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Sodium in PDB 5ogl: Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog

Enzymatic activity of Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog

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

Protein crystallography data

The structure of Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog, PDB code: 5ogl was solved by M.Napiorkowska, J.Boilevin, T.Sovdat, T.Darbre, J.-L.Reymond, M.Aebi, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.77 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.940, 116.180, 172.020, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.4

Other elements in 5ogl:

The structure of Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An 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 Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog (pdb code 5ogl). 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 Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog, PDB code: 5ogl:

Sodium binding site 1 out of 1 in 5ogl

Go back to Sodium Binding Sites List in 5ogl
Sodium binding site 1 out of 1 in the Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An 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 Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:55.2
occ:1.00
 OE2 A:GLU43 2.9 65.5 1.0
OE1 A:GLU43 2.9 65.5 1.0
CD A:GLU43 3.3 65.2 1.0
CE2 A:TYR42 3.8 67.1 1.0
CD2 A:PHE41 4.1 70.2 1.0
CD2 A:TYR42 4.2 67.2 1.0
CZ A:TYR42 4.4 66.7 1.0
OH A:TYR42 4.7 66.8 1.0
CG A:GLU43 4.8 64.6 1.0
CE2 A:PHE41 4.9 71.1 1.0
CB A:PHE41 4.9 69.1 1.0
CA A:PHE41 4.9 68.7 1.0

Reference:

M.Napiorkowska, J.Boilevin, T.Sovdat, T.Darbre, J.L.Reymond, M.Aebi, K.P.Locher. Molecular Basis of Lipid-Linked Oligosaccharide Recognition and Processing By Bacterial Oligosaccharyltransferase. Nat. Struct. Mol. Biol. V. 24 1100 2017.
ISSN: ESSN 1545-9985
PubMed: 29058712
DOI: 10.1038/NSMB.3491
Page generated: Tue Dec 15 11:24:44 2020

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