Cobalt in PDB 5m1o: Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Cobalt

The structure of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Cobalt, PDB code: 5m1o 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)	42.92 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.937, 53.895, 69.751, 90.00, 91.62, 90.00
R / Rfree (%)	18.5 / 22.4

The binding sites of Cobalt atom in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Cobalt (pdb code 5m1o). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Cobalt, PDB code: 5m1o:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:20.4 occ:0.70 O A:HOH648 2.0 24.8 1.0 OD1 A:ASP429 2.0 15.9 1.0 O A:HOH700 2.1 25.0 1.0 OD2 A:ASP294 2.1 19.1 0.7 O A:HOH608 2.1 28.6 1.0 O A:HOH652 2.2 30.8 1.0 CG A:ASP294 3.0 18.8 0.7 CG A:ASP429 3.1 14.2 1.0 OD1 A:ASP294 3.3 19.7 0.7 CB A:ASP429 3.5 13.8 1.0 CA A:ASP429 3.8 13.3 1.0 O B:HOH740 3.9 40.9 1.0 OD1 A:ASP294 4.0 14.7 0.3 CG A:ASP294 4.1 14.5 0.3 OD2 A:ASP429 4.2 14.6 1.0 O A:TYR301 4.2 18.4 1.0 NH2 B:ARG284 4.2 36.2 1.0 O B:HOH645 4.2 21.4 1.0 O A:PHE295 4.2 20.9 1.0 OD2 A:ASP294 4.2 14.3 0.3 O A:HOH733 4.3 29.5 1.0 OD1 A:ASP428 4.4 18.8 1.0 CB A:ASP294 4.4 17.5 0.7 N A:ASP429 4.4 14.2 1.0 CB A:ASP294 4.6 15.0 0.3 OD2 A:ASP300 4.9 35.8 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ B:Co501 b:33.5 occ:0.70 O B:HOH647 2.1 42.6 1.0 OD2 B:ASP294 2.2 31.1 1.0 OD1 B:ASP429 2.2 32.3 1.0 O B:HOH690 2.2 38.8 1.0 O B:HOH677 2.3 35.8 1.0 O B:HOH725 2.3 28.4 1.0 CG B:ASP294 3.2 31.5 1.0 CG B:ASP429 3.3 30.5 1.0 OD1 B:ASP294 3.5 36.0 1.0 CB B:ASP429 3.6 28.4 1.0 CA B:ASP429 3.8 26.7 1.0 O B:TYR301 4.2 32.0 1.0 OD2 B:ASP429 4.4 34.5 1.0 OD1 B:ASP428 4.4 38.2 1.0 O B:PHE295 4.5 29.1 1.0 N B:ASP429 4.5 27.6 1.0 CB B:ASP294 4.5 27.3 1.0 O B:HOH680 4.8 29.1 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