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Manganese 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:

Magnesium (Mg) 4 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 5vyz

Go back to Manganese Binding Sites List in 5vyz
Manganese 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 Manganese with other atoms in the Mn 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:Mn1201

b:50.4
occ:1.00
 OD2 A:ASP534 2.4 25.2 1.0
NE2 A:HIS732 2.6 20.1 1.0
NE2 A:HIS734 2.6 25.0 1.0
NZ A:LYS703 2.9 30.1 1.0
CG A:ASP534 3.3 23.3 1.0
CE1 A:HIS734 3.3 25.2 1.0
CE1 A:HIS732 3.3 19.3 1.0
OD1 A:ASP534 3.5 21.2 1.0
CD2 A:HIS732 3.6 20.9 1.0
CD2 A:HIS734 3.7 26.6 1.0
O A:HOH1477 4.1 37.1 1.0
CE A:LYS703 4.2 26.7 1.0
NH2 A:ARG533 4.3 21.0 1.0
NE2 A:GLN768 4.4 15.9 1.0
ND1 A:HIS732 4.4 20.2 1.0
ND1 A:HIS734 4.5 24.6 1.0
CG A:HIS732 4.6 21.0 1.0
CB A:ASP534 4.6 19.7 1.0
CA A:MET705 4.6 21.9 1.0
CG A:HIS734 4.8 25.1 1.0
CB A:MET705 4.9 23.0 1.0
O A:MET705 4.9 22.6 1.0

Manganese binding site 2 out of 4 in 5vyz

Go back to Manganese Binding Sites List in 5vyz
Manganese 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 Manganese with other atoms in the Mn 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:Mn1201

b:50.1
occ:1.00
 NE2 B:HIS732 2.5 19.9 1.0
OD2 B:ASP534 2.5 20.6 1.0
NE2 B:HIS734 2.5 18.2 1.0
NZ B:LYS703 2.9 37.8 1.0
CE1 B:HIS732 3.3 20.6 1.0
CE1 B:HIS734 3.3 17.1 1.0
CG B:ASP534 3.4 18.7 1.0
CD2 B:HIS732 3.5 18.6 1.0
OD1 B:ASP534 3.6 19.2 1.0
CD2 B:HIS734 3.7 19.6 1.0
O B:HOH1485 4.1 41.4 1.0
CE B:LYS703 4.1 37.4 1.0
NH2 B:ARG533 4.4 21.9 1.0
ND1 B:HIS732 4.4 19.6 1.0
NE2 B:GLN768 4.4 19.9 1.0
CA B:MET705 4.5 23.3 1.0
ND1 B:HIS734 4.5 21.0 1.0
CG B:HIS732 4.6 19.5 1.0
CB B:ASP534 4.7 17.3 1.0
CG B:HIS734 4.7 18.9 1.0
CB B:MET705 4.7 24.9 1.0
O B:MET705 4.8 22.9 1.0

Manganese binding site 3 out of 4 in 5vyz

Go back to Manganese Binding Sites List in 5vyz
Manganese 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 Manganese with other atoms in the Mn 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:Mn1201

b:45.8
occ:1.00
 OD2 C:ASP534 2.3 29.8 1.0
NE2 C:HIS732 2.5 18.6 1.0
NE2 C:HIS734 2.6 23.1 1.0
NZ C:LYS703 3.0 34.1 1.0
CG C:ASP534 3.2 27.1 1.0
CE1 C:HIS734 3.3 21.0 1.0
CE1 C:HIS732 3.3 19.0 1.0
OD1 C:ASP534 3.5 25.4 1.0
CD2 C:HIS732 3.5 19.5 1.0
CD2 C:HIS734 3.7 22.4 1.0
CE C:LYS703 4.2 32.0 1.0
NE2 C:GLN768 4.3 18.7 1.0
NH2 C:ARG533 4.4 26.5 1.0
ND1 C:HIS732 4.4 17.9 1.0
ND1 C:HIS734 4.5 25.5 1.0
O C:HOH1325 4.5 34.8 1.0
CG C:HIS732 4.6 18.7 1.0
CA C:MET705 4.6 21.9 1.0
CB C:ASP534 4.6 21.6 1.0
CG C:HIS734 4.7 23.4 1.0
CB C:MET705 4.8 23.0 1.0
O C:MET705 4.9 18.1 1.0

Manganese binding site 4 out of 4 in 5vyz

Go back to Manganese Binding Sites List in 5vyz
Manganese 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 Manganese with other atoms in the Mn 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:Mn1202

b:45.6
occ:1.00
 OD2 D:ASP534 2.4 28.2 1.0
NE2 D:HIS732 2.5 19.5 1.0
NE2 D:HIS734 2.6 22.4 1.0
NZ D:LYS703 2.9 33.9 1.0
CE1 D:HIS732 3.3 18.1 1.0
CG D:ASP534 3.3 22.0 1.0
CE1 D:HIS734 3.4 21.2 1.0
O D:HOH1448 3.5 30.3 1.0
CD2 D:HIS732 3.5 19.5 1.0
OD1 D:ASP534 3.6 24.2 1.0
CD2 D:HIS734 3.7 24.8 1.0
CE D:LYS703 4.1 31.0 1.0
NH2 D:ARG533 4.4 23.5 1.0
ND1 D:HIS732 4.4 18.8 1.0
NE2 D:GLN768 4.4 20.4 1.0
O D:HOH1413 4.4 39.8 1.0
CG D:HIS732 4.5 19.1 1.0
ND1 D:HIS734 4.6 25.9 1.0
CA D:MET705 4.6 24.5 1.0
CB D:ASP534 4.6 19.4 1.0
CG D:HIS734 4.8 23.4 1.0
CB D:MET705 4.9 27.4 1.0
O D:MET705 4.9 24.4 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: Sun Oct 6 03:13:49 2024

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