Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa, PDB code: 7zyy:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 7zyy
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Magnesium Binding Sites List in 7zyy
Magnesium binding site 1 out
of 8 in the Cryo-Em Structure 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 Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1201
b:49.9
occ:1.00
|
O
|
A:VAL519
|
2.3
|
52.8
|
1.0
|
O
|
A:HOH1317
|
2.6
|
42.1
|
1.0
|
O
|
A:THR522
|
2.8
|
52.9
|
1.0
|
OD2
|
A:ASP753
|
2.9
|
44.5
|
1.0
|
O
|
A:HOH1346
|
3.4
|
43.7
|
1.0
|
C
|
A:VAL519
|
3.4
|
45.8
|
1.0
|
CG
|
A:ASP753
|
3.8
|
45.2
|
1.0
|
C
|
A:THR522
|
3.9
|
48.4
|
1.0
|
O
|
A:LYS520
|
3.9
|
53.0
|
1.0
|
CA
|
A:LYS520
|
4.0
|
45.2
|
1.0
|
CB
|
A:ASP753
|
4.0
|
39.1
|
1.0
|
C
|
A:LYS520
|
4.0
|
48.7
|
1.0
|
N
|
A:LYS520
|
4.1
|
46.2
|
1.0
|
N
|
A:THR522
|
4.1
|
49.4
|
1.0
|
CG1
|
A:VAL519
|
4.2
|
50.2
|
1.0
|
CB
|
A:THR522
|
4.3
|
47.8
|
1.0
|
CA
|
A:ASP753
|
4.3
|
39.0
|
1.0
|
CA
|
A:THR522
|
4.3
|
48.5
|
1.0
|
CA
|
A:VAL519
|
4.5
|
43.7
|
1.0
|
O
|
A:GLU524
|
4.5
|
52.5
|
1.0
|
NH2
|
A:ARG783
|
4.7
|
34.0
|
1.0
|
N
|
A:ASN521
|
4.8
|
43.2
|
1.0
|
OD1
|
A:ASP753
|
4.9
|
49.3
|
1.0
|
O
|
A:ASP753
|
5.0
|
34.6
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 7zyy
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Magnesium Binding Sites List in 7zyy
Magnesium binding site 2 out
of 8 in the Cryo-Em Structure 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 Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1204
b:62.9
occ:1.00
|
O1A
|
A:ADP1203
|
2.1
|
77.3
|
1.0
|
O1B
|
A:ADP1203
|
2.1
|
73.0
|
1.0
|
OE1
|
A:GLU274
|
2.4
|
67.7
|
1.0
|
OE2
|
A:GLU286
|
2.6
|
66.4
|
1.0
|
CD
|
A:GLU286
|
2.9
|
66.6
|
1.0
|
OE1
|
A:GLU286
|
3.0
|
68.4
|
1.0
|
O3A
|
A:ADP1203
|
3.0
|
75.8
|
1.0
|
PA
|
A:ADP1203
|
3.1
|
85.3
|
1.0
|
PB
|
A:ADP1203
|
3.1
|
78.9
|
1.0
|
CD
|
A:GLU274
|
3.2
|
66.9
|
1.0
|
OE2
|
A:GLU274
|
3.3
|
67.8
|
1.0
|
O2B
|
A:ADP1203
|
3.9
|
75.3
|
1.0
|
CG
|
A:GLU286
|
4.0
|
63.7
|
1.0
|
O2A
|
A:ADP1203
|
4.1
|
80.1
|
1.0
|
O5'
|
A:ADP1203
|
4.2
|
76.4
|
1.0
|
O3B
|
A:ADP1203
|
4.3
|
76.4
|
1.0
|
CB
|
A:GLU286
|
4.3
|
61.3
|
1.0
|
OD1
|
A:ASN288
|
4.5
|
55.0
|
1.0
|
CG
|
A:GLU274
|
4.6
|
62.0
|
1.0
|
ND2
|
A:ASN288
|
4.6
|
52.4
|
1.0
|
C5'
|
A:ADP1203
|
4.9
|
73.5
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 7zyy
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Magnesium Binding Sites List in 7zyy
Magnesium binding site 3 out
of 8 in the Cryo-Em Structure 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 Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1201
b:26.0
occ:1.00
|
O
|
B:VAL519
|
2.3
|
39.9
|
1.0
|
O
|
B:HOH1350
|
2.6
|
22.7
|
1.0
|
O
|
B:THR522
|
2.7
|
36.0
|
1.0
|
OD1
|
B:ASP753
|
2.9
|
27.8
|
1.0
|
O
|
B:HOH1436
|
3.3
|
36.3
|
1.0
|
C
|
B:VAL519
|
3.4
|
23.8
|
1.0
|
O
|
B:LYS520
|
3.7
|
38.4
|
1.0
|
C
|
B:THR522
|
3.8
|
30.4
|
1.0
|
CG
|
B:ASP753
|
3.9
|
29.0
|
1.0
|
C
|
B:LYS520
|
3.9
|
29.4
|
1.0
|
CA
|
B:LYS520
|
4.0
|
17.7
|
1.0
|
CB
|
B:ASP753
|
4.1
|
12.5
|
1.0
|
N
|
B:THR522
|
4.1
|
31.9
|
1.0
|
N
|
B:LYS520
|
4.2
|
24.6
|
1.0
|
CB
|
B:THR522
|
4.3
|
28.8
|
1.0
|
CA
|
B:THR522
|
4.3
|
29.3
|
1.0
|
CG1
|
B:VAL519
|
4.4
|
25.1
|
1.0
|
CA
|
B:ASP753
|
4.4
|
15.5
|
1.0
|
O
|
B:GLU524
|
4.5
|
37.6
|
1.0
|
CA
|
B:VAL519
|
4.5
|
17.2
|
1.0
|
NH2
|
B:ARG783
|
4.6
|
16.7
|
1.0
|
N
|
B:ASN521
|
4.8
|
24.4
|
1.0
|
N
|
B:LYS523
|
4.9
|
26.4
|
1.0
|
O
|
B:ASP753
|
5.0
|
17.9
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 7zyy
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Magnesium Binding Sites List in 7zyy
Magnesium binding site 4 out
of 8 in the Cryo-Em Structure 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 Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1204
b:39.3
occ:1.00
|
O3A
|
B:ADP1203
|
2.1
|
60.6
|
1.0
|
OE2
|
B:GLU286
|
2.2
|
43.6
|
1.0
|
OE1
|
B:GLU274
|
2.2
|
40.6
|
1.0
|
O1A
|
B:ADP1203
|
2.6
|
52.9
|
1.0
|
PA
|
B:ADP1203
|
2.9
|
61.3
|
1.0
|
CD
|
B:GLU274
|
3.1
|
37.9
|
1.0
|
PB
|
B:ADP1203
|
3.1
|
69.8
|
1.0
|
OE2
|
B:GLU274
|
3.2
|
41.7
|
1.0
|
O1B
|
B:ADP1203
|
3.3
|
54.6
|
1.0
|
CD
|
B:GLU286
|
3.3
|
44.3
|
1.0
|
O2B
|
B:ADP1203
|
3.3
|
45.6
|
1.0
|
CG
|
B:GLU286
|
3.9
|
35.3
|
1.0
|
O2A
|
B:ADP1203
|
4.0
|
45.2
|
1.0
|
O5'
|
B:ADP1203
|
4.0
|
48.4
|
1.0
|
OE1
|
B:GLU286
|
4.2
|
51.8
|
1.0
|
OD1
|
B:ASN288
|
4.4
|
34.8
|
1.0
|
O3B
|
B:ADP1203
|
4.4
|
53.9
|
1.0
|
CG
|
B:GLU274
|
4.5
|
29.9
|
1.0
|
O
|
B:HOH1411
|
4.5
|
27.8
|
1.0
|
ND2
|
B:ASN288
|
4.5
|
28.6
|
1.0
|
C5'
|
B:ADP1203
|
4.6
|
48.6
|
1.0
|
CG
|
B:ASN288
|
4.9
|
32.7
|
1.0
|
CE1
|
B:HIS207
|
5.0
|
26.0
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 7zyy
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Magnesium Binding Sites List in 7zyy
Magnesium binding site 5 out
of 8 in the Cryo-Em Structure 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 Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1201
b:38.6
occ:1.00
|
OD1
|
C:ASP753
|
2.2
|
39.7
|
1.0
|
O
|
C:VAL519
|
2.3
|
43.6
|
1.0
|
O
|
C:HOH1325
|
2.6
|
27.8
|
1.0
|
O
|
C:THR522
|
2.7
|
40.4
|
1.0
|
CG
|
C:ASP753
|
3.4
|
35.2
|
1.0
|
C
|
C:VAL519
|
3.4
|
30.7
|
1.0
|
O
|
C:LYS520
|
3.8
|
41.2
|
1.0
|
C
|
C:THR522
|
3.8
|
34.8
|
1.0
|
C
|
C:LYS520
|
4.0
|
34.9
|
1.0
|
CA
|
C:LYS520
|
4.0
|
23.7
|
1.0
|
CB
|
C:ASP753
|
4.0
|
26.7
|
1.0
|
N
|
C:THR522
|
4.1
|
35.6
|
1.0
|
N
|
C:LYS520
|
4.2
|
28.4
|
1.0
|
CB
|
C:THR522
|
4.2
|
34.9
|
1.0
|
CA
|
C:THR522
|
4.2
|
36.5
|
1.0
|
OD2
|
C:ASP753
|
4.3
|
38.7
|
1.0
|
CG1
|
C:VAL519
|
4.4
|
35.9
|
1.0
|
CA
|
C:ASP753
|
4.4
|
25.4
|
1.0
|
O
|
C:GLU524
|
4.5
|
44.5
|
1.0
|
CA
|
C:VAL519
|
4.5
|
26.1
|
1.0
|
NH2
|
C:ARG783
|
4.6
|
21.6
|
1.0
|
N
|
C:ASN521
|
4.8
|
29.2
|
1.0
|
N
|
C:LYS523
|
4.9
|
30.7
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 7zyy
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Magnesium Binding Sites List in 7zyy
Magnesium binding site 6 out
of 8 in the Cryo-Em Structure 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 Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1204
b:59.0
occ:1.00
|
O2A
|
C:ADP1203
|
2.0
|
61.2
|
1.0
|
OE1
|
C:GLU274
|
2.1
|
45.2
|
1.0
|
CD
|
C:GLU274
|
2.7
|
44.2
|
1.0
|
OE2
|
C:GLU274
|
2.7
|
46.0
|
1.0
|
OE1
|
C:GLU286
|
3.1
|
50.9
|
1.0
|
CD
|
C:GLU286
|
3.3
|
48.9
|
1.0
|
OE2
|
C:GLU286
|
3.4
|
52.0
|
1.0
|
PA
|
C:ADP1203
|
3.5
|
64.3
|
1.0
|
O2B
|
C:ADP1203
|
3.5
|
60.3
|
1.0
|
O3B
|
C:ADP1203
|
3.6
|
54.8
|
1.0
|
OD1
|
C:ASN288
|
3.7
|
38.0
|
1.0
|
ND2
|
C:ASN288
|
4.0
|
29.1
|
1.0
|
PB
|
C:ADP1203
|
4.0
|
70.8
|
1.0
|
CG
|
C:GLU274
|
4.1
|
38.4
|
1.0
|
CG
|
C:GLU286
|
4.2
|
42.8
|
1.0
|
CG
|
C:ASN288
|
4.2
|
32.4
|
1.0
|
O3A
|
C:ADP1203
|
4.2
|
61.4
|
1.0
|
O5'
|
C:ADP1203
|
4.4
|
55.4
|
1.0
|
O1A
|
C:ADP1203
|
4.4
|
55.3
|
1.0
|
CB
|
C:GLU286
|
4.7
|
35.8
|
1.0
|
NZ
|
C:LYS236
|
4.8
|
36.3
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 7zyy
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Magnesium Binding Sites List in 7zyy
Magnesium binding site 7 out
of 8 in the Cryo-Em Structure 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 Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1201
b:41.1
occ:1.00
|
O
|
D:VAL519
|
2.3
|
47.5
|
1.0
|
O
|
D:HOH1321
|
2.6
|
37.4
|
1.0
|
OD1
|
D:ASP753
|
2.7
|
40.1
|
1.0
|
O
|
D:THR522
|
2.7
|
45.0
|
1.0
|
C
|
D:VAL519
|
3.4
|
36.8
|
1.0
|
CG
|
D:ASP753
|
3.7
|
36.0
|
1.0
|
C
|
D:THR522
|
3.8
|
39.0
|
1.0
|
O
|
D:LYS520
|
3.9
|
43.5
|
1.0
|
CB
|
D:ASP753
|
4.0
|
28.3
|
1.0
|
CA
|
D:LYS520
|
4.0
|
33.2
|
1.0
|
C
|
D:LYS520
|
4.0
|
37.2
|
1.0
|
N
|
D:THR522
|
4.1
|
42.7
|
1.0
|
N
|
D:LYS520
|
4.2
|
35.6
|
1.0
|
CB
|
D:THR522
|
4.2
|
39.5
|
1.0
|
CA
|
D:THR522
|
4.3
|
41.2
|
1.0
|
CA
|
D:ASP753
|
4.3
|
28.5
|
1.0
|
CG1
|
D:VAL519
|
4.3
|
39.1
|
1.0
|
CA
|
D:VAL519
|
4.5
|
33.2
|
1.0
|
O
|
D:GLU524
|
4.5
|
44.1
|
1.0
|
NH2
|
D:ARG783
|
4.7
|
26.7
|
1.0
|
N
|
D:ASN521
|
4.8
|
31.8
|
1.0
|
OD2
|
D:ASP753
|
4.9
|
41.0
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 7zyy
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Magnesium Binding Sites List in 7zyy
Magnesium binding site 8 out
of 8 in the Cryo-Em Structure of Lactococcus Lactis Pyruvate Carboxylase with Acetyl-Coa
Mono view
Stereo pair view
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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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1204
b:92.6
occ:1.00
|
O2A
|
D:ADP1203
|
2.0
|
90.1
|
1.0
|
O2B
|
D:ADP1203
|
2.0
|
89.0
|
1.0
|
OE1
|
D:GLU274
|
2.0
|
86.8
|
1.0
|
OE2
|
D:GLU286
|
2.1
|
90.4
|
1.0
|
CD
|
D:GLU286
|
2.3
|
90.1
|
1.0
|
OE1
|
D:GLU286
|
2.3
|
89.3
|
1.0
|
PA
|
D:ADP1203
|
2.9
|
98.0
|
1.0
|
CD
|
D:GLU274
|
3.0
|
84.9
|
1.0
|
PB
|
D:ADP1203
|
3.2
|
93.5
|
1.0
|
OE2
|
D:GLU274
|
3.3
|
83.0
|
1.0
|
O1A
|
D:ADP1203
|
3.3
|
86.8
|
1.0
|
O3A
|
D:ADP1203
|
3.4
|
91.6
|
1.0
|
CG
|
D:GLU286
|
3.4
|
87.5
|
1.0
|
O1B
|
D:ADP1203
|
3.7
|
86.5
|
1.0
|
CB
|
D:GLU286
|
4.0
|
83.2
|
1.0
|
O5'
|
D:ADP1203
|
4.3
|
92.5
|
1.0
|
CG
|
D:GLU274
|
4.4
|
83.0
|
1.0
|
O3B
|
D:ADP1203
|
4.4
|
89.5
|
1.0
|
OD1
|
D:ASN288
|
4.7
|
73.3
|
1.0
|
ND2
|
D:ASN288
|
4.9
|
72.1
|
1.0
|
CB
|
D:GLU274
|
5.0
|
81.8
|
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 17:07:27 2024
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