Sodium 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:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na611 b:54.5 occ:1.00 O A:HOH869 2.3 59.6 1.0 O3 A:PO4606 2.3 30.0 1.0 O A:HOH779 2.6 71.7 1.0 OG1 A:THR217 2.7 64.9 1.0 O A:HOH856 2.9 57.3 1.0 O A:HOH803 3.2 53.0 1.0 P A:PO4606 3.6 34.3 1.0 CB A:THR217 3.6 63.7 1.0 OE2 A:GLU10 3.6 33.5 1.0 CG2 A:THR218 3.6 62.8 1.0 OD2 A:ASP94 3.8 34.6 1.0 O2 A:PO4606 3.8 38.4 1.0 MG A:MG605 3.9 29.2 1.0 O A:HOH784 4.3 39.4 1.0 CE1 A:HIS155 4.3 32.1 1.0 O A:HOH867 4.3 58.1 1.0 O1 A:PO4606 4.3 30.6 1.0 CG2 A:THR217 4.5 61.9 1.0 CD A:GLU10 4.5 29.9 1.0 C A:THR217 4.6 62.7 1.0 O A:THR217 4.6 62.1 1.0 O4 A:PO4606 4.6 29.4 1.0 O A:HOH765 4.7 70.4 1.0 OE1 A:GLU10 4.7 29.3 1.0 CA A:THR217 4.7 62.6 1.0 CG A:ASP94 4.7 36.6 1.0 NH2 A:ARG227 4.8 47.3 1.0 NE2 A:HIS155 4.8 30.4 1.0 N A:THR218 5.0 63.3 1.0 OD1 A:ASP94 5.0 39.6 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