Magnesium in PDB 5lrt: Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate

The structure of Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate, PDB code: 5lrt was solved by M.Bolten, C.Vahlensieck, C.Lipp, M.Leibundgut, N.Ban, E.Weber-Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.20 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.398, 72.398, 215.250, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 19.8

The structure of Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate (pdb code 5lrt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate, PDB code: 5lrt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate


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 Adp and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:39.5 occ:1.00 O3B A:ADP601 1.9 35.6 1.0 O A:HOH864 2.0 44.3 1.0 OE2 A:GLU229 2.1 42.9 1.0 O A:HOH721 2.2 42.5 1.0 O A:HOH738 2.2 36.6 1.0 O A:HOH796 2.2 39.1 1.0 CD A:GLU229 3.1 51.2 1.0 PB A:ADP601 3.2 33.2 1.0 OE1 A:GLU229 3.3 55.8 1.0 O2B A:ADP601 3.6 33.0 1.0 NH2 A:ARG239 4.0 38.0 1.0 O3A A:ADP601 4.0 32.1 1.0 NE2 A:HIS231 4.1 41.5 1.0 O A:HOH748 4.2 48.5 1.0 NH1 A:ARG227 4.3 36.9 1.0 O1B A:ADP601 4.3 32.3 1.0 O1A A:ADP601 4.4 32.9 1.0 O A:HOH858 4.4 61.1 1.0 CG A:GLU229 4.5 49.4 1.0 NH1 A:ARG90 4.5 33.4 1.0 O A:HOH917 4.6 49.2 1.0 O A:HOH909 4.7 72.0 1.0 CE1 A:HIS231 4.7 41.3 1.0 PA A:ADP601 4.8 31.3 1.0

Magnesium binding site 2 out of 4 in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate


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 Adp and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:29.6 occ:1.00 OE1 A:GLU99 2.0 29.5 1.0 O2A A:ADP601 2.0 29.4 1.0 O4 A:PO4606 2.0 29.4 1.0 OH A:TYR92 2.1 30.4 1.0 O2B A:ADP601 2.1 33.0 1.0 OE1 A:GLU8 2.1 28.5 1.0 CD A:GLU99 3.0 27.7 1.0 PA A:ADP601 3.2 31.3 1.0 CD A:GLU8 3.2 32.7 1.0 CZ A:TYR92 3.2 32.8 1.0 PB A:ADP601 3.2 33.2 1.0 P A:PO4606 3.4 34.3 1.0 O3A A:ADP601 3.4 32.1 1.0 OE2 A:GLU99 3.5 27.0 1.0 CE1 A:TYR92 3.6 28.4 1.0 MG A:MG605 3.6 29.2 1.0 O A:HOH840 3.7 30.9 1.0 O1 A:PO4606 3.7 30.6 1.0 MG A:MG604 3.7 31.9 1.0 O1B A:ADP601 3.8 32.3 1.0 CG A:GLU8 3.8 27.8 1.0 O A:HOH726 3.9 35.8 1.0 OG A:SER101 4.0 27.7 1.0 O2 A:PO4606 4.1 38.4 1.0 O1A A:ADP601 4.2 32.9 1.0 OE2 A:GLU8 4.2 31.1 1.0 O5' A:ADP601 4.2 29.9 1.0 CB A:GLU8 4.2 27.0 1.0 O A:HOH738 4.3 36.6 1.0 CG A:GLU99 4.3 27.8 1.0 O3 A:PO4606 4.4 30.0 1.0 CE2 A:TYR92 4.4 34.3 1.0 O3B A:ADP601 4.5 35.6 1.0 NH1 A:ARG90 4.6 33.4 1.0 OD2 A:ASP94 4.7 34.6 1.0

Magnesium binding site 3 out of 4 in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:31.9 occ:1.00 O1 A:PO4606 2.0 30.6 1.0 O1B A:ADP601 2.1 32.3 1.0 NE2 A:HIS241 2.2 32.4 1.0 OE2 A:GLU8 2.2 31.1 1.0 OE1 A:GLU8 2.2 28.5 1.0 ND1 A:HIS155 2.4 29.9 1.0 CD A:GLU8 2.5 32.7 1.0 CE1 A:HIS241 3.1 35.8 1.0 CD2 A:HIS241 3.2 34.1 1.0 CE1 A:HIS155 3.2 32.1 1.0 PB A:ADP601 3.2 33.2 1.0 P A:PO4606 3.3 34.3 1.0 CG A:HIS155 3.4 30.1 1.0 O2B A:ADP601 3.5 33.0 1.0 O4 A:PO4606 3.5 29.4 1.0 NH1 A:ARG227 3.6 36.9 1.0 MG A:MG603 3.7 29.6 1.0 CB A:HIS155 3.8 30.1 1.0 O3A A:ADP601 3.9 32.1 1.0 O A:HOH840 4.0 30.9 1.0 CG A:GLU8 4.0 27.8 1.0 O3 A:PO4606 4.2 30.0 1.0 ND1 A:HIS241 4.3 36.9 1.0 O2 A:PO4606 4.3 38.4 1.0 CG A:HIS241 4.3 35.7 1.0 NE2 A:HIS155 4.4 30.4 1.0 O3B A:ADP601 4.5 35.6 1.0 CD2 A:HIS155 4.5 29.2 1.0 CZ A:ARG227 4.6 44.7 1.0 NH1 A:ARG239 4.6 33.1 1.0 CB A:GLU8 4.6 27.0 1.0 O2A A:ADP601 4.7 29.4 1.0 OE1 A:GLU99 4.9 29.5 1.0 MG A:MG605 4.9 29.2 1.0 NH2 A:ARG227 5.0 47.3 1.0

Magnesium binding site 4 out of 4 in the Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-Like Modification Pathway in Complex with Adp and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:29.2 occ:1.00 OE2 A:GLU10 2.0 33.5 1.0 OD2 A:ASP94 2.0 34.6 1.0 OE2 A:GLU99 2.0 27.0 1.0 O4 A:PO4606 2.1 29.4 1.0 O3 A:PO4606 2.1 30.0 1.0 O A:HOH840 2.2 30.9 1.0 P A:PO4606 2.7 34.3 1.0 CD A:GLU99 3.0 27.7 1.0 CD A:GLU10 3.1 29.9 1.0 CG A:ASP94 3.1 36.6 1.0 OE1 A:GLU99 3.3 29.5 1.0 CG A:GLU10 3.5 28.1 1.0 MG A:MG603 3.6 29.6 1.0 CB A:ASP94 3.7 32.6 1.0 O2 A:PO4606 3.7 38.4 1.0 O1 A:PO4606 3.8 30.6 1.0 OH A:TYR92 3.9 30.4 1.0 NA A:NA611 3.9 54.5 1.0 O A:HOH869 3.9 59.6 1.0 OD1 A:ASP94 4.2 39.6 1.0 OE1 A:GLU10 4.2 29.3 1.0 O A:HOH726 4.2 35.8 1.0 OE1 A:GLU8 4.2 28.5 1.0 CG A:GLU99 4.3 27.8 1.0 O A:HOH856 4.3 57.3 1.0 CE1 A:HIS155 4.4 32.1 1.0 O A:HOH867 4.5 58.1 1.0 CZ A:TYR92 4.7 32.8 1.0 ND1 A:HIS155 4.7 29.9 1.0 CB A:GLU99 4.8 29.1 1.0 O2B A:ADP601 4.9 33.0 1.0 MG A:MG604 4.9 31.9 1.0

M.Bolten, C.Vahlensieck, C.Lipp, M.Leibundgut, N.Ban, E.Weber-Ban. Depupylase Dop Requires Inorganic Phosphate in the Active Site For Catalysis. J. Biol. Chem. V. 292 4044 2017.
ISSN: ESSN 1083-351X
PubMed: 28119453
DOI: 10.1074/JBC.M116.755645