Magnesium in PDB 5obw: Mycoplasma Genitalium Dnak-Nbd in Complex with Atp

The structure of Mycoplasma Genitalium Dnak-Nbd in Complex with Atp, PDB code: 5obw was solved by M.Adell, B.Calisto, I.Fita, L.Martinelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.96 / 1.40
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	157.916, 157.916, 57.504, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 19.7

The binding sites of Magnesium atom in the Mycoplasma Genitalium Dnak-Nbd in Complex with Atp (pdb code 5obw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Mycoplasma Genitalium Dnak-Nbd in Complex with Atp, PDB code: 5obw:

Magnesium binding site 1 out of 1 in the Mycoplasma Genitalium Dnak-Nbd 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 Mycoplasma Genitalium Dnak-Nbd in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:16.3 occ:1.00 O1B A:ADP402 2.0 16.8 1.0 O A:HOH582 2.1 15.0 1.0 O A:HOH559 2.1 16.5 1.0 O A:HOH713 2.1 19.8 1.0 O A:HOH545 2.1 16.0 1.0 O2 A:PO4403 2.1 15.0 1.0 P A:PO4403 3.3 15.3 1.0 PB A:ADP402 3.5 15.5 1.0 O4 A:PO4403 3.6 14.1 1.0 O A:HOH681 3.9 17.8 1.0 O A:HOH659 4.1 17.0 1.0 O A:HOH530 4.1 24.3 1.0 O3B A:ADP402 4.1 17.7 1.0 O1A A:ADP402 4.1 16.5 1.0 O1 A:PO4403 4.1 15.9 1.0 OE1 A:GLU154 4.2 15.0 1.0 OD1 A:ASP177 4.2 15.2 1.0 OD2 A:ASP177 4.3 15.6 1.0 O2B A:ADP402 4.3 15.6 1.0 O3A A:ADP402 4.5 17.1 1.0 O3 A:PO4403 4.5 15.4 1.0 OD2 A:ASP12 4.5 14.4 1.0 OD1 A:ASP12 4.5 13.6 1.0 CG A:ASP177 4.7 14.3 1.0 CD A:GLU154 4.8 14.2 1.0 O A:HOH529 5.0 18.8 1.0 PA A:ADP402 5.0 16.4 1.0 CG A:ASP12 5.0 14.0 1.0

M.Adell, B.M.Calisto, I.Fita, L.Martinelli. The Nucleotide-Bound/Substrate-Bound Conformation of the Mycoplasma Genitalium Dnak Chaperone. Protein Sci. V. 27 1000 2018.
ISSN: ESSN 1469-896X
PubMed: 29520883
DOI: 10.1002/PRO.3401