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Sodium in PDB 6gxc: Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog

Enzymatic activity of Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog

All present enzymatic activity of Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog:
2.4.99.19;

Protein crystallography data

The structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog, PDB code: 6gxc was solved by M.Napiorkowska, K.P.Locher, J.Boilevin, T.Darbre, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.09 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.810, 116.540, 173.890, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 28.3

Other elements in 6gxc:

The structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog (pdb code 6gxc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog, PDB code: 6gxc:

Sodium binding site 1 out of 1 in 6gxc

Go back to Sodium Binding Sites List in 6gxc
Sodium binding site 1 out of 1 in the Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na803

b:75.9
occ:1.00
 OE1 A:GLU43 3.2 0.2 1.0
OE2 A:GLU43 3.5 0.2 1.0
CD A:GLU43 3.7 0.9 1.0
CD2 A:TYR42 3.8 0.1 1.0
CE2 A:TYR42 3.9 0.1 1.0
CD2 A:PHE41 4.1 0.9 1.0
CA A:PHE41 4.4 0.4 1.0
N A:TYR42 4.5 1.0 1.0
CB A:PHE41 4.7 99.8 1.0
O A:GLU40 4.8 0.2 1.0
CG A:TYR42 4.9 0.6 1.0
CG A:PHE41 4.9 0.8 1.0
C A:PHE41 5.0 0.4 1.0
CE2 A:PHE41 5.0 0.8 1.0
CZ A:TYR42 5.0 0.6 1.0

Reference:

M.Napiorkowska, J.Boilevin, T.Darbre, J.L.Reymond, K.P.Locher. Structure of Bacterial Oligosaccharyltransferase Pglb Bound to A Reactive Llo and An Inhibitory Peptide. Sci Rep V. 8 16297 2018.
ISSN: ESSN 2045-2322
PubMed: 30389987
DOI: 10.1038/S41598-018-34534-0
Page generated: Tue Oct 8 09:08:19 2024

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