Magnesium in PDB 4b0t: Structure of the Pup Ligase Pafa of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp

The structure of Structure of the Pup Ligase Pafa of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp, PDB code: 4b0t 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)	49.417 / 2.16
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.100, 118.810, 163.020, 90.00, 90.00, 90.00
R / Rfree (%)	17.73 / 21.91

The binding sites of Magnesium atom in the Structure of the Pup Ligase Pafa of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp (pdb code 4b0t). 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 Pup Ligase Pafa of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp, PDB code: 4b0t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Pup Ligase Pafa of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp


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 Pup Ligase Pafa of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1479 b:45.6 occ:1.00 O1A A:ADP1478 2.1 31.9 0.6 O A:HOH2053 2.2 43.7 1.0 O A:HOH2250 2.3 37.8 1.0 O A:HOH2251 2.3 45.8 1.0 OE1 B:GLU16 2.3 40.9 1.0 O A:HOH2063 2.5 64.9 1.0 O2B A:ADP1478 2.5 33.5 0.4 CD B:GLU16 3.3 40.3 1.0 PA A:ADP1478 3.6 36.3 0.6 OE2 B:GLU16 3.6 36.4 1.0 PB A:ADP1478 3.7 37.7 0.4 O3B A:ADP1478 3.7 43.3 0.6 O3B A:ADP1478 3.7 42.9 0.4 NH2 A:ARG60 3.8 38.7 1.0 O1B A:ADP1478 4.0 42.0 0.6 O2A A:ADP1478 4.0 40.4 0.4 O5' A:ADP1478 4.1 42.4 0.4 OE2 A:GLU70 4.1 54.3 1.0 OE1 A:GLU70 4.2 50.7 1.0 PB A:ADP1478 4.3 46.2 0.6 O3A A:ADP1478 4.4 39.5 0.6 O5' A:ADP1478 4.5 42.4 0.6 O2A A:ADP1478 4.5 38.1 0.6 PA A:ADP1478 4.5 41.2 0.4 O3A A:ADP1478 4.5 37.6 0.4 CD A:GLU70 4.6 48.5 1.0 CG B:GLU16 4.7 37.6 1.0 ND2 B:ASN446 4.8 67.0 1.0 O1B A:ADP1478 4.8 41.6 0.4 C5' A:ADP1478 4.9 39.9 0.6 NH1 B:ARG447 4.9 95.4 1.0 O B:ASN446 4.9 58.7 1.0 CZ A:ARG60 4.9 37.8 1.0 CB B:ASN446 4.9 55.7 1.0 NH2 B:ARG447 5.0 90.7 1.0 C5' A:ADP1478 5.0 40.4 0.4

Magnesium binding site 2 out of 2 in the Structure of the Pup Ligase Pafa of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp


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 Pup Ligase Pafa of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1480 b:60.2 occ:1.00 O A:HOH2018 2.4 44.5 1.0 O1B B:ADP1479 2.4 46.3 1.0 O A:HOH2016 2.4 47.5 1.0 OE1 A:GLU16 2.5 46.8 1.0 O A:HOH2235 2.7 64.3 1.0 O A:HOH2017 2.8 59.0 1.0 CD A:GLU16 3.4 43.2 1.0 O2A B:ADP1479 3.4 58.8 1.0 OE2 A:GLU16 3.5 41.4 1.0 PB B:ADP1479 3.7 56.1 1.0 O5' B:ADP1479 3.8 49.0 1.0 NH2 B:ARG60 3.9 39.5 1.0 O2B B:ADP1479 4.0 64.3 1.0 PA B:ADP1479 4.1 56.8 1.0 O3A B:ADP1479 4.5 56.5 1.0 O B:HOH2014 4.6 48.3 1.0 OE1 B:GLU70 4.7 55.3 1.0 H5'1 B:ADP1479 4.8 49.1 1.0 O3B B:ADP1479 4.8 48.3 1.0 CG A:GLU16 4.8 38.2 1.0 O A:PRO448 4.9 79.0 1.0 O A:ASN446 4.9 64.8 1.0 C5' B:ADP1479 4.9 41.1 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: ISSN 2041-1723
PubMed: 22910360
DOI: 10.1038/NCOMMS2009