Go back to
Manganese Binding Sites List in 7zyy
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 7zyy
Go back to
Manganese Binding Sites List in 7zyy
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 7zyy
Go back to
Manganese Binding Sites List in 7zyy
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
|
|
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 11:13:50 2024
|