Magnesium in PDB 4b0s: Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Atp

The structure of Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Atp, PDB code: 4b0s was solved by D.Ozcelik, J.Barandun, N.Schmitz, M.Sutter, E.Guth, F.F.Damberger, F.H.-T.Allain, N.Ban, E.Weber-Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.360, 70.410, 93.520, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 24.6

The binding sites of Magnesium atom in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Atp (pdb code 4b0s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Atp, PDB code: 4b0s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1502 b:39.2 occ:0.71 O2G A:ATP1501 2.1 0.4 0.7 OE2 A:GLU8 2.3 0.2 1.0 ND1 A:HIS155 2.4 71.4 1.0 CD A:GLU8 2.5 87.3 1.0 NE2 A:HIS241 2.6 41.5 1.0 OE1 A:GLU8 2.6 91.1 1.0 CE1 A:HIS241 3.0 55.1 1.0 MG A:MG1503 3.1 92.2 0.7 CE1 A:HIS155 3.1 70.3 1.0 CG A:HIS155 3.3 60.1 1.0 O3A A:ATP1501 3.3 0.4 0.7 O A:HOH2001 3.3 54.3 0.7 PG A:ATP1501 3.3 0.9 0.7 O3B A:ATP1501 3.5 0.7 0.7 CB A:HIS155 3.7 31.7 1.0 CG A:GLU8 3.7 70.0 1.0 CD2 A:HIS241 4.0 44.0 1.0 PB A:ATP1501 4.0 68.1 0.7 O1G A:ATP1501 4.1 0.7 0.7 NE2 A:HIS155 4.2 67.7 1.0 O2B A:ATP1501 4.2 71.1 0.7 OE2 A:GLU99 4.2 75.5 1.0 ND1 A:HIS241 4.3 63.4 1.0 CD2 A:HIS155 4.3 59.9 1.0 PA A:ATP1501 4.5 0.2 0.7 O3G A:ATP1501 4.5 0.5 0.7 O2A A:ATP1501 4.5 0.5 0.7 CB A:GLU8 4.6 50.7 1.0 O5' A:ATP1501 4.6 78.2 0.7 CG A:HIS241 4.8 50.2 1.0 OH A:TYR92 4.8 67.3 1.0 OD2 A:ASP94 5.0 84.9 1.0

Magnesium binding site 2 out of 2 in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1503 b:92.2 occ:0.71 OH A:TYR92 1.9 67.3 1.0 O2A A:ATP1501 2.0 0.5 0.7 O A:HOH2001 2.1 54.3 0.7 OE1 A:GLU8 2.1 91.1 1.0 OE2 A:GLU99 2.2 75.5 1.0 OE1 A:GLU99 2.5 93.0 1.0 CD A:GLU99 2.6 76.5 1.0 O3A A:ATP1501 2.7 0.4 0.7 O2G A:ATP1501 2.9 0.4 0.7 PA A:ATP1501 2.9 0.2 0.7 CD A:GLU8 3.1 87.3 1.0 MG A:MG1502 3.1 39.2 0.7 CZ A:TYR92 3.2 55.0 1.0 CB A:GLU8 3.6 50.7 1.0 O5' A:ATP1501 3.7 78.2 0.7 CG A:GLU8 3.8 70.0 1.0 OG A:SER101 3.9 49.4 1.0 OE2 A:GLU8 3.9 0.2 1.0 PG A:ATP1501 4.0 0.9 0.7 OD2 A:ASP94 4.0 84.9 1.0 CE2 A:TYR92 4.1 49.4 1.0 O3G A:ATP1501 4.1 0.5 0.7 CE1 A:TYR92 4.1 45.3 1.0 CG A:GLU99 4.2 60.4 1.0 O1A A:ATP1501 4.2 0.7 0.7 ND1 A:HIS155 4.3 71.4 1.0 PB A:ATP1501 4.3 68.1 0.7 O3B A:ATP1501 4.5 0.7 0.7 H5'1 A:ATP1501 4.6 0.5 0.7 C5' A:ATP1501 4.7 77.8 0.7 CG A:ASP94 4.8 87.2 1.0 H4' A:ATP1501 4.8 1.0 0.7 CB A:GLU99 5.0 43.3 1.0 CA A:GLU8 5.0 37.0 1.0 CE1 A:HIS155 5.0 70.3 1.0

D.Ozcelik, J.Barandun, N.Schmitz, M.Sutter, E.Guth, F.F.Damberger, F.H.-T.Allain, N.Ban, E.Weber-Ban. Structures of Pup Ligase Pafa and Depupylase Dop From the Prokaryotic Ubiquitin-Like Modification Pathway. Nat.Commun. V. 3 1014 2012.
ISSN: ESSN 2041-1723
PubMed: 22910360
DOI: 10.1038/NCOMMS2009