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:

Manganese (Mn) 4 atoms

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 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 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 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 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 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 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 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

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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: Fri Apr 7 05:03:53 2023

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