Manganese in PDB 5c15: K428A Muntant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese

The structure of K428A Muntant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese, PDB code: 5c15 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)	18.92 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.766, 57.365, 46.646, 90.00, 98.71, 90.00
R / Rfree (%)	16.4 / 18.6

The binding sites of Manganese atom in the K428A Muntant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese (pdb code 5c15). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the K428A Muntant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese, PDB code: 5c15:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the K428A Muntant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of K428A Muntant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn800 b:65.0 occ:0.68 O A:HOH923 1.9 32.8 1.0 O A:HOH976 2.0 25.7 1.0 OD2 A:ASP296 2.0 26.4 1.0 O A:HOH999 2.5 37.2 1.0 MN A:MN801 2.6 31.9 0.9 OD1 A:ASP244 3.0 39.6 1.0 O A:HOH918 3.0 43.3 1.0 CG A:ASP296 3.1 24.1 1.0 OD2 A:ASP244 3.3 25.8 1.0 CG A:ASP244 3.4 35.9 1.0 HB3 A:ASP296 3.5 23.3 1.0 O A:HOH1096 3.6 42.6 1.0 CB A:ASP296 3.7 19.4 1.0 HB2 A:ASP296 3.7 23.3 1.0 O A:HOH1127 4.0 38.5 1.0 OD1 A:ASP296 4.2 26.2 1.0 OD2 A:ASP444 4.3 31.6 1.0 HA A:ASP244 4.5 23.5 1.0 O A:SER246 4.6 57.0 1.0 O A:HOH1087 4.6 55.1 1.0 CB A:ASP244 4.6 22.1 1.0 OD1 A:ASN441 4.7 39.1 1.0 HB3 A:ASP444 4.7 22.4 1.0 CD A:PRO245 4.8 21.2 1.0 HB2 A:ASP244 4.8 26.5 1.0 C A:SER246 4.8 66.7 1.0 N A:SER246 4.8 33.1 1.0 O A:HOH943 4.8 26.8 1.0 CA A:ASP244 5.0 19.6 1.0

Manganese binding site 2 out of 2 in the K428A Muntant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of K428A Muntant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:31.9 occ:0.89 OD2 A:ASP244 2.0 25.8 1.0 OD2 A:ASP444 2.2 31.6 1.0 O A:HOH923 2.2 32.8 1.0 O A:HOH1096 2.3 42.6 1.0 O A:HOH976 2.3 25.7 1.0 OD1 A:ASN441 2.6 39.1 1.0 MN A:MN800 2.6 65.0 0.7 CG A:ASP244 3.0 35.9 1.0 CG A:ASP444 3.2 30.6 1.0 OD1 A:ASP244 3.3 39.6 1.0 HB2 A:ASP444 3.3 22.4 1.0 HA A:ASN441 3.4 26.1 1.0 HB3 A:ASP444 3.6 22.4 1.0 CB A:ASP444 3.6 18.7 1.0 CG A:ASN441 3.7 36.3 1.0 O A:HOH1087 4.0 55.1 1.0 O A:HOH940 4.1 43.1 1.0 CA A:ASN441 4.3 21.7 1.0 OD1 A:ASP444 4.3 25.0 1.0 CB A:ASP244 4.4 22.1 1.0 HB3 A:SER439 4.4 48.4 1.0 O A:HOH1127 4.4 38.5 1.0 CB A:ASN441 4.4 30.2 1.0 HB2 A:ASP244 4.4 26.5 1.0 OD2 A:ASP296 4.4 26.4 1.0 HB3 A:ASN441 4.4 36.2 1.0 HD2 A:PRO440 4.7 37.5 1.0 ND2 A:ASN441 4.7 37.4 1.0 HB2 A:ALA428 4.7 46.3 1.0 HH12 A:ARG361 4.7 38.4 1.0 HD22 A:ASN441 4.7 44.8 1.0 O A:PRO440 4.8 25.0 1.0 HB3 A:ASP244 4.8 26.5 1.0 N A:ASN441 4.8 24.4 1.0 O A:HOH918 4.8 43.3 1.0 O A:HOH999 4.8 37.2 1.0 HG2 A:PRO440 4.9 40.6 1.0 C A:PRO440 4.9 25.0 1.0 O A:HOH1093 5.0 36.0 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