Magnesium in PDB 5oby: Mycoplasma Genitalium Dnak-Nbd in Complex with Amp-Pnp

The structure of Mycoplasma Genitalium Dnak-Nbd in Complex with Amp-Pnp, PDB code: 5oby 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)	78.53 / 1.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	157.065, 157.065, 56.782, 90.00, 90.00, 120.00
R / Rfree (%)	14.1 / 16.1

The binding sites of Magnesium atom in the Mycoplasma Genitalium Dnak-Nbd in Complex with Amp-Pnp (pdb code 5oby). 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 Amp-Pnp, PDB code: 5oby:

Magnesium binding site 1 out of 1 in the Mycoplasma Genitalium Dnak-Nbd in Complex with Amp-Pnp


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 Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:19.5 occ:0.50 O A:HOH652 1.8 20.2 1.0 O A:HOH593 1.9 16.8 1.0 O A:HOH549 2.3 24.0 1.0 O A:HOH580 2.4 24.4 1.0 O1B A:ANP402 2.5 17.5 1.0 N3B A:ANP402 2.8 19.5 1.0 PB A:ANP402 3.3 14.0 1.0 O A:HOH509 3.5 29.3 1.0 O A:HOH511 3.7 34.2 1.0 O A:HOH520 3.9 37.4 1.0 OD1 A:ASP177 4.0 16.0 1.0 O1A A:ANP402 4.0 15.9 1.0 PG A:ANP402 4.1 17.8 1.0 O A:HOH685 4.1 19.1 1.0 OD2 A:ASP177 4.2 17.6 1.0 OD2 A:ASP12 4.2 16.2 1.0 O3A A:ANP402 4.3 15.7 1.0 OD1 A:ASP12 4.3 15.9 1.0 O2G A:ANP402 4.4 20.0 1.0 O1G A:ANP402 4.4 19.4 1.0 O2B A:ANP402 4.5 15.0 1.0 OE1 A:GLU154 4.5 18.4 1.0 CG A:ASP177 4.5 15.2 1.0 O A:HOH622 4.6 41.5 1.0 CG A:ASP12 4.7 14.9 1.0 PA A:ANP402 4.8 15.2 1.0 CD A:GLU154 4.9 15.7 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