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Chlorine 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:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the HK620 Tail Needle Crystallized at pH 9 (Crystal Form II), PDB code: 5bvz:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5bvz

Go back to Chlorine Binding Sites List in 5bvz
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl302

b:23.8
occ:1.00
ND2 A:ASN80 3.1 23.9 1.0
ND2 C:ASN80 3.2 31.8 1.0
ND2 B:ASN80 3.3 26.2 1.0
CB A:ASN80 3.7 27.5 1.0
CG A:ASN80 3.9 29.5 1.0
CB B:ASN80 3.9 23.3 1.0
CA A:ILE77 4.0 22.4 1.0
CB C:ASN80 4.0 22.6 1.0
CG1 B:ILE77 4.0 40.7 1.0
CG C:ASN80 4.1 26.4 1.0
CG1 A:ILE77 4.1 24.7 1.0
CA B:ILE77 4.1 36.3 1.0
CG B:ASN80 4.1 26.9 1.0
CG2 B:ILE77 4.2 24.7 1.0
CG1 C:ILE77 4.2 29.1 1.0
CG2 A:ILE77 4.2 23.7 1.0
CA C:ILE77 4.3 30.2 1.0
CB A:ILE77 4.3 25.9 1.0
CB B:ILE77 4.3 34.5 1.0
CG2 C:ILE77 4.4 24.1 1.0
CB C:ILE77 4.5 31.1 1.0
O A:ILE77 4.6 25.8 1.0
O B:ILE77 4.7 29.6 1.0
C A:ILE77 4.8 22.0 1.0
O C:ILE77 4.9 30.2 1.0
N A:ILE77 4.9 21.1 1.0
C B:ILE77 4.9 33.5 1.0
O A:ARG76 4.9 32.3 1.0

Chlorine binding site 2 out of 2 in 5bvz

Go back to Chlorine Binding Sites List in 5bvz
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl302

b:55.6
occ:1.00
ND2 E:ASN80 2.7 29.2 1.0
ND2 D:ASN80 3.0 34.8 1.0
ND2 F:ASN80 3.3 24.7 1.0
CB E:ASN80 3.6 26.9 1.0
CG E:ASN80 3.6 31.6 1.0
CB D:ASN80 3.8 22.2 1.0
CG D:ASN80 3.9 25.3 1.0
CB F:ASN80 3.9 23.5 1.0
CA E:ILE77 4.1 35.9 1.0
CG F:ASN80 4.1 29.4 1.0
CA F:ILE77 4.2 24.6 1.0
CG1 E:ILE77 4.2 28.9 1.0
CG1 F:ILE77 4.2 26.7 1.0
CG2 F:ILE77 4.3 25.9 1.0
CA D:ILE77 4.3 23.8 1.0
CG1 D:ILE77 4.3 27.0 1.0
CG2 E:ILE77 4.4 25.0 1.0
CB F:ILE77 4.5 30.5 1.0
CB E:ILE77 4.5 25.2 1.0
CG2 D:ILE77 4.5 25.0 1.0
O F:ILE77 4.5 28.1 1.0
CB D:ILE77 4.6 28.6 1.0
O E:ILE77 4.6 23.7 1.0
O D:ILE77 4.8 27.7 1.0
OD1 E:ASN80 4.8 24.7 1.0
C F:ILE77 4.9 35.9 1.0
C E:ILE77 4.9 34.7 1.0
N E:ILE77 5.0 36.2 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 11:33:22 2020

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