Manganese in PDB 5m1n: Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Manganese

The structure of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Manganese, PDB code: 5m1n 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 (°)	43.804, 53.936, 70.079, 90.00, 92.06, 90.00
R / Rfree (%)	16.9 / 18.2

The binding sites of Manganese atom in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Manganese (pdb code 5m1n). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Manganese, PDB code: 5m1n:
Jump to Manganese binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:10.2 occ:1.00 O A:HOH753 2.1 13.3 1.0 OD1 A:ASP429 2.1 8.2 1.0 OD2 A:ASP294 2.2 9.9 1.0 O A:HOH605 2.2 12.3 1.0 O A:HOH654 2.2 12.2 1.0 O A:HOH645 2.2 11.1 1.0 CG A:ASP294 3.1 10.0 1.0 CG A:ASP429 3.2 7.4 1.0 OD1 A:ASP294 3.4 11.5 1.0 CB A:ASP429 3.6 7.2 1.0 CA A:ASP429 4.0 6.9 1.0 O A:TYR301 4.2 9.7 1.0 O B:HOH828 4.2 26.6 1.0 O A:PHE295 4.3 11.3 1.0 O A:HOH751 4.3 10.0 1.0 OD2 A:ASP429 4.3 7.9 1.0 O A:HOH747 4.3 24.4 1.0 NH1 B:ARG284 4.4 16.1 1.0 O A:HOH797 4.5 23.1 1.0 OD1 A:ASP428 4.5 10.5 1.0 CB A:ASP294 4.5 9.4 1.0 N A:ASP429 4.5 7.2 1.0 OD2 A:ASP300 4.8 17.5 1.0 O A:HOH756 5.0 30.8 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:9.5 occ:1.00 OD2 B:ASP294 2.1 9.4 1.0 OD1 B:ASP429 2.2 8.6 1.0 O B:HOH770 2.2 11.6 1.0 O B:HOH666 2.2 10.5 1.0 O B:HOH796 2.2 12.2 1.0 O B:HOH808 2.2 10.6 1.0 CG B:ASP294 3.1 9.2 1.0 CG B:ASP429 3.2 8.5 1.0 OD1 B:ASP294 3.3 11.0 1.0 CB B:ASP429 3.6 8.1 1.0 CA B:ASP429 3.9 8.0 1.0 O B:HOH831 4.0 19.4 1.0 O B:PHE295 4.1 11.3 1.0 O B:TYR301 4.2 10.6 1.0 O B:HOH862 4.3 14.6 0.5 O B:HOH702 4.3 23.4 1.0 OD2 B:ASP429 4.4 9.0 1.0 O B:HOH780 4.4 13.4 1.0 O B:HOH835 4.4 26.0 1.0 CB B:ASP294 4.5 8.6 1.0 O B:HOH715 4.6 13.1 1.0 N B:ASP429 4.6 8.5 1.0 OD1 B:ASP428 4.6 13.6 1.0 C B:PHE295 4.8 10.5 1.0 O B:HOH692 4.9 13.8 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