Calcium in PDB 5m1p: Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Calcium

The structure of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Calcium, PDB code: 5m1p 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)	43.43 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.453, 53.597, 69.852, 90.00, 91.80, 90.00
R / Rfree (%)	22.2 / 23.5

The binding sites of Calcium atom in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Calcium (pdb code 5m1p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Calcium, PDB code: 5m1p:
Jump to Calcium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:12.1 occ:0.85 OD1 A:ASP294 2.3 13.6 1.0 O A:TYR301 2.3 10.6 1.0 O A:HOH762 2.3 18.1 1.0 OD2 A:ASP300 2.4 14.7 1.0 O A:PHE295 2.4 13.3 1.0 OD2 A:ASP429 2.4 11.8 1.0 CG A:ASP429 3.4 10.1 1.0 CG A:ASP294 3.5 13.0 1.0 CG A:ASP300 3.5 15.1 1.0 C A:PHE295 3.5 13.0 1.0 C A:TYR301 3.5 10.1 1.0 CB A:ASP429 3.9 9.7 1.0 CB A:ASP300 3.9 14.3 1.0 OD2 A:ASP294 4.1 14.8 1.0 CA A:GLY296 4.2 13.9 1.0 N A:TYR301 4.2 11.1 1.0 O A:HOH686 4.2 19.3 1.0 N A:GLY296 4.2 13.3 1.0 O A:ASP294 4.3 12.6 1.0 C A:ASP294 4.3 11.6 1.0 N A:PHE295 4.4 11.5 1.0 CA A:TYR301 4.4 10.6 1.0 N A:SER302 4.5 9.3 1.0 C A:ASP300 4.5 12.3 1.0 OD1 A:ASP429 4.5 10.3 1.0 OD1 A:ASP300 4.6 15.7 1.0 O A:HOH782 4.6 22.7 1.0 CA A:PHE295 4.6 12.1 1.0 CB A:ASP294 4.6 12.1 1.0 CA A:SER302 4.6 9.6 1.0 N A:LYS297 4.7 15.8 1.0 CA A:ASP429 4.7 9.2 1.0 O A:ASP300 4.9 12.6 1.0 O A:HOH721 4.9 17.9 1.0 CA A:ASP300 4.9 13.7 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:13.1 occ:0.90 O B:HOH775 2.4 16.2 1.0 O B:HOH678 2.4 15.8 1.0 O B:PHE295 2.4 12.8 1.0 O B:HOH788 2.5 18.1 1.0 O B:HOH823 2.5 15.9 1.0 O B:HOH773 2.5 15.2 1.0 O B:HOH822 2.6 15.8 1.0 O B:HOH675 2.6 12.8 1.0 C B:PHE295 3.6 12.0 1.0 N B:PHE295 4.2 10.5 1.0 O B:HOH637 4.3 24.5 0.5 O B:HOH637 4.3 16.0 0.5 O B:HOH772 4.4 17.5 1.0 N B:GLY296 4.4 13.0 1.0 O B:HOH776 4.4 17.8 1.0 CA B:PHE295 4.5 11.2 1.0 CA B:GLY296 4.5 14.4 1.0 OD1 B:ASP429 4.6 12.3 1.0 O B:HOH705 4.6 15.9 1.0 O B:HOH609 4.7 12.8 1.0 CB B:ASP294 4.7 10.6 1.0 OD2 B:ASP347 4.8 10.9 1.0 O B:HOH611 4.8 12.7 1.0 O B:HOH664 4.8 16.2 1.0 O B:TYR301 4.9 11.9 1.0 O B:HOH660 4.9 18.6 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