Calcium in PDB 5c2d: K428A Mutant GP2C of Large Terminase Subunit From Bacteriophage SF6 with Calcium

The structure of K428A Mutant GP2C of Large Terminase Subunit From Bacteriophage SF6 with Calcium, PDB code: 5c2d 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)	18.95 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.078, 57.437, 46.568, 90.00, 98.99, 90.00
R / Rfree (%)	16 / 19.2

The binding sites of Calcium atom in the K428A Mutant GP2C of Large Terminase Subunit From Bacteriophage SF6 with Calcium (pdb code 5c2d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the K428A Mutant GP2C of Large Terminase Subunit From Bacteriophage SF6 with Calcium, PDB code: 5c2d:

Calcium binding site 1 out of 1 in the K428A Mutant GP2C of Large Terminase Subunit From Bacteriophage SF6 with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of K428A Mutant GP2C of Large Terminase Subunit From Bacteriophage SF6 with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:33.1 occ:1.00 O A:HOH606 2.2 23.8 1.0 OD2 A:ASP244 2.4 31.8 1.0 O A:HOH798 2.4 34.0 1.0 OD2 A:ASP296 2.5 22.0 1.0 OD2 A:ASP444 2.6 24.9 1.0 O A:HOH759 2.6 52.0 1.0 O A:HOH815 2.6 63.6 1.0 O A:HOH601 2.9 45.2 1.0 CG A:ASP244 3.4 30.2 1.0 CG A:ASP296 3.6 19.5 1.0 CG A:ASP444 3.6 21.4 1.0 O A:HOH802 3.6 44.8 1.0 OD1 A:ASP244 3.7 28.3 1.0 CB A:ASP444 3.8 17.4 1.0 O A:HOH671 3.9 33.4 1.0 CB A:ASP296 4.2 15.3 1.0 O A:HOH612 4.4 34.2 1.0 OD1 A:ASP296 4.5 20.5 1.0 O A:HOH785 4.5 16.8 1.0 NH1 A:ARG361 4.5 25.8 1.0 O A:HOH786 4.5 30.4 1.0 CB A:ASP244 4.7 16.5 1.0 OD1 A:ASP444 4.7 20.2 1.0 OD1 A:ASN441 4.7 25.1 1.0 O A:HOH628 4.8 32.4 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