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Calcium in PDB 5lsf: Sacbrood Honeybee Virus

Protein crystallography data

The structure of Sacbrood Honeybee Virus, PDB code: 5lsf was solved by P.Plevka, M.Veselikova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group C 1 2 1 2
Cell size a, b, c (Å), α, β, γ (°) 487.850, 360.970, 338.160, 90.00, 133.07, 90.00
R / Rfree (%) 19.4 / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Sacbrood Honeybee Virus (pdb code 5lsf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Sacbrood Honeybee Virus, PDB code: 5lsf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5lsf

Go back to Calcium Binding Sites List in 5lsf
Calcium binding site 1 out of 2 in the Sacbrood Honeybee Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sacbrood Honeybee Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:56.3
occ:1.00
O A:HOH508 3.0 43.0 1.0
N A:ASN14 3.7 21.5 1.0
O A:ASN14 3.9 22.0 1.0
CA A:ALA13 4.1 19.8 1.0
C A:ALA13 4.4 21.1 1.0
CB A:ALA13 4.5 17.1 1.0
CA A:ASN14 4.6 22.1 1.0
C A:ASN14 4.6 22.0 1.0
CB A:ASN14 4.8 23.3 1.0

Calcium binding site 2 out of 2 in 5lsf

Go back to Calcium Binding Sites List in 5lsf
Calcium binding site 2 out of 2 in the Sacbrood Honeybee Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sacbrood Honeybee Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:66.3
occ:1.00
O B:HOH488 4.6 40.1 1.0

Reference:

M.Prochazkova, T.Fuzik, K.Skubnik, J.Moravcova, Z.Ubiparip, A.Pridal, P.Plevka. Virion Structure and Genome Delivery Mechanism of Sacbrood Honeybee Virus. Proc. Natl. Acad. Sci. V. 115 7759 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29987012
DOI: 10.1073/PNAS.1722018115
Page generated: Wed Jul 9 07:59:56 2025

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