Calcium in PDB 5bvz: HK620 Tail Needle Crystallized at pH 9 (Crystal Form II)

The structure of HK620 Tail Needle Crystallized at pH 9 (Crystal Form II), PDB code: 5bvz was solved by A.Bhardwaj, G.Cingolani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.002, 73.812, 77.633, 83.21, 66.41, 70.66
R / Rfree (%)	20.9 / 26

The structure of HK620 Tail Needle Crystallized at pH 9 (Crystal Form II) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the HK620 Tail Needle Crystallized at pH 9 (Crystal Form II) (pdb code 5bvz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the HK620 Tail Needle Crystallized at pH 9 (Crystal Form II), PDB code: 5bvz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the HK620 Tail Needle Crystallized at pH 9 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of HK620 Tail Needle Crystallized at pH 9 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:37.9 occ:1.00 OD1 A:ASN63 2.3 32.8 1.0 OE1 C:GLN66 2.3 38.9 1.0 OE1 A:GLN66 2.3 45.9 1.0 OD1 C:ASN63 2.4 41.5 1.0 OE1 B:GLN66 2.4 54.0 1.0 OD1 B:ASN63 2.5 39.7 1.0 CD C:GLN66 3.4 38.8 1.0 CD A:GLN66 3.5 48.0 1.0 CG A:ASN63 3.5 38.5 1.0 CD B:GLN66 3.5 42.8 1.0 CG C:ASN63 3.6 38.8 1.0 CG B:ASN63 3.7 38.3 1.0 NE2 C:GLN66 4.0 33.1 1.0 NE2 A:GLN66 4.1 53.2 1.0 NE2 B:GLN66 4.1 46.0 1.0 ND2 A:ASN63 4.3 40.5 1.0 CA A:ASN63 4.4 32.9 1.0 CA C:ASN63 4.4 37.0 1.0 ND2 C:ASN63 4.4 34.4 1.0 CB A:ASN63 4.5 31.8 1.0 ND2 B:ASN63 4.5 50.2 1.0 CB C:ASN63 4.6 42.3 1.0 CA B:ASN63 4.6 45.0 1.0 CG A:GLN66 4.7 41.4 1.0 CG C:GLN66 4.7 31.4 1.0 CB B:ASN63 4.7 36.6 1.0 CB A:GLN66 4.8 33.5 1.0 N C:ASN63 4.8 33.0 1.0 CG B:GLN66 4.8 41.2 1.0 CB C:GLN66 4.9 39.4 1.0 N A:ASN63 4.9 35.8 1.0 CB B:GLN66 4.9 37.9 1.0

Calcium binding site 2 out of 2 in the HK620 Tail Needle Crystallized at pH 9 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of HK620 Tail Needle Crystallized at pH 9 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:43.2 occ:1.00 OD1 F:ASN63 2.3 53.2 1.0 OE1 D:GLN66 2.3 38.4 1.0 OE1 E:GLN66 2.4 44.3 1.0 OD1 E:ASN63 2.4 42.8 1.0 OE1 F:GLN66 2.4 41.9 1.0 OD1 D:ASN63 2.5 43.6 1.0 CG F:ASN63 3.5 49.3 1.0 CD D:GLN66 3.5 45.1 1.0 CD E:GLN66 3.5 43.0 1.0 CD F:GLN66 3.6 46.2 1.0 CG E:ASN63 3.6 43.1 1.0 CG D:ASN63 3.7 47.9 1.0 NE2 D:GLN66 4.1 45.0 1.0 NE2 F:GLN66 4.1 48.9 1.0 NE2 E:GLN66 4.2 43.3 1.0 ND2 F:ASN63 4.3 45.5 1.0 ND2 E:ASN63 4.4 53.8 1.0 CA F:ASN63 4.4 43.6 1.0 ND2 D:ASN63 4.5 42.4 1.0 CB F:ASN63 4.5 45.9 1.0 CA D:ASN63 4.6 47.8 1.0 CA E:ASN63 4.6 45.6 1.0 CB E:ASN63 4.6 38.5 1.0 CB D:ASN63 4.7 50.5 1.0 CG D:GLN66 4.7 39.7 1.0 CG E:GLN66 4.8 42.5 1.0 CG F:GLN66 4.8 41.0 1.0 CB D:GLN66 4.8 36.7 1.0 CB E:GLN66 4.8 37.5 1.0 N F:ASN63 4.9 46.6 1.0 CB F:GLN66 4.9 38.6 1.0 N E:ASN63 5.0 40.9 1.0 N D:ASN63 5.0 48.0 1.0

A.Bhardwaj, R.S.Sankhala, A.S.Olia, D.Brooke, S.R.Casjens, D.J.Taylor, P.E.Prevelige, G.Cingolani. Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions. J.Biol.Chem. V. 291 215 2016.
ISSN: ESSN 1083-351X
PubMed: 26574546
DOI: 10.1074/JBC.M115.696260