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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:

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 (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 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 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 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 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 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 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 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 site 8 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 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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