Manganese in PDB 5c2f: K428A Mutant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese and Beta-Thujaplicinol

The structure of K428A Mutant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese and Beta-Thujaplicinol, PDB code: 5c2f 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)	19.26 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.589, 58.418, 53.384, 90.00, 96.43, 90.00
R / Rfree (%)	16.8 / 20.8

The binding sites of Manganese atom in the K428A Mutant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese and Beta-Thujaplicinol (pdb code 5c2f). 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 Mutant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese and Beta-Thujaplicinol, PDB code: 5c2f:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the K428A Mutant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese and Beta-Thujaplicinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of K428A Mutant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese and Beta-Thujaplicinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:25.7 occ:1.00 O1 A:JTH503 2.1 31.6 1.0 OD1 A:ASP244 2.1 24.5 1.0 OD2 A:ASP296 2.1 27.8 1.0 O7 A:JTH503 2.1 24.8 1.0 O A:HOH633 2.2 28.1 1.0 O A:HOH670 2.2 27.1 1.0 C1 A:JTH503 3.0 31.7 1.0 C7 A:JTH503 3.0 34.2 1.0 CG A:ASP244 3.1 27.1 1.0 CG A:ASP296 3.2 25.0 1.0 OD2 A:ASP244 3.5 23.5 1.0 CB A:ASP296 3.7 21.6 1.0 MN A:MN502 3.7 27.4 1.0 O A:PRO245 4.2 22.9 1.0 O A:HOH718 4.3 39.5 1.0 OD1 A:ASP296 4.3 25.4 1.0 C2 A:JTH503 4.3 35.0 1.0 C6 A:JTH503 4.3 29.5 1.0 OD2 A:ASP444 4.5 27.3 1.0 CB A:ASP244 4.5 25.9 1.0 O A:HOH622 4.6 30.2 1.0 O A:HOH605 4.6 31.0 1.0 O2 A:JTH503 4.6 29.0 1.0 O A:HOH636 4.7 28.8 1.0 CA A:ASP244 4.8 22.4 1.0 CD A:PRO245 4.8 24.2 1.0

Manganese binding site 2 out of 2 in the K428A Mutant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese and Beta-Thujaplicinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of K428A Mutant Nuclease Domain of the Large Terminase Subunit GP2 of Bacterial Virus SF6 with Manganese and Beta-Thujaplicinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:27.4 occ:1.00 OD2 A:ASP244 2.0 23.5 1.0 O2 A:JTH503 2.1 29.0 1.0 O1 A:JTH503 2.2 31.6 1.0 OD1 A:ASN441 2.3 30.2 1.0 O A:HOH636 2.3 28.8 1.0 O A:HOH622 2.3 30.2 1.0 CG A:ASP244 3.0 27.1 1.0 C2 A:JTH503 3.0 35.0 1.0 C1 A:JTH503 3.0 31.7 1.0 CG A:ASN441 3.3 25.2 1.0 OD1 A:ASP244 3.4 24.5 1.0 OG A:SER439 3.5 38.5 1.0 CB A:ASN441 3.7 24.3 1.0 MN A:MN501 3.7 25.7 1.0 CA A:ASN441 3.9 24.6 1.0 O A:HOH633 4.2 28.1 1.0 CB A:ASP244 4.3 25.9 1.0 OD2 A:ASP444 4.3 27.3 1.0 C3 A:JTH503 4.3 37.8 1.0 C7 A:JTH503 4.3 34.2 1.0 O A:ALA252 4.4 30.2 1.0 N A:ASN441 4.4 23.4 1.0 CB A:SER439 4.5 34.9 1.0 O A:PRO245 4.5 22.9 1.0 ND2 A:ASN441 4.5 29.8 1.0 O7 A:JTH503 4.7 24.8 1.0 O A:HOH670 4.7 27.1 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