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Manganese 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:

Magnesium (Mg) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp, PDB code: 5vz0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5vz0

Go back to Manganese Binding Sites List in 5vz0
Manganese binding site 1 out of 4 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 Manganese with other atoms in the Mn 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:Mn1201

b:35.4
occ:1.00
 OD2 A:ASP534 2.2 32.6 1.0
NE2 A:HIS732 2.3 26.9 1.0
NE2 A:HIS734 2.4 21.9 1.0
O A:HOH1361 2.4 30.0 1.0
NZ A:LYS703 2.9 34.0 1.0
CE1 A:HIS734 3.1 22.7 1.0
CE1 A:HIS732 3.1 27.1 1.0
CG A:ASP534 3.2 25.6 1.0
CD2 A:HIS732 3.4 24.9 1.0
OD1 A:ASP534 3.5 27.0 1.0
CD2 A:HIS734 3.5 26.5 1.0
NE2 A:GLN768 4.0 25.3 1.0
ND1 A:HIS734 4.3 23.0 1.0
ND1 A:HIS732 4.3 24.2 1.0
NH2 A:ARG533 4.4 23.9 1.0
CE A:LYS703 4.4 31.2 1.0
CG A:HIS732 4.4 23.2 1.0
CB A:ASP534 4.5 21.4 1.0
O A:HOH1562 4.5 40.8 1.0
CG A:HIS734 4.5 22.5 1.0
O A:HOH1378 4.7 30.4 1.0
CA A:MET705 4.7 21.3 1.0
O A:MET705 4.9 21.4 1.0

Manganese binding site 2 out of 4 in 5vz0

Go back to Manganese Binding Sites List in 5vz0
Manganese binding site 2 out of 4 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 Manganese with other atoms in the Mn 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:Mn1202

b:33.6
occ:1.00
 OD2 B:ASP534 2.2 20.5 1.0
NE2 B:HIS732 2.3 27.2 1.0
NE2 B:HIS734 2.4 21.6 1.0
O B:HOH1419 2.4 34.7 1.0
NZ B:LYS703 2.9 38.8 1.0
CE1 B:HIS732 3.0 27.9 1.0
CE1 B:HIS734 3.1 22.2 1.0
CG B:ASP534 3.2 20.1 1.0
CD2 B:HIS732 3.3 26.2 1.0
OD1 B:ASP534 3.5 27.1 1.0
CD2 B:HIS734 3.5 22.9 1.0
O B:HOH1548 3.6 39.5 1.0
NE2 B:GLN768 4.0 23.9 1.0
ND1 B:HIS732 4.2 29.2 1.0
O B:HOH1607 4.2 37.0 1.0
ND1 B:HIS734 4.3 21.5 1.0
NH2 B:ARG533 4.3 22.4 1.0
CE B:LYS703 4.3 32.4 1.0
CG B:HIS732 4.4 23.0 1.0
CG B:HIS734 4.5 20.3 1.0
CB B:ASP534 4.5 18.8 1.0
O B:HOH1524 4.5 33.9 1.0
CA B:MET705 4.7 24.5 1.0
O B:HOH1335 4.9 43.6 1.0
O B:MET705 4.9 27.1 1.0

Manganese binding site 3 out of 4 in 5vz0

Go back to Manganese Binding Sites List in 5vz0
Manganese binding site 3 out of 4 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 Manganese with other atoms in the Mn 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
C:Mn1201

b:32.8
occ:1.00
 OD2 C:ASP534 2.2 34.6 1.0
NE2 C:HIS732 2.3 21.4 1.0
NE2 C:HIS734 2.4 22.9 1.0
O C:HOH1376 2.4 32.0 1.0
NZ C:LYS703 2.9 32.7 1.0
CE1 C:HIS734 3.1 20.4 1.0
CE1 C:HIS732 3.1 21.9 1.0
CG C:ASP534 3.1 29.7 1.0
CD2 C:HIS732 3.4 21.3 1.0
OD1 C:ASP534 3.5 30.4 1.0
CD2 C:HIS734 3.5 22.4 1.0
O C:HOH1545 3.8 34.4 1.0
NE2 C:GLN768 4.0 23.9 1.0
ND1 C:HIS734 4.3 21.5 1.0
ND1 C:HIS732 4.3 20.7 1.0
CE C:LYS703 4.4 29.1 1.0
CG C:HIS732 4.4 21.9 1.0
NH2 C:ARG533 4.4 20.4 1.0
CB C:ASP534 4.5 27.2 1.0
CG C:HIS734 4.5 22.5 1.0
O C:HOH1335 4.6 33.3 1.0
CA C:MET705 4.7 21.1 1.0
O C:MET705 4.9 19.4 1.0

Manganese binding site 4 out of 4 in 5vz0

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Manganese binding site 4 out of 4 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 Manganese with other atoms in the Mn binding site number 4 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:Mn1201

b:33.2
occ:1.00
 OD2 D:ASP534 2.2 20.0 1.0
NE2 D:HIS732 2.3 23.2 1.0
NE2 D:HIS734 2.3 22.3 1.0
O D:HOH1430 2.5 29.7 1.0
NZ D:LYS703 2.9 31.5 1.0
CE1 D:HIS734 3.1 21.4 1.0
CE1 D:HIS732 3.1 24.0 1.0
CG D:ASP534 3.2 16.2 1.0
CD2 D:HIS732 3.4 20.3 1.0
CD2 D:HIS734 3.5 22.6 1.0
OD1 D:ASP534 3.6 22.5 1.0
O D:HOH1559 3.9 28.5 1.0
NE2 D:GLN768 4.1 22.9 1.0
ND1 D:HIS732 4.2 21.5 1.0
ND1 D:HIS734 4.3 22.8 1.0
CE D:LYS703 4.4 28.9 1.0
NH2 D:ARG533 4.4 22.7 1.0
CG D:HIS732 4.4 19.7 1.0
CG D:HIS734 4.5 23.4 1.0
CB D:ASP534 4.5 16.3 1.0
O D:HOH1567 4.5 29.6 1.0
CA D:MET705 4.7 26.4 1.0
O D:MET705 4.9 26.9 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: Sun Oct 6 03:13:48 2024

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