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Magnesium in PDB 5gmy: Crystal Structure of the Archaeoglobus Fulgidus Oligosaccharyltransferase (O29867_ARCFU) Tethered with An Acceptor Peptide Containing the Nvt Sequon Via A Disulfide Bond

Enzymatic activity of Crystal Structure of the Archaeoglobus Fulgidus Oligosaccharyltransferase (O29867_ARCFU) Tethered with An Acceptor Peptide Containing the Nvt Sequon Via A Disulfide Bond

All present enzymatic activity of Crystal Structure of the Archaeoglobus Fulgidus Oligosaccharyltransferase (O29867_ARCFU) Tethered with An Acceptor Peptide Containing the Nvt Sequon Via A Disulfide Bond:
2.4.99.18;

Protein crystallography data

The structure of Crystal Structure of the Archaeoglobus Fulgidus Oligosaccharyltransferase (O29867_ARCFU) Tethered with An Acceptor Peptide Containing the Nvt Sequon Via A Disulfide Bond, PDB code: 5gmy was solved by S.Matsumoto, D.Kohda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.10 / 3.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.549, 121.549, 181.344, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 27.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Archaeoglobus Fulgidus Oligosaccharyltransferase (O29867_ARCFU) Tethered with An Acceptor Peptide Containing the Nvt Sequon Via A Disulfide Bond (pdb code 5gmy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Archaeoglobus Fulgidus Oligosaccharyltransferase (O29867_ARCFU) Tethered with An Acceptor Peptide Containing the Nvt Sequon Via A Disulfide Bond, PDB code: 5gmy:

Magnesium binding site 1 out of 1 in 5gmy

Go back to Magnesium Binding Sites List in 5gmy
Magnesium binding site 1 out of 1 in the Crystal Structure of the Archaeoglobus Fulgidus Oligosaccharyltransferase (O29867_ARCFU) Tethered with An Acceptor Peptide Containing the Nvt Sequon Via A Disulfide Bond


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Archaeoglobus Fulgidus Oligosaccharyltransferase (O29867_ARCFU) Tethered with An Acceptor Peptide Containing the Nvt Sequon Via A Disulfide Bond within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1200

b:28.9
occ:1.00
 OD2 A:ASP161 2.9 55.3 1.0
OD2 A:ASP47 3.1 42.9 1.0
NE2 A:HIS163 3.1 43.7 1.0
CG A:ASP47 3.5 71.4 1.0
OE1 A:GLU360 3.5 0.0 1.0
CD2 A:HIS163 3.7 52.1 1.0
CB B:ASN13 3.7 93.5 1.0
OE2 A:GLU360 3.8 1.0 1.0
OD1 A:ASP47 3.8 76.5 1.0
CD A:GLU360 3.9 0.1 1.0
ND2 B:ASN13 4.0 87.5 1.0
N B:ASN13 4.0 0.7 1.0
NH2 A:ARG154 4.0 66.3 1.0
CZ A:ARG154 4.1 59.8 1.0
NE A:ARG154 4.1 52.1 1.0
CG A:ASP161 4.2 56.5 1.0
CB A:ASP47 4.2 69.7 1.0
CE1 A:HIS163 4.3 43.6 1.0
CZ A:PHE159 4.3 39.2 1.0
CA B:ASN13 4.4 97.8 1.0
CG B:ASN13 4.4 88.4 1.0
CE2 A:PHE159 4.7 39.2 1.0
C B:TYR12 4.7 0.1 1.0
NH1 A:ARG154 4.7 57.8 1.0
CD A:ARG154 4.9 48.0 1.0
CB B:TYR12 4.9 0.3 1.0
CG A:HIS163 5.0 53.0 1.0
CB A:ASP161 5.0 57.3 1.0

Reference:

S.Matsumoto, Y.Taguchi, A.Shimada, M.Igura, D.Kohda. Tethering An N-Glycosylation Sequon-Containing Peptide Creates A Catalytically Competent Oligosaccharyltransferase Complex Biochemistry V. 56 602 2017.
ISSN: ISSN 1520-4995
PubMed: 27997792
DOI: 10.1021/ACS.BIOCHEM.6B01089
Page generated: Tue Aug 12 10:21:33 2025

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