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Calcium in PDB 5bu8: HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon

Protein crystallography data

The structure of HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon, PDB code: 5bu8 was solved by R.S.Sankhala, G.Cingolani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.99 / 2.20
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 43.642, 43.642, 271.063, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 25.1

Other elements in 5bu8:

The structure of HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon also contains other interesting chemical elements:

Xenon (Xe) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon (pdb code 5bu8). 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 7.5 and Derivatized with Xenon, PDB code: 5bu8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5bu8

Go back to Calcium Binding Sites List in 5bu8
Calcium binding site 1 out of 2 in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon


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 7.5 and Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:3.2
occ:0.33
OD1 A:ASN63 2.4 14.7 1.0
OE1 A:GLN66 2.5 10.4 1.0
CD A:GLN66 3.6 4.5 1.0
CG A:ASN63 3.7 15.9 1.0
NE2 A:GLN66 4.1 4.2 1.0
ND2 A:ASN63 4.5 18.2 1.0
CB A:ASN63 4.6 6.0 1.0
CA A:ASN63 4.7 10.7 1.0
CG A:GLN66 4.9 3.7 1.0

Calcium binding site 2 out of 2 in 5bu8

Go back to Calcium Binding Sites List in 5bu8
Calcium binding site 2 out of 2 in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon


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 7.5 and Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:18.3
occ:0.33
OE1 B:GLN66 2.4 9.4 1.0
OD1 B:ASN63 2.5 11.8 1.0
CD B:GLN66 3.5 10.5 1.0
CG B:ASN63 3.7 10.3 1.0
NE2 B:GLN66 4.0 12.0 1.0
O B:HOH453 4.4 31.7 1.0
O B:HOH521 4.5 11.6 0.3
CA B:ASN63 4.6 9.9 1.0
ND2 B:ASN63 4.6 23.7 1.0
CB B:ASN63 4.7 4.6 1.0
CG B:GLN66 4.8 7.2 1.0
CB B:GLN66 4.9 10.9 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: Wed Oct 28 09:08:05 2020

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