Magnesium in PDB 7zz3: Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
Enzymatic activity of Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
All present enzymatic activity of Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa:
6.4.1.1;
Other elements in 7zz3:
The structure of Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
(pdb code 7zz3). 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 "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa, PDB code: 7zz3:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 7zz3
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Magnesium Binding Sites List in 7zz3
Magnesium binding site 1 out
of 8 in the Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
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 "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1202
b:68.4
occ:1.00
|
O
|
A:VAL519
|
2.4
|
78.7
|
1.0
|
O
|
A:THR522
|
2.6
|
77.4
|
1.0
|
OD1
|
A:ASP753
|
2.8
|
73.1
|
1.0
|
C
|
A:VAL519
|
3.6
|
69.8
|
1.0
|
C
|
A:THR522
|
3.7
|
71.1
|
1.0
|
CG
|
A:ASP753
|
3.8
|
68.9
|
1.0
|
CB
|
A:THR522
|
3.9
|
68.2
|
1.0
|
N
|
A:THR522
|
4.0
|
73.6
|
1.0
|
O
|
A:LYS520
|
4.0
|
72.7
|
1.0
|
CB
|
A:ASP753
|
4.0
|
62.7
|
1.0
|
CA
|
A:THR522
|
4.1
|
69.5
|
1.0
|
C
|
A:LYS520
|
4.2
|
71.0
|
1.0
|
CA
|
A:LYS520
|
4.3
|
68.0
|
1.0
|
CA
|
A:ASP753
|
4.3
|
63.1
|
1.0
|
O
|
A:GLU524
|
4.4
|
73.8
|
1.0
|
N
|
A:LYS520
|
4.4
|
69.2
|
1.0
|
CG1
|
A:VAL519
|
4.4
|
69.2
|
1.0
|
NH2
|
A:ARG783
|
4.4
|
60.8
|
1.0
|
CA
|
A:VAL519
|
4.6
|
64.8
|
1.0
|
OG1
|
A:THR522
|
4.7
|
71.9
|
1.0
|
N
|
A:LYS523
|
4.8
|
66.8
|
1.0
|
O
|
A:ASP753
|
4.9
|
64.1
|
1.0
|
OD2
|
A:ASP753
|
5.0
|
66.8
|
1.0
|
N
|
A:ASN521
|
5.0
|
64.0
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 7zz3
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Magnesium Binding Sites List in 7zz3
Magnesium binding site 2 out
of 8 in the Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
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 "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1205
b:49.7
occ:1.00
|
OE1
|
A:GLU274
|
2.4
|
63.1
|
1.0
|
O3B
|
A:ATP1204
|
2.5
|
63.5
|
1.0
|
OE1
|
A:GLU286
|
2.6
|
56.1
|
1.0
|
O3A
|
A:ATP1204
|
2.7
|
52.7
|
1.0
|
O1A
|
A:ATP1204
|
2.7
|
63.6
|
1.0
|
O2G
|
A:ATP1204
|
3.1
|
63.6
|
1.0
|
CD
|
A:GLU274
|
3.2
|
61.9
|
1.0
|
OE2
|
A:GLU274
|
3.3
|
63.8
|
1.0
|
PA
|
A:ATP1204
|
3.3
|
62.5
|
1.0
|
PB
|
A:ATP1204
|
3.3
|
53.7
|
1.0
|
PG
|
A:ATP1204
|
3.4
|
81.9
|
1.0
|
CD
|
A:GLU286
|
3.8
|
62.2
|
1.0
|
O5'
|
A:ATP1204
|
4.1
|
54.2
|
1.0
|
O1B
|
A:ATP1204
|
4.2
|
61.9
|
1.0
|
O2B
|
A:ATP1204
|
4.3
|
53.9
|
1.0
|
OD1
|
A:ASN288
|
4.4
|
62.2
|
1.0
|
O1G
|
A:ATP1204
|
4.4
|
68.9
|
1.0
|
C5'
|
A:ATP1204
|
4.4
|
52.4
|
1.0
|
OE2
|
A:GLU286
|
4.4
|
69.8
|
1.0
|
O3G
|
A:ATP1204
|
4.4
|
54.5
|
1.0
|
O2A
|
A:ATP1204
|
4.5
|
59.4
|
1.0
|
CG
|
A:GLU274
|
4.6
|
49.1
|
1.0
|
CE1
|
A:HIS207
|
4.6
|
47.9
|
1.0
|
CB
|
A:GLU286
|
4.9
|
50.5
|
1.0
|
NE2
|
A:HIS207
|
4.9
|
50.0
|
1.0
|
CG
|
A:GLU286
|
4.9
|
57.1
|
1.0
|
ND2
|
A:ASN288
|
5.0
|
56.0
|
1.0
|
NZ
|
A:LYS236
|
5.0
|
54.6
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 7zz3
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Magnesium Binding Sites List in 7zz3
Magnesium binding site 3 out
of 8 in the Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
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 "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1201
b:55.9
occ:1.00
|
OD1
|
B:ASP753
|
2.1
|
61.2
|
1.0
|
O
|
B:VAL519
|
2.4
|
66.8
|
1.0
|
O
|
B:THR522
|
2.7
|
64.9
|
1.0
|
CG
|
B:ASP753
|
3.3
|
53.8
|
1.0
|
C
|
B:VAL519
|
3.6
|
54.9
|
1.0
|
C
|
B:THR522
|
3.8
|
58.7
|
1.0
|
O
|
B:LYS520
|
3.9
|
63.0
|
1.0
|
CB
|
B:ASP753
|
3.9
|
41.5
|
1.0
|
CA
|
B:LYS520
|
4.1
|
49.2
|
1.0
|
C
|
B:LYS520
|
4.1
|
56.7
|
1.0
|
N
|
B:THR522
|
4.2
|
60.5
|
1.0
|
CA
|
B:ASP753
|
4.2
|
38.5
|
1.0
|
OD2
|
B:ASP753
|
4.3
|
55.5
|
1.0
|
N
|
B:LYS520
|
4.3
|
54.3
|
1.0
|
CB
|
B:THR522
|
4.3
|
58.6
|
1.0
|
CA
|
B:THR522
|
4.3
|
57.0
|
1.0
|
NH2
|
B:ARG783
|
4.4
|
49.1
|
1.0
|
CG1
|
B:VAL519
|
4.4
|
50.9
|
1.0
|
O
|
B:GLU524
|
4.5
|
66.2
|
1.0
|
CA
|
B:VAL519
|
4.7
|
44.6
|
1.0
|
O
|
B:ASP753
|
4.9
|
44.4
|
1.0
|
N
|
B:ASN521
|
4.9
|
52.0
|
1.0
|
N
|
B:LYS523
|
4.9
|
57.6
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 7zz3
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Magnesium Binding Sites List in 7zz3
Magnesium binding site 4 out
of 8 in the Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
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 "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1204
b:64.7
occ:1.00
|
O3A
|
B:ADP1203
|
2.1
|
86.6
|
1.0
|
OE1
|
B:GLU274
|
2.1
|
73.7
|
1.0
|
OE2
|
B:GLU286
|
2.1
|
73.7
|
1.0
|
O1A
|
B:ADP1203
|
2.7
|
88.4
|
1.0
|
PB
|
B:ADP1203
|
3.0
|
90.1
|
1.0
|
PA
|
B:ADP1203
|
3.0
|
93.2
|
1.0
|
CD
|
B:GLU274
|
3.1
|
71.0
|
1.0
|
CD
|
B:GLU286
|
3.1
|
75.5
|
1.0
|
O1B
|
B:ADP1203
|
3.1
|
83.7
|
1.0
|
O2B
|
B:ADP1203
|
3.1
|
80.2
|
1.0
|
OE2
|
B:GLU274
|
3.4
|
65.8
|
1.0
|
CG
|
B:GLU286
|
3.8
|
64.9
|
1.0
|
O2A
|
B:ADP1203
|
4.0
|
82.8
|
1.0
|
OE1
|
B:GLU286
|
4.1
|
78.6
|
1.0
|
O5'
|
B:ADP1203
|
4.1
|
76.4
|
1.0
|
O3B
|
B:ADP1203
|
4.3
|
82.4
|
1.0
|
OD1
|
B:ASN288
|
4.3
|
63.7
|
1.0
|
CG
|
B:GLU274
|
4.4
|
61.7
|
1.0
|
ND2
|
B:ASN288
|
4.5
|
51.2
|
1.0
|
C5'
|
B:ADP1203
|
4.7
|
76.3
|
1.0
|
CG
|
B:ASN288
|
4.8
|
56.3
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 7zz3
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Magnesium Binding Sites List in 7zz3
Magnesium binding site 5 out
of 8 in the Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
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 "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1201
b:65.1
occ:1.00
|
O
|
C:VAL519
|
2.4
|
68.7
|
1.0
|
O
|
C:THR522
|
2.5
|
70.9
|
1.0
|
OD1
|
C:ASP753
|
2.8
|
64.9
|
1.0
|
C
|
C:THR522
|
3.6
|
64.1
|
1.0
|
C
|
C:VAL519
|
3.6
|
57.7
|
1.0
|
CG
|
C:ASP753
|
3.8
|
63.3
|
1.0
|
N
|
C:THR522
|
4.0
|
64.3
|
1.0
|
O
|
C:LYS520
|
4.0
|
66.0
|
1.0
|
CB
|
C:ASP753
|
4.1
|
56.8
|
1.0
|
CA
|
C:LYS520
|
4.1
|
51.3
|
1.0
|
CA
|
C:THR522
|
4.1
|
62.7
|
1.0
|
C
|
C:LYS520
|
4.1
|
55.7
|
1.0
|
CB
|
C:THR522
|
4.1
|
62.2
|
1.0
|
O
|
C:GLU524
|
4.3
|
70.3
|
1.0
|
N
|
C:LYS520
|
4.3
|
55.9
|
1.0
|
CA
|
C:ASP753
|
4.4
|
53.3
|
1.0
|
NH2
|
C:ARG783
|
4.4
|
53.6
|
1.0
|
CG1
|
C:VAL519
|
4.6
|
57.6
|
1.0
|
CA
|
C:VAL519
|
4.7
|
53.0
|
1.0
|
N
|
C:LYS523
|
4.7
|
59.0
|
1.0
|
N
|
C:ASN521
|
4.8
|
50.8
|
1.0
|
OD2
|
C:ASP753
|
4.9
|
65.7
|
1.0
|
CG2
|
C:THR522
|
5.0
|
62.8
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 7zz3
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Magnesium Binding Sites List in 7zz3
Magnesium binding site 6 out
of 8 in the Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
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 "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1204
b:78.3
occ:1.00
|
O3A
|
C:ADP1203
|
2.1
|
86.6
|
1.0
|
OE2
|
C:GLU286
|
2.1
|
63.5
|
1.0
|
O3B
|
C:ADP1203
|
2.7
|
81.2
|
1.0
|
PB
|
C:ADP1203
|
2.7
|
90.9
|
1.0
|
OE2
|
C:GLU274
|
2.8
|
62.4
|
1.0
|
O2B
|
C:ADP1203
|
3.0
|
73.6
|
1.0
|
OE1
|
C:GLU274
|
3.0
|
62.5
|
1.0
|
O2A
|
C:ADP1203
|
3.3
|
84.9
|
1.0
|
CD
|
C:GLU274
|
3.3
|
56.6
|
1.0
|
PA
|
C:ADP1203
|
3.3
|
88.4
|
1.0
|
CD
|
C:GLU286
|
3.3
|
61.6
|
1.0
|
OE1
|
C:GLU286
|
4.1
|
69.3
|
1.0
|
O1B
|
C:ADP1203
|
4.1
|
77.7
|
1.0
|
O1A
|
C:ADP1203
|
4.2
|
81.2
|
1.0
|
CG
|
C:GLU286
|
4.3
|
47.1
|
1.0
|
O5'
|
C:ADP1203
|
4.4
|
77.6
|
1.0
|
OD1
|
C:ASN288
|
4.4
|
54.4
|
1.0
|
C5'
|
C:ADP1203
|
4.7
|
75.5
|
1.0
|
CG
|
C:GLU274
|
4.7
|
45.4
|
1.0
|
CE1
|
C:HIS207
|
4.8
|
50.4
|
1.0
|
NZ
|
C:LYS236
|
5.0
|
50.8
|
1.0
|
ND2
|
C:ASN288
|
5.0
|
45.0
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 7zz3
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Magnesium Binding Sites List in 7zz3
Magnesium binding site 7 out
of 8 in the Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
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 "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1201
b:75.9
occ:1.00
|
O
|
D:THR522
|
2.3
|
75.6
|
1.0
|
O
|
D:VAL519
|
2.5
|
73.8
|
1.0
|
OD1
|
D:ASP753
|
3.0
|
67.8
|
1.0
|
C
|
D:THR522
|
3.4
|
65.5
|
1.0
|
C
|
D:VAL519
|
3.7
|
65.3
|
1.0
|
O
|
D:LYS520
|
3.9
|
67.4
|
1.0
|
CB
|
D:THR522
|
4.0
|
63.3
|
1.0
|
CG
|
D:ASP753
|
4.0
|
65.7
|
1.0
|
CA
|
D:THR522
|
4.0
|
64.8
|
1.0
|
N
|
D:THR522
|
4.0
|
66.9
|
1.0
|
O
|
D:GLU524
|
4.1
|
71.9
|
1.0
|
C
|
D:LYS520
|
4.2
|
62.7
|
1.0
|
CB
|
D:ASP753
|
4.3
|
58.9
|
1.0
|
NH2
|
D:ARG783
|
4.3
|
56.5
|
1.0
|
CA
|
D:LYS520
|
4.4
|
58.6
|
1.0
|
CA
|
D:ASP753
|
4.4
|
54.8
|
1.0
|
N
|
D:LYS520
|
4.5
|
60.8
|
1.0
|
N
|
D:LYS523
|
4.5
|
60.2
|
1.0
|
CG2
|
D:THR522
|
4.6
|
64.7
|
1.0
|
CG1
|
D:VAL519
|
4.7
|
65.3
|
1.0
|
CA
|
D:VAL519
|
4.8
|
60.6
|
1.0
|
CA
|
D:LYS523
|
4.8
|
65.7
|
1.0
|
C
|
D:LYS523
|
5.0
|
70.4
|
1.0
|
C
|
D:ASN521
|
5.0
|
65.4
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 7zz3
Go back to
Magnesium Binding Sites List in 7zz3
Magnesium binding site 8 out
of 8 in the Cryo-Em Structure of "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
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 "Bc React" Conformation of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1204
b:139.8
occ:1.00
|
O3A
|
D:ADP1203
|
2.1
|
135.2
|
1.0
|
OE1
|
D:GLU286
|
2.1
|
125.3
|
1.0
|
OE1
|
D:GLU274
|
2.2
|
123.5
|
1.0
|
OE2
|
D:GLU274
|
2.2
|
124.0
|
1.0
|
CD
|
D:GLU274
|
2.5
|
122.9
|
1.0
|
O3B
|
D:ADP1203
|
2.6
|
132.0
|
1.0
|
PB
|
D:ADP1203
|
2.8
|
135.2
|
1.0
|
CD
|
D:GLU286
|
3.3
|
122.9
|
1.0
|
O2B
|
D:ADP1203
|
3.3
|
129.9
|
1.0
|
PA
|
D:ADP1203
|
3.3
|
137.9
|
1.0
|
O2A
|
D:ADP1203
|
3.4
|
132.7
|
1.0
|
OE2
|
D:GLU286
|
3.9
|
121.6
|
1.0
|
CG
|
D:GLU274
|
4.0
|
119.1
|
1.0
|
OD1
|
D:ASN288
|
4.2
|
109.2
|
1.0
|
O1B
|
D:ADP1203
|
4.2
|
131.4
|
1.0
|
O5'
|
D:ADP1203
|
4.2
|
133.2
|
1.0
|
CB
|
D:GLU286
|
4.3
|
118.4
|
1.0
|
CG
|
D:GLU286
|
4.4
|
120.4
|
1.0
|
O1A
|
D:ADP1203
|
4.4
|
133.1
|
1.0
|
ND2
|
D:ASN288
|
4.4
|
103.4
|
1.0
|
CE1
|
D:HIS207
|
4.5
|
107.1
|
1.0
|
C5'
|
D:ADP1203
|
4.7
|
131.1
|
1.0
|
CB
|
D:GLU274
|
4.7
|
118.2
|
1.0
|
CG
|
D:ASN288
|
4.7
|
106.0
|
1.0
|
OE2
|
D:GLU209
|
4.9
|
109.0
|
1.0
|
NE2
|
D:HIS207
|
5.0
|
108.3
|
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 17:08:00 2024
|