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

Protein crystallography data

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

Other elements in 5bvz:

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

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

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 5bvz

Go back to Calcium Binding Sites List in 5bvz
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 5bvz

Go back to Calcium Binding Sites List in 5bvz
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

Reference:

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
Page generated: Sat Dec 12 05:18:56 2020

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