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

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

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

Protein crystallography data

The structure of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase in Complex with Cyclic-Di-Amp, PDB code: 5vyz 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) 48.60 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 97.270, 130.431, 133.367, 66.08, 89.05, 70.60
R / Rfree (%) 18.3 / 22.1

Other elements in 5vyz:

The structure of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase 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 in Complex with Cyclic-Di-Amp (pdb code 5vyz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase in Complex with Cyclic-Di-Amp, PDB code: 5vyz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5vyz

Go back to Magnesium Binding Sites List in 5vyz
Magnesium binding site 1 out of 4 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase 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 in Complex with Cyclic-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1203

b:35.3
occ:1.00
 O2B A:ADP1202 1.7 44.9 1.0
OE1 A:GLU286 1.9 44.0 1.0
O2A A:ADP1202 2.0 46.8 1.0
O A:HOH1304 2.1 38.6 1.0
OE2 A:GLU274 2.3 42.6 1.0
PB A:ADP1202 3.0 61.5 1.0
CD A:GLU286 3.1 42.7 1.0
CD A:GLU274 3.2 37.6 1.0
PA A:ADP1202 3.2 50.0 1.0
OE1 A:GLU274 3.4 45.5 1.0
O3A A:ADP1202 3.6 48.6 1.0
O1B A:ADP1202 3.7 59.2 1.0
OE2 A:GLU286 3.9 40.7 1.0
O5' A:ADP1202 4.0 43.5 1.0
C5' A:ADP1202 4.1 41.0 1.0
O3B A:ADP1202 4.2 66.1 1.0
CG A:GLU286 4.2 45.4 1.0
OD1 A:ASN288 4.3 43.2 1.0
O1A A:ADP1202 4.5 41.5 1.0
CE1 A:HIS207 4.5 43.7 1.0
ND2 A:ASN288 4.5 31.6 1.0
CG A:GLU274 4.6 34.1 1.0
CB A:GLU286 4.8 40.6 1.0
CG A:ASN288 4.9 33.6 1.0
NZ A:LYS236 4.9 38.5 1.0

Magnesium binding site 2 out of 4 in 5vyz

Go back to Magnesium Binding Sites List in 5vyz
Magnesium binding site 2 out of 4 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase 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 in Complex with Cyclic-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1203

b:31.9
occ:1.00
 O3B B:ADP1202 1.8 58.4 1.0
OE1 B:GLU286 1.9 36.8 1.0
OE2 B:GLU274 2.1 37.2 1.0
O B:HOH1422 2.1 37.6 1.0
O2A B:ADP1202 2.2 57.7 1.0
CD B:GLU274 3.1 38.4 1.0
CD B:GLU286 3.1 42.0 1.0
PB B:ADP1202 3.2 63.8 1.0
OE1 B:GLU274 3.3 47.0 1.0
PA B:ADP1202 3.4 52.1 1.0
O3A B:ADP1202 3.6 59.9 1.0
CG B:GLU286 3.9 40.6 1.0
O1B B:ADP1202 4.0 65.7 1.0
C5' B:ADP1202 4.0 43.1 1.0
OE2 B:GLU286 4.1 33.2 1.0
O5' B:ADP1202 4.1 51.0 1.0
CE1 B:HIS207 4.1 38.9 1.0
O2B B:ADP1202 4.3 61.0 1.0
OD1 B:ASN288 4.5 38.3 1.0
CG B:GLU274 4.5 38.6 1.0
O1A B:ADP1202 4.7 56.2 1.0
NZ B:LYS236 4.8 40.0 1.0
ND2 B:ASN288 4.8 36.5 1.0
NE2 B:HIS207 4.8 40.0 1.0
CE B:LYS236 4.8 39.7 1.0

Magnesium binding site 3 out of 4 in 5vyz

Go back to Magnesium Binding Sites List in 5vyz
Magnesium binding site 3 out of 4 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase 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 in Complex with Cyclic-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1203

b:47.9
occ:1.00
 OE1 C:GLU286 1.6 60.4 1.0
O2B C:ADP1202 1.8 65.5 1.0
O1A C:ADP1202 2.3 73.0 1.0
OE2 C:GLU274 2.4 54.1 1.0
CD C:GLU286 2.9 50.9 1.0
PB C:ADP1202 3.2 77.5 1.0
CD C:GLU274 3.2 44.2 1.0
OE1 C:GLU274 3.4 47.4 1.0
PA C:ADP1202 3.5 72.3 1.0
O3A C:ADP1202 3.6 70.8 1.0
OE2 C:GLU286 3.7 49.4 1.0
CG C:GLU286 3.9 48.1 1.0
OD1 C:ASN288 3.9 47.3 1.0
ND2 C:ASN288 4.0 45.8 1.0
O1B C:ADP1202 4.1 68.1 1.0
O3B C:ADP1202 4.2 66.8 1.0
C5' C:ADP1202 4.3 72.0 1.0
CG C:ASN288 4.4 41.3 1.0
O5' C:ADP1202 4.4 72.1 1.0
CG C:GLU274 4.6 39.0 1.0
O2A C:ADP1202 4.7 73.2 1.0
NZ C:LYS236 4.9 48.2 1.0
NE2 C:HIS207 5.0 46.1 1.0

Magnesium binding site 4 out of 4 in 5vyz

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Magnesium binding site 4 out of 4 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase 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 4 of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase in Complex with Cyclic-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1204

b:31.9
occ:1.00
 O1B D:ADP1203 1.8 46.6 1.0
OE2 D:GLU274 2.1 35.4 1.0
O1A D:ADP1203 2.1 51.2 1.0
OE1 D:GLU286 2.1 47.5 1.0
CD D:GLU274 3.0 35.1 1.0
PB D:ADP1203 3.1 57.6 1.0
OE1 D:GLU274 3.2 43.0 1.0
PA D:ADP1203 3.4 53.6 1.0
CD D:GLU286 3.4 49.0 1.0
O3A D:ADP1203 3.6 53.7 1.0
O2B D:ADP1203 3.8 56.5 1.0
O5' D:ADP1203 4.2 46.3 1.0
CE1 D:HIS207 4.2 37.4 1.0
OE2 D:GLU286 4.2 44.8 1.0
C5' D:ADP1203 4.3 40.8 1.0
OD1 D:ASN288 4.3 39.0 1.0
O3B D:ADP1203 4.5 51.3 1.0
CG D:GLU274 4.5 34.6 1.0
CG D:GLU286 4.5 50.5 1.0
NZ D:LYS236 4.6 49.4 1.0
O2A D:ADP1203 4.6 57.8 1.0
CE D:LYS236 4.7 45.2 1.0
ND2 D:ASN288 4.7 29.6 1.0
NE2 D:HIS207 4.8 32.7 1.0
CG D:ASN288 5.0 31.8 1.0
CB D:GLU286 5.0 44.4 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 06:22:18 2024

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