Magnesium in PDB 5c12: Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6

The structure of Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6, PDB code: 5c12 was solved by H.Zhao, L.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.97 / 1.52
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.645, 57.519, 46.598, 90.00, 98.76, 90.00
R / Rfree (%)	15.8 / 18.3

The binding sites of Magnesium atom in the Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 (pdb code 5c12). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6, PDB code: 5c12:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg800 b:45.5 occ:0.96 O A:HOH910 1.7 19.6 1.0 O A:HOH995 1.9 21.6 1.0 OD2 A:ASP296 2.0 16.0 1.0 MG A:MG801 2.4 19.6 0.9 O A:HOH972 2.9 27.9 1.0 O A:HOH1027 3.1 26.8 1.0 CG A:ASP296 3.2 15.1 1.0 OD1 A:ASP244 3.3 22.0 1.0 O A:HOH942 3.3 31.3 1.0 OD2 A:ASP244 3.3 15.7 1.0 CG A:ASP244 3.5 18.7 1.0 OD1 A:ASP247 3.5 36.2 1.0 HB3 A:ASP296 3.6 15.9 1.0 O A:HOH1158 3.7 31.2 1.0 HD2 A:PRO245 3.7 15.6 1.0 CB A:ASP296 3.8 13.3 1.0 HB2 A:ASP296 3.8 15.9 1.0 OD2 A:ASP444 4.1 19.4 1.0 O A:HOH908 4.2 30.5 1.0 O A:HOH1175 4.2 24.6 1.0 OD1 A:ASP296 4.2 14.8 1.0 O A:HOH1122 4.3 40.8 1.0 O A:SER246 4.5 27.6 1.0 H A:SER246 4.5 24.9 1.0 HA A:ASP244 4.5 15.4 1.0 HB3 A:ASP444 4.7 14.4 1.0 CB A:ASP244 4.7 13.5 1.0 CD A:PRO245 4.7 13.0 1.0 C A:SER246 4.7 39.8 1.0 CG A:ASP247 4.8 41.9 1.0 HB2 A:ASP244 4.8 16.2 1.0 HG2 A:PRO245 4.9 21.9 1.0 O A:HOH977 5.0 18.3 1.0

Magnesium binding site 2 out of 2 in the Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:19.6 occ:0.88 O A:HOH910 1.9 19.6 1.0 OD2 A:ASP244 2.0 15.7 1.0 O A:HOH1027 2.1 26.8 1.0 O A:HOH908 2.1 30.5 1.0 O A:HOH995 2.2 21.6 1.0 OD2 A:ASP444 2.2 19.4 1.0 MG A:MG800 2.4 45.5 1.0 CG A:ASP244 3.0 18.7 1.0 CG A:ASP444 3.3 19.1 1.0 OD1 A:ASP244 3.3 22.0 1.0 HB2 A:ASP444 3.4 14.4 1.0 HB3 A:ASP444 3.5 14.4 1.0 HA A:ASN441 3.6 18.9 1.0 CB A:ASP444 3.6 12.0 1.0 OD1 A:ASP247 3.7 36.2 1.0 HG A:SER439 4.0 44.9 1.0 OD1 A:ASN441 4.1 26.4 1.0 O A:HOH947 4.1 33.1 1.0 O A:HOH1158 4.1 31.2 1.0 OG A:SER439 4.1 37.4 1.0 OD2 A:ASP296 4.3 16.0 1.0 CB A:ASP244 4.3 13.5 1.0 HB2 A:ASP244 4.3 16.2 1.0 OD1 A:ASP444 4.4 17.9 1.0 O A:HOH1175 4.4 24.6 1.0 CA A:ASN441 4.5 15.8 1.0 HD2 A:PRO440 4.6 28.0 1.0 CG A:ASP247 4.6 41.9 1.0 HH12 A:ARG361 4.7 28.7 1.0 HB2 A:ALA428 4.7 38.9 1.0 OD2 A:ASP247 4.8 56.2 1.0 HB3 A:ASN441 4.8 18.5 1.0 HB3 A:ASP244 4.8 16.2 1.0 O A:PRO440 4.8 15.2 1.0 HA A:SER246 4.8 35.0 1.0 CG A:ASN441 4.9 31.1 1.0 H A:SER246 4.9 24.9 1.0 HG2 A:PRO440 4.9 26.2 1.0 O A:HOH972 5.0 27.9 1.0

H.Zhao, Z.Lin, A.Y.Lynn, B.Varnado, J.A.Beutler, R.P.Murelli, S.F.Le Grice, L.Tang. Two Distinct Modes of Metal Ion Binding in the Nuclease Active Site of A Viral Dna-Packaging Terminase: Insight Into the Two-Metal-Ion Catalytic Mechanism. Nucleic Acids Res. V. 43 11003 2015.
ISSN: ESSN 1362-4962
PubMed: 26450964
DOI: 10.1093/NAR/GKV1018