Magnesium in PDB 5m1k: Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Magnesium

The structure of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Magnesium, PDB code: 5m1k was solved by R.G.Xu, H.T.Jenkins, M.Chechik, E.V.Blagova, S.J.Greive, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.78 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.807, 54.057, 69.950, 90.00, 91.94, 90.00
R / Rfree (%)	18.3 / 20.9

The binding sites of Magnesium atom in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Magnesium (pdb code 5m1k). 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 Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Magnesium, PDB code: 5m1k:

Magnesium binding site 1 out of 1 in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Magnesium


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 Large Terminase Nuclease From Thermophilic Phage G20C with Bound Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:14.9 occ:0.40 O B:HOH658 1.9 28.1 1.0 O B:HOH790 2.0 30.3 1.0 O B:HOH795 2.1 27.2 1.0 OD2 B:ASP294 2.2 12.6 0.4 O B:HOH791 2.2 32.6 1.0 OD1 B:ASP429 2.4 16.3 1.0 CG B:ASP294 3.2 11.7 0.4 CG B:ASP429 3.4 14.4 1.0 OD1 B:ASP294 3.5 12.9 0.4 OD2 B:ASP294 3.8 14.8 0.6 CB B:ASP429 3.8 12.9 1.0 CA B:ASP429 4.1 12.2 1.0 CG B:ASP294 4.2 13.3 0.6 O B:TYR301 4.2 14.5 1.0 O B:PHE295 4.3 16.8 1.0 CB B:ASP294 4.5 11.2 0.4 CB B:ASP294 4.5 12.9 0.6 OD2 B:ASP429 4.6 16.1 1.0 O B:HOH722 4.6 16.9 1.0 O B:HOH789 4.6 25.6 1.0 OD1 B:ASP294 4.7 14.3 0.6 N B:ASP429 4.8 12.7 1.0 C B:PHE295 4.9 14.4 1.0 OD1 B:ASP428 4.9 20.1 1.0

R.G.Xu, H.T.Jenkins, M.Chechik, E.V.Blagova, A.Lopatina, E.Klimuk, L.Minakhin, K.Severinov, S.J.Greive, A.A.Antson. Viral Genome Packaging Terminase Cleaves Dna Using the Canonical Ruvc-Like Two-Metal Catalysis Mechanism. Nucleic Acids Res. V. 45 3580 2017.
ISSN: ESSN 1362-4962
PubMed: 28100693
DOI: 10.1093/NAR/GKW1354