Magnesium 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 Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa and Cyclic Di-Amp, PDB code: 7zz8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 7zz8
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Magnesium Binding Sites List in 7zz8
Magnesium binding site 1 out
of 8 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 Magnesium with other atoms in the Mg 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:Mg1201
b:74.2
occ:1.00
|
O
|
A:THR522
|
2.1
|
77.3
|
1.0
|
OD1
|
A:ASP753
|
2.8
|
84.8
|
1.0
|
O
|
A:VAL519
|
3.0
|
79.3
|
1.0
|
C
|
A:THR522
|
3.3
|
74.9
|
1.0
|
NH2
|
A:ARG783
|
3.3
|
65.4
|
1.0
|
CA
|
A:THR522
|
4.0
|
76.4
|
1.0
|
N
|
A:THR522
|
4.0
|
78.9
|
1.0
|
CG
|
A:ASP753
|
4.0
|
82.6
|
1.0
|
O
|
A:GLU524
|
4.1
|
77.4
|
1.0
|
O
|
A:LYS520
|
4.1
|
77.6
|
1.0
|
CB
|
A:THR522
|
4.1
|
74.7
|
1.0
|
C
|
A:VAL519
|
4.2
|
76.5
|
1.0
|
C
|
A:LYS520
|
4.3
|
77.6
|
1.0
|
N
|
A:LYS523
|
4.3
|
68.0
|
1.0
|
O
|
A:LYS523
|
4.4
|
74.6
|
1.0
|
CA
|
A:LYS520
|
4.5
|
77.5
|
1.0
|
CZ
|
A:ARG783
|
4.5
|
64.2
|
1.0
|
C
|
A:LYS523
|
4.5
|
73.7
|
1.0
|
CA
|
A:LYS523
|
4.6
|
69.2
|
1.0
|
CB
|
A:ASP753
|
4.6
|
75.6
|
1.0
|
CA
|
A:ASP753
|
4.7
|
70.4
|
1.0
|
N
|
A:LYS520
|
4.8
|
77.2
|
1.0
|
CG2
|
A:THR522
|
4.9
|
71.0
|
1.0
|
OD2
|
A:ASP753
|
4.9
|
81.4
|
1.0
|
C
|
A:GLU524
|
5.0
|
72.6
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 7zz8
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Magnesium Binding Sites List in 7zz8
Magnesium binding site 2 out
of 8 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 Magnesium with other atoms in the Mg 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
|
A:Mg1204
b:88.9
occ:1.00
|
OE1
|
A:GLU274
|
2.1
|
67.0
|
1.0
|
O3A
|
A:ADP1203
|
2.1
|
108.9
|
1.0
|
OE1
|
A:GLU286
|
2.4
|
66.5
|
1.0
|
OE2
|
A:GLU274
|
2.6
|
53.4
|
1.0
|
CD
|
A:GLU274
|
2.6
|
63.6
|
1.0
|
O1A
|
A:ADP1203
|
2.8
|
95.8
|
1.0
|
PA
|
A:ADP1203
|
2.9
|
112.8
|
1.0
|
PB
|
A:ADP1203
|
3.3
|
109.1
|
1.0
|
O1B
|
A:ADP1203
|
3.3
|
98.9
|
1.0
|
O5'
|
A:ADP1203
|
3.5
|
100.7
|
1.0
|
CD
|
A:GLU286
|
3.6
|
63.9
|
1.0
|
O3B
|
A:ADP1203
|
3.9
|
98.9
|
1.0
|
NE2
|
A:HIS207
|
4.0
|
52.8
|
1.0
|
CG
|
A:GLU274
|
4.1
|
57.5
|
1.0
|
OD1
|
A:ASN288
|
4.3
|
52.6
|
1.0
|
CB
|
A:GLU286
|
4.3
|
56.9
|
1.0
|
O2A
|
A:ADP1203
|
4.3
|
102.6
|
1.0
|
OE2
|
A:GLU286
|
4.4
|
62.8
|
1.0
|
CE1
|
A:HIS207
|
4.4
|
49.3
|
1.0
|
O2B
|
A:ADP1203
|
4.5
|
97.6
|
1.0
|
CG
|
A:GLU286
|
4.5
|
58.3
|
1.0
|
CB
|
A:GLU274
|
4.7
|
42.7
|
1.0
|
C5'
|
A:ADP1203
|
4.8
|
97.0
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 7zz8
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Magnesium Binding Sites List in 7zz8
Magnesium binding site 3 out
of 8 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 Magnesium with other atoms in the Mg 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
|
B:Mg1201
b:62.2
occ:1.00
|
O
|
B:THR522
|
2.1
|
65.2
|
1.0
|
OD1
|
B:ASP753
|
2.4
|
83.7
|
1.0
|
O
|
B:VAL519
|
2.9
|
60.8
|
1.0
|
C
|
B:THR522
|
3.3
|
66.8
|
1.0
|
NH2
|
B:ARG783
|
3.5
|
59.7
|
1.0
|
CG
|
B:ASP753
|
3.7
|
79.9
|
1.0
|
O
|
B:LYS520
|
3.9
|
61.3
|
1.0
|
N
|
B:THR522
|
4.0
|
73.7
|
1.0
|
CA
|
B:THR522
|
4.0
|
70.0
|
1.0
|
C
|
B:VAL519
|
4.1
|
60.9
|
1.0
|
C
|
B:LYS520
|
4.2
|
61.1
|
1.0
|
CB
|
B:THR522
|
4.2
|
64.0
|
1.0
|
O
|
B:GLU524
|
4.3
|
74.7
|
1.0
|
CA
|
B:LYS520
|
4.3
|
58.7
|
1.0
|
N
|
B:LYS523
|
4.3
|
68.0
|
1.0
|
OD2
|
B:ASP753
|
4.5
|
77.5
|
1.0
|
CB
|
B:ASP753
|
4.5
|
69.9
|
1.0
|
CA
|
B:ASP753
|
4.6
|
65.7
|
1.0
|
CA
|
B:LYS523
|
4.6
|
71.8
|
1.0
|
CZ
|
B:ARG783
|
4.6
|
60.8
|
1.0
|
N
|
B:LYS520
|
4.7
|
60.1
|
1.0
|
C
|
B:LYS523
|
4.8
|
76.6
|
1.0
|
N
|
B:ASN521
|
5.0
|
59.7
|
1.0
|
O
|
B:VAL752
|
5.0
|
65.7
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 7zz8
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Magnesium Binding Sites List in 7zz8
Magnesium binding site 4 out
of 8 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 Magnesium with other atoms in the Mg 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
|
B:Mg1204
b:95.1
occ:1.00
|
O1B
|
B:ADP1203
|
2.1
|
124.4
|
1.0
|
OE1
|
B:GLU274
|
2.1
|
90.1
|
1.0
|
CD
|
B:GLU274
|
2.9
|
89.8
|
1.0
|
OE2
|
B:GLU274
|
3.0
|
87.8
|
1.0
|
OE1
|
B:GLU286
|
3.1
|
89.0
|
1.0
|
PB
|
B:ADP1203
|
3.4
|
131.5
|
1.0
|
O2B
|
B:ADP1203
|
3.8
|
124.7
|
1.0
|
C5'
|
B:ADP1203
|
3.9
|
125.6
|
1.0
|
NE2
|
B:HIS207
|
4.0
|
69.5
|
1.0
|
O1A
|
B:ADP1203
|
4.1
|
125.1
|
1.0
|
CD
|
B:GLU286
|
4.3
|
88.1
|
1.0
|
O3B
|
B:ADP1203
|
4.3
|
125.5
|
1.0
|
CG
|
B:GLU274
|
4.3
|
85.0
|
1.0
|
CB
|
B:GLU286
|
4.4
|
83.4
|
1.0
|
O3A
|
B:ADP1203
|
4.5
|
128.9
|
1.0
|
CE1
|
B:HIS207
|
4.7
|
69.6
|
1.0
|
O5'
|
B:ADP1203
|
4.7
|
128.4
|
1.0
|
PA
|
B:ADP1203
|
4.7
|
134.8
|
1.0
|
CB
|
B:GLU274
|
4.8
|
75.6
|
1.0
|
C3'
|
B:ADP1203
|
4.9
|
123.5
|
1.0
|
CG
|
B:GLU286
|
5.0
|
85.5
|
1.0
|
C4'
|
B:ADP1203
|
5.0
|
124.1
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 7zz8
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Magnesium Binding Sites List in 7zz8
Magnesium binding site 5 out
of 8 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 Magnesium with other atoms in the Mg binding
site number 5 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:Mg1202
b:87.9
occ:1.00
|
O
|
C:THR522
|
2.1
|
73.9
|
1.0
|
O
|
C:VAL519
|
2.5
|
76.5
|
1.0
|
C
|
C:THR522
|
3.0
|
68.4
|
1.0
|
N
|
C:THR522
|
3.4
|
74.2
|
1.0
|
CB
|
C:THR522
|
3.4
|
70.7
|
1.0
|
CA
|
C:THR522
|
3.4
|
71.2
|
1.0
|
C
|
C:VAL519
|
3.7
|
72.1
|
1.0
|
NH2
|
C:ARG783
|
3.9
|
64.9
|
1.0
|
C
|
C:LYS520
|
4.0
|
74.7
|
1.0
|
O
|
C:LYS520
|
4.0
|
74.6
|
1.0
|
O
|
C:GLU524
|
4.0
|
74.4
|
1.0
|
OG1
|
C:THR522
|
4.2
|
75.1
|
1.0
|
CA
|
C:LYS520
|
4.2
|
73.2
|
1.0
|
N
|
C:LYS523
|
4.3
|
62.9
|
1.0
|
N
|
C:LYS520
|
4.4
|
74.0
|
1.0
|
OD2
|
C:ASP753
|
4.5
|
87.2
|
1.0
|
N
|
C:ASN521
|
4.5
|
67.2
|
1.0
|
C
|
C:ASN521
|
4.5
|
70.2
|
1.0
|
CG2
|
C:THR522
|
4.5
|
70.5
|
1.0
|
C
|
C:LYS523
|
4.8
|
71.4
|
1.0
|
CA
|
C:LYS523
|
4.8
|
68.0
|
1.0
|
CA
|
C:VAL519
|
4.8
|
68.0
|
1.0
|
O
|
C:LYS523
|
4.8
|
72.0
|
1.0
|
CG1
|
C:VAL519
|
5.0
|
70.0
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 7zz8
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Magnesium Binding Sites List in 7zz8
Magnesium binding site 6 out
of 8 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 Magnesium with other atoms in the Mg binding
site number 6 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:Mg1205
b:88.7
occ:1.00
|
OE1
|
C:GLU274
|
2.1
|
68.1
|
1.0
|
O3A
|
C:ADP1204
|
2.4
|
107.8
|
1.0
|
OE2
|
C:GLU286
|
2.5
|
71.4
|
1.0
|
O2A
|
C:ADP1204
|
2.6
|
97.7
|
1.0
|
CD
|
C:GLU274
|
2.9
|
65.5
|
1.0
|
OE2
|
C:GLU274
|
3.0
|
60.6
|
1.0
|
PA
|
C:ADP1204
|
3.0
|
112.0
|
1.0
|
CD
|
C:GLU286
|
3.6
|
69.5
|
1.0
|
O5'
|
C:ADP1204
|
3.7
|
102.1
|
1.0
|
PB
|
C:ADP1204
|
3.7
|
109.7
|
1.0
|
O3B
|
C:ADP1204
|
3.8
|
100.0
|
1.0
|
CG
|
C:GLU286
|
4.0
|
65.5
|
1.0
|
O2B
|
C:ADP1204
|
4.2
|
96.1
|
1.0
|
C5'
|
C:ADP1204
|
4.3
|
97.8
|
1.0
|
CE1
|
C:HIS207
|
4.3
|
52.7
|
1.0
|
CG
|
C:GLU274
|
4.3
|
58.7
|
1.0
|
O1A
|
C:ADP1204
|
4.4
|
101.5
|
1.0
|
OD1
|
C:ASN288
|
4.6
|
56.8
|
1.0
|
OE1
|
C:GLU286
|
4.6
|
68.5
|
1.0
|
O1B
|
C:ADP1204
|
4.8
|
99.7
|
1.0
|
NE2
|
C:HIS207
|
4.8
|
56.4
|
1.0
|
CB
|
C:GLU274
|
4.9
|
45.2
|
1.0
|
NZ
|
C:LYS236
|
5.0
|
58.9
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 7zz8
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Magnesium Binding Sites List in 7zz8
Magnesium binding site 7 out
of 8 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 Magnesium with other atoms in the Mg binding
site number 7 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:Mg1201
b:57.6
occ:1.00
|
O
|
D:THR522
|
2.1
|
67.8
|
1.0
|
OD1
|
D:ASP753
|
2.7
|
79.5
|
1.0
|
O
|
D:VAL519
|
2.8
|
57.5
|
1.0
|
OG1
|
D:THR522
|
3.0
|
67.2
|
1.0
|
C
|
D:THR522
|
3.2
|
62.8
|
1.0
|
NH2
|
D:ARG783
|
3.4
|
64.0
|
1.0
|
N
|
D:THR522
|
3.7
|
69.0
|
1.0
|
CA
|
D:THR522
|
3.8
|
65.2
|
1.0
|
CB
|
D:THR522
|
3.9
|
65.1
|
1.0
|
CG
|
D:ASP753
|
4.0
|
76.5
|
1.0
|
C
|
D:VAL519
|
4.0
|
56.0
|
1.0
|
O
|
D:GLU524
|
4.1
|
75.1
|
1.0
|
C
|
D:LYS520
|
4.3
|
60.0
|
1.0
|
O
|
D:LYS520
|
4.3
|
66.0
|
1.0
|
N
|
D:LYS523
|
4.4
|
60.3
|
1.0
|
CA
|
D:LYS520
|
4.4
|
58.5
|
1.0
|
CZ
|
D:ARG783
|
4.5
|
63.3
|
1.0
|
N
|
D:LYS520
|
4.7
|
58.2
|
1.0
|
CA
|
D:LYS523
|
4.7
|
68.1
|
1.0
|
C
|
D:LYS523
|
4.7
|
68.4
|
1.0
|
N
|
D:ASN521
|
4.7
|
57.5
|
1.0
|
O
|
D:LYS523
|
4.8
|
65.0
|
1.0
|
CB
|
D:ASP753
|
4.8
|
67.2
|
1.0
|
CA
|
D:ASP753
|
4.8
|
61.5
|
1.0
|
OD2
|
D:ASP753
|
4.8
|
74.8
|
1.0
|
C
|
D:ASN521
|
4.9
|
64.2
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 7zz8
Go back to
Magnesium Binding Sites List in 7zz8
Magnesium binding site 8 out
of 8 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 Magnesium with other atoms in the Mg binding
site number 8 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:Mg1204
b:111.2
occ:1.00
|
OE1
|
D:GLU274
|
2.1
|
84.4
|
1.0
|
O3A
|
D:ADP1203
|
2.2
|
121.0
|
1.0
|
O2A
|
D:ADP1203
|
2.3
|
116.0
|
1.0
|
OE2
|
D:GLU286
|
2.7
|
88.5
|
1.0
|
OE2
|
D:GLU274
|
2.7
|
79.0
|
1.0
|
PA
|
D:ADP1203
|
2.7
|
124.6
|
1.0
|
CD
|
D:GLU274
|
2.7
|
83.5
|
1.0
|
O5'
|
D:ADP1203
|
3.3
|
117.4
|
1.0
|
PB
|
D:ADP1203
|
3.7
|
121.8
|
1.0
|
CD
|
D:GLU286
|
3.7
|
86.8
|
1.0
|
O3B
|
D:ADP1203
|
3.9
|
114.6
|
1.0
|
CE1
|
D:HIS207
|
4.0
|
68.0
|
1.0
|
CG
|
D:GLU286
|
4.1
|
83.8
|
1.0
|
C5'
|
D:ADP1203
|
4.1
|
115.6
|
1.0
|
O1A
|
D:ADP1203
|
4.1
|
114.0
|
1.0
|
O2B
|
D:ADP1203
|
4.1
|
112.9
|
1.0
|
CG
|
D:GLU274
|
4.2
|
79.2
|
1.0
|
NE2
|
D:HIS207
|
4.3
|
72.1
|
1.0
|
O1B
|
D:ADP1203
|
4.7
|
113.5
|
1.0
|
OE2
|
D:GLU209
|
4.7
|
77.3
|
1.0
|
CB
|
D:GLU274
|
4.8
|
71.4
|
1.0
|
OE1
|
D:GLU286
|
4.8
|
85.0
|
1.0
|
OD1
|
D:ASN288
|
4.9
|
74.4
|
1.0
|
C3'
|
D:ADP1203
|
4.9
|
113.2
|
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: Thu Oct 3 17:08:11 2024
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