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:

Manganese (Mn) 4 atoms

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 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 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 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 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 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 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 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

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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

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