Magnesium in PDB 4bjr: Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa

The structure of Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa, PDB code: 4bjr was solved by J.Barandun, C.L.Delley, N.Ban, E.Weber-Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.131 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.840, 84.020, 215.110, 90.00, 90.00, 90.00
R / Rfree (%)	21.31 / 24.75

The binding sites of Magnesium atom in the Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa (pdb code 4bjr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa, PDB code: 4bjr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa


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 Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1517 b:68.1 occ:1.00 O1B A:ATP1516 2.0 85.8 1.0 OH A:TYR62 2.0 70.7 1.0 O2A A:ATP1516 2.1 81.5 1.0 OE2 A:GLU70 2.4 56.9 1.0 OE1 A:GLU16 2.4 72.4 1.0 CD A:GLU16 3.2 60.1 1.0 CZ A:TYR62 3.3 53.6 1.0 PB A:ATP1516 3.4 87.4 1.0 PA A:ATP1516 3.4 71.6 1.0 CD A:GLU70 3.5 66.2 1.0 O3A A:ATP1516 3.8 78.7 1.0 CG A:GLU16 3.9 54.9 1.0 O2G A:ATP1516 4.0 0.6 1.0 OE2 A:GLU16 4.0 57.1 1.0 CE1 A:TYR62 4.0 50.7 1.0 OE1 A:GLU70 4.1 65.7 1.0 O5' A:ATP1516 4.1 63.9 1.0 O1G A:ATP1516 4.2 97.8 1.0 NH1 A:ARG60 4.2 64.8 1.0 CE2 A:TYR62 4.3 51.0 1.0 O3B A:ATP1516 4.4 1.0 1.0 O2B A:ATP1516 4.4 85.3 1.0 PG A:ATP1516 4.5 0.2 1.0 CG A:GLU70 4.5 60.0 1.0 CB A:GLU16 4.6 58.0 1.0 O1A A:ATP1516 4.7 74.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1517 b:77.6 occ:1.00 OH B:TYR62 1.9 72.1 1.0 O3G B:ATP1516 2.0 84.9 1.0 OE2 B:GLU70 2.3 57.1 1.0 OE1 B:GLU16 2.5 70.5 1.0 O2A B:ATP1516 2.7 63.6 1.0 CD B:GLU70 3.3 66.2 1.0 CZ B:TYR62 3.3 55.2 1.0 CD B:GLU16 3.3 58.0 1.0 O3A B:ATP1516 3.5 63.2 1.0 PG B:ATP1516 3.5 0.5 1.0 PA B:ATP1516 3.7 55.6 1.0 OE1 B:GLU70 3.8 65.6 1.0 MG B:MG1518 3.8 76.1 1.0 CG B:GLU16 4.0 52.4 1.0 O3B B:ATP1516 4.0 79.5 1.0 CE1 B:TYR62 4.1 52.7 1.0 OE2 B:GLU16 4.2 56.4 1.0 CE2 B:TYR62 4.2 52.7 1.0 O1G B:ATP1516 4.3 0.1 1.0 CG B:GLU70 4.4 60.2 1.0 O5' B:ATP1516 4.5 61.2 1.0 PB B:ATP1516 4.5 89.0 1.0 O2G B:ATP1516 4.5 77.5 1.0 CB B:GLU16 4.6 55.7 1.0 NH1 B:ARG60 4.6 66.4 1.0 O1A B:ATP1516 4.9 63.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1518 b:76.1 occ:1.00 OE1 B:GLU16 2.7 70.5 1.0 O B:HOH2006 2.9 65.1 1.0 OE2 B:GLU16 3.2 56.4 1.0 CD B:GLU16 3.4 58.0 1.0 NE2 B:HIS221 3.5 60.6 1.0 CE1 B:HIS221 3.6 56.2 1.0 O3B B:ATP1516 3.6 79.5 1.0 MG B:MG1517 3.8 77.6 1.0 O3G B:ATP1516 3.9 84.9 1.0 O1G B:ATP1516 4.1 0.1 1.0 O3A B:ATP1516 4.1 63.2 1.0 PG B:ATP1516 4.2 0.5 1.0 ND1 B:HIS130 4.3 63.6 1.0 CD A:GLU515 4.3 0.2 1.0 OE1 A:GLU515 4.3 0.7 1.0 CD2 B:HIS221 4.5 58.0 1.0 PB B:ATP1516 4.5 89.0 1.0 ND1 B:HIS221 4.5 59.1 1.0 CG A:GLU515 4.6 0.2 1.0 OE2 A:GLU515 4.6 1.0 1.0 O1B B:ATP1516 4.6 81.3 1.0 CE1 B:HIS130 4.8 67.2 1.0 CG B:GLU16 4.9 52.4 1.0 CG B:HIS221 5.0 55.6 1.0

J.Barandun, C.L.Delley, N.Ban, E.Weber-Ban. Crystal Structure of the Complex Between Prokaryotic Ubiquitin-Like Protein Pup and Its Ligase Pafa. J.Am.Chem.Soc. V. 135 6794 2013.
ISSN: ISSN 0002-7863
PubMed: 23601177
DOI: 10.1021/JA4024012