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Xenon 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:

Calcium (Ca) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon 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 Xenon atom.
In total 6 binding sites of Xenon where determined in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon, PDB code: 5bu8:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6;

Xenon binding site 1 out of 6 in 5bu8

Go back to Xenon Binding Sites List in 5bu8
Xenon binding site 1 out of 6 in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe 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:Xe302

b:74.8
occ:0.33
CD2 A:LEU108 3.6 26.4 1.0
CB A:LEU108 4.1 11.7 1.0
CG A:LEU108 4.4 16.1 1.0
CA A:VAL105 4.9 17.9 1.0
CG2 A:VAL105 5.0 31.9 1.0

Xenon binding site 2 out of 6 in 5bu8

Go back to Xenon Binding Sites List in 5bu8
Xenon binding site 2 out of 6 in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe 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
A:Xe303

b:32.4
occ:0.33
CD2 A:LEU155 3.9 12.2 1.0
CD1 A:LEU155 4.3 7.9 1.0
CD1 A:LEU151 4.4 11.4 1.0
CG1 A:VAL141 4.7 35.8 1.0
CG A:LEU155 4.8 7.7 1.0

Xenon binding site 3 out of 6 in 5bu8

Go back to Xenon Binding Sites List in 5bu8
Xenon binding site 3 out of 6 in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 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:Xe304

b:20.3
occ:0.33
CG A:TYR161 3.7 8.9 1.0
CG2 A:VAL169 3.8 6.5 1.0
CD2 A:TYR161 3.8 11.4 1.0
CB A:TYR161 4.0 8.0 1.0
CD1 A:TYR161 4.1 19.2 1.0
CB A:VAL169 4.3 12.1 1.0
CE2 A:TYR161 4.3 14.1 1.0
CE1 A:TYR161 4.5 10.8 1.0
CZ A:TYR161 4.6 7.1 1.0
CG1 A:VAL169 4.7 6.5 1.0

Xenon binding site 4 out of 6 in 5bu8

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Xenon binding site 4 out of 6 in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 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:Xe305

b:88.3
occ:0.33
CB A:ALA94 3.7 28.3 1.0
CG A:LEU91 4.1 22.9 1.0
CA A:LEU91 4.5 13.1 1.0
CD1 A:LEU91 4.5 37.7 1.0
CB A:LEU91 4.7 13.1 1.0
O A:LEU91 4.8 32.4 1.0

Xenon binding site 5 out of 6 in 5bu8

Go back to Xenon Binding Sites List in 5bu8
Xenon binding site 5 out of 6 in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 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:Xe302

b:13.9
occ:0.33
CG B:TYR161 3.7 6.7 1.0
CG2 B:VAL169 3.7 7.9 1.0
CD2 B:TYR161 3.8 8.2 1.0
CB B:TYR161 3.9 6.0 1.0
CD1 B:TYR161 4.1 6.2 1.0
CB B:VAL169 4.2 5.5 1.0
CE2 B:TYR161 4.3 15.3 1.0
CG1 B:VAL169 4.6 5.5 1.0
CE1 B:TYR161 4.6 6.2 1.0
CZ B:TYR161 4.7 6.2 1.0

Xenon binding site 6 out of 6 in 5bu8

Go back to Xenon Binding Sites List in 5bu8
Xenon binding site 6 out of 6 in the HK620 Tail Needle Crystallized at pH 7.5 and Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 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:Xe303

b:0.8
occ:0.33
CG B:LEU91 3.8 14.5 1.0
CB B:ALA94 3.9 17.7 1.0
CA B:LEU91 4.2 15.5 1.0
CD1 B:LEU91 4.3 22.1 1.0
CB B:LEU91 4.3 17.8 1.0
CD2 B:LEU91 4.8 13.4 1.0
O B:LEU91 4.8 20.6 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: Sun Nov 1 12:23:43 2020

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