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Magnesium in PDB 5vz0: Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp

Enzymatic activity of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp

All present enzymatic activity of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp:
6.4.1.1;

Protein crystallography data

The structure of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp, PDB code: 5vz0 was solved by P.H.Choi, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.55 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 97.155, 130.390, 134.271, 65.99, 88.67, 70.14
R / Rfree (%) 19.1 / 21.8

Other elements in 5vz0:

The structure of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp (pdb code 5vz0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp, PDB code: 5vz0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5vz0

Go back to Magnesium Binding Sites List in 5vz0
Magnesium binding site 1 out of 3 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with 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 Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1203

b:48.0
occ:1.00
 O2B A:ADP1202 1.8 66.1 1.0
O2A A:ADP1202 1.9 58.9 1.0
OE2 A:GLU274 2.2 44.1 1.0
OE1 A:GLU286 2.4 56.3 1.0
CD A:GLU274 3.1 35.4 1.0
PB A:ADP1202 3.1 74.5 1.0
OE1 A:GLU274 3.3 45.8 1.0
PA A:ADP1202 3.3 57.4 1.0
CD A:GLU286 3.7 56.5 1.0
O3A A:ADP1202 3.7 63.1 1.0
O1B A:ADP1202 3.7 81.2 1.0
O5' A:ADP1202 4.2 55.7 1.0
CE1 A:HIS207 4.3 38.2 1.0
OE2 A:GLU286 4.3 60.6 1.0
C5' A:ADP1202 4.3 51.0 1.0
ND2 A:ASN288 4.3 43.7 1.0
OD1 A:ASN288 4.3 49.9 1.0
O3B A:ADP1202 4.4 61.6 1.0
O1A A:ADP1202 4.5 53.7 1.0
CG A:GLU274 4.6 35.4 1.0
NZ A:LYS236 4.6 48.6 1.0
CG A:ASN288 4.8 40.3 1.0
CG A:GLU286 4.8 52.5 1.0
CE A:LYS236 4.9 51.2 1.0
NE2 A:HIS207 4.9 39.8 1.0
CB A:GLU286 4.9 42.4 1.0

Magnesium binding site 2 out of 3 in 5vz0

Go back to Magnesium Binding Sites List in 5vz0
Magnesium binding site 2 out of 3 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with 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 Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1204

b:34.5
occ:1.00
 O3B B:ADP1203 1.8 62.1 1.0
O B:HOH1311 1.9 42.2 1.0
O2A B:ADP1203 2.0 65.0 1.0
OE2 B:GLU274 2.2 49.2 1.0
OE1 B:GLU286 2.2 54.2 1.0
PB B:ADP1203 3.1 58.0 1.0
PA B:ADP1203 3.2 58.0 1.0
CD B:GLU274 3.2 50.0 1.0
CD B:GLU286 3.5 61.8 1.0
O3A B:ADP1203 3.5 60.4 1.0
OE1 B:GLU274 3.6 56.0 1.0
O1B B:ADP1203 3.7 59.3 1.0
O5' B:ADP1203 4.1 53.0 1.0
C5' B:ADP1203 4.1 49.3 1.0
OE2 B:GLU286 4.2 54.6 1.0
CE1 B:HIS207 4.3 38.8 1.0
O2B B:ADP1203 4.3 58.9 1.0
O1A B:ADP1203 4.4 53.6 1.0
ND2 B:ASN288 4.5 34.5 1.0
CG B:GLU274 4.6 46.6 1.0
CG B:GLU286 4.6 62.3 1.0
CB B:GLU286 4.6 49.1 1.0
OD1 B:ASN288 4.6 48.1 1.0
NE2 B:HIS207 5.0 39.0 1.0

Magnesium binding site 3 out of 3 in 5vz0

Go back to Magnesium Binding Sites List in 5vz0
Magnesium binding site 3 out of 3 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with 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 Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1203

b:36.5
occ:1.00
 O D:HOH1301 1.8 37.8 1.0
O1B D:ADP1202 1.9 56.2 1.0
OE1 D:GLU286 2.0 56.2 1.0
OE2 D:GLU274 2.1 40.4 1.0
O1A D:ADP1202 2.3 54.7 1.0
O2B D:ADP1202 2.7 60.8 1.0
PB D:ADP1202 2.8 63.8 1.0
CD D:GLU274 3.2 39.2 1.0
CD D:GLU286 3.3 53.2 1.0
PA D:ADP1202 3.4 55.3 1.0
OE1 D:GLU274 3.5 48.2 1.0
O3A D:ADP1202 3.6 56.2 1.0
OE2 D:GLU286 3.9 63.4 1.0
O3B D:ADP1202 4.2 47.9 1.0
ND2 D:ASN288 4.2 41.7 1.0
OD1 D:ASN288 4.3 46.0 1.0
O5' D:ADP1202 4.4 51.4 1.0
CG D:GLU286 4.4 52.9 1.0
O2A D:ADP1202 4.5 59.6 1.0
CG D:GLU274 4.5 35.9 1.0
CB D:GLU286 4.6 46.9 1.0
CE1 D:HIS207 4.6 43.8 1.0
C5' D:ADP1202 4.7 46.3 1.0
CG D:ASN288 4.7 39.8 1.0
NZ D:LYS236 4.9 51.6 1.0

Reference:

P.H.Choi, T.M.N.Vu, H.T.Pham, J.J.Woodward, M.S.Turner, L.Tong. Structural and Functional Studies of Pyruvate Carboxylase Regulation By Cyclic Di-Amp in Lactic Acid Bacteria. Proc. Natl. Acad. Sci. V. 114 E7226 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28808024
DOI: 10.1073/PNAS.1704756114
Page generated: Mon Sep 30 06:22:52 2024

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