Atomistry » Manganese » PDB 5nha-5raa » 5ogl
Atomistry »
  Manganese »
    PDB 5nha-5raa »
      5ogl »

Manganese 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:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog, PDB code: 5ogl:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5ogl

Go back to Manganese Binding Sites List in 5ogl
Manganese binding site 1 out of 2 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 Manganese with other atoms in the Mn 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:Mn801

b:48.9
occ:1.00
 O A:HOH903 2.2 44.3 1.0
O A:HOH910 2.2 58.5 1.0
OD1 A:ASP154 2.2 55.8 1.0
O A:HOH902 2.4 56.8 1.0
OD2 A:ASP56 2.6 57.4 1.0
CG A:ASP56 3.3 57.9 1.0
CG A:ASP154 3.3 56.3 1.0
CB A:ASP56 3.6 57.9 1.0
OE2 A:GLU319 3.6 58.7 1.0
OD2 A:ASP154 3.7 56.5 1.0
OD1 A:ASP56 4.2 58.6 1.0
OD1 A:ASP156 4.3 57.9 1.0
CD A:GLU319 4.5 58.3 1.0
OE1 A:GLU319 4.5 58.3 1.0
CB A:ASP154 4.7 57.2 1.0
NH1 A:ARG147 4.7 57.9 1.0
CB B:ASN13 4.8 57.3 1.0
O27 A:9UB803 4.8 73.7 1.0

Manganese binding site 2 out of 2 in 5ogl

Go back to Manganese Binding Sites List in 5ogl
Manganese binding site 2 out of 2 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 Manganese with other atoms in the Mn binding site number 2 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:Mn802

b:70.0
occ:0.74
 O A:HOH906 2.2 62.7 1.0
OD1 A:ASP475 2.3 70.2 1.0
OD2 A:ASP76 2.4 70.7 1.0
OE1 A:GLN73 2.6 72.0 1.0
CG A:ASP475 3.4 69.3 1.0
CG A:ASP76 3.5 71.5 1.0
NH2 A:ARG65 3.5 66.4 1.0
OD2 A:ASP475 3.8 68.9 1.0
CD A:GLN73 3.8 72.8 1.0
OE2 A:GLU62 4.0 66.2 1.0
OD2 A:ASP66 4.0 71.0 1.0
N A:GLN73 4.2 71.7 1.0
CB A:ASP76 4.2 72.7 1.0
OD1 A:ASP66 4.4 70.3 1.0
OD1 A:ASP76 4.4 71.3 1.0
CB A:GLN73 4.5 74.7 1.0
CB A:ASP475 4.6 68.9 1.0
CG A:ASP66 4.6 70.5 1.0
CG A:GLN73 4.7 74.5 1.0
NE2 A:GLN73 4.7 72.2 1.0
CA A:ASP475 4.7 66.2 1.0
CB A:HIS72 4.7 71.2 1.0
C A:ASP475 4.7 68.0 1.0
CZ A:ARG65 4.8 65.4 1.0
CA A:HIS72 4.8 74.3 1.0
O A:ASP475 4.8 68.7 1.0
CG A:ARG456 4.9 72.3 1.0
C A:HIS72 5.0 75.5 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: Sun Oct 6 02:20:24 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy