Chlorine in PDB 8gih: Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24

Protein crystallography data

The structure of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24, PDB code: 8gih was solved by P.L.Shaffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.90 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.78, 87.57, 103.26, 90, 103.48, 90
R / Rfree (%) 20.5 / 25.3

Other elements in 8gih:

The structure of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Bromine (Br) 6 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 (pdb code 8gih). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24, PDB code: 8gih:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 8gih

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Chlorine binding site 1 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:77.2
occ:1.00
 N A:ASP40 3.4 66.0 1.0
N A:ARG39 3.6 59.1 1.0
CB A:ASP40 3.7 78.6 1.0
CG A:ASP40 3.7 86.2 1.0
OD1 A:ASP40 3.9 82.2 1.0
O A:LEU37 4.0 61.0 1.0
CA A:ASP40 4.1 67.6 1.0
C A:TYR38 4.2 57.7 1.0
OD2 A:ASP40 4.2 92.5 1.0
CB A:ARG39 4.3 61.9 0.5
CA A:ARG39 4.3 56.9 0.5
CA A:ARG39 4.3 56.9 0.5
C A:ARG39 4.3 57.7 1.0
C A:LEU37 4.3 56.3 1.0
CB A:ARG39 4.3 61.7 0.5
N A:TYR38 4.4 50.4 1.0
CA A:TYR38 4.4 51.9 1.0
O A:ALA36 4.7 61.2 1.0
O A:ALA35 4.7 55.6 1.0
O A:TYR38 4.9 54.2 1.0

Chlorine binding site 2 out of 12 in 8gih

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Chlorine binding site 2 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:53.9
occ:1.00
 N A:ALA137 3.7 56.7 1.0
O A:PRO135 3.9 48.8 1.0
CB A:ALA137 4.1 50.5 1.0
CA A:ASN136 4.4 50.0 1.0
CH2 A:TRP125 4.5 42.9 1.0
C A:ASN136 4.6 48.3 1.0
CA A:ALA137 4.6 57.7 1.0
CZ2 A:TRP125 4.8 47.6 1.0
C A:PRO135 4.9 50.5 1.0
OD1 A:ASN136 4.9 62.6 1.0

Chlorine binding site 3 out of 12 in 8gih

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Chlorine binding site 3 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:81.8
occ:1.00
 CG B:ASP40 3.5 90.7 1.0
N B:ASP40 3.6 74.0 1.0
CB B:ASP40 3.7 78.5 1.0
OD1 B:ASP40 3.7 93.3 1.0
OD2 B:ASP40 3.9 96.2 1.0
N B:ARG39 3.9 67.4 1.0
CG B:ARG39 4.0 83.7 1.0
CA B:ASP40 4.3 71.0 1.0
O B:LEU37 4.3 66.5 1.0
C B:TYR38 4.4 68.9 1.0
O B:ALA35 4.5 57.8 1.0
O B:ALA36 4.5 63.1 1.0
C B:LEU37 4.5 62.8 1.0
C B:ARG39 4.5 69.8 1.0
N B:TYR38 4.6 55.0 1.0
CA B:ARG39 4.6 64.3 1.0
CA B:TYR38 4.7 55.2 1.0
CB B:ARG39 4.7 65.8 1.0

Chlorine binding site 4 out of 12 in 8gih

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Chlorine binding site 4 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:60.9
occ:1.00
 O C:ARG133 3.4 51.4 1.0
N B:ALA137 3.7 54.8 1.0
O B:PRO135 4.0 60.4 1.0
CB B:ALA137 4.0 60.3 1.0
CD C:PRO135 4.1 57.4 1.0
CA B:ASN136 4.4 63.5 1.0
C C:ARG133 4.5 47.7 1.0
CA B:ALA137 4.5 58.5 1.0
N C:PRO135 4.6 58.5 1.0
C B:ASN136 4.6 59.0 1.0
CH2 B:TRP125 4.6 54.1 1.0
CA C:PRO134 4.6 57.2 1.0
CZ2 B:TRP125 4.8 54.6 1.0
C C:PRO134 4.9 55.1 1.0
O C:ALA131 4.9 71.3 1.0
CG C:PRO135 5.0 60.7 1.0
OD1 B:ASN136 5.0 73.6 1.0
N C:PRO134 5.0 46.4 1.0

Chlorine binding site 5 out of 12 in 8gih

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Chlorine binding site 5 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:88.0
occ:1.00
 N C:ASP40 3.8 60.5 1.0
N C:ARG39 3.9 61.8 1.0
CG C:ASP40 3.9 70.4 1.0
OD1 C:ASP40 4.0 70.7 1.0
O C:LEU37 4.1 54.0 1.0
CB C:ASP40 4.1 61.4 1.0
OD2 C:ASP40 4.3 72.5 1.0
CB C:ARG39 4.3 61.6 1.0
O C:ALA36 4.3 56.3 1.0
C C:LEU37 4.3 62.6 1.0
O C:ALA35 4.4 52.3 1.0
N C:TYR38 4.5 62.0 1.0
CA C:ARG39 4.5 56.8 1.0
C C:TYR38 4.5 68.8 1.0
CA C:ASP40 4.6 56.9 1.0
C C:ARG39 4.7 60.1 1.0
CA C:TYR38 4.7 60.6 1.0
C C:ALA36 4.9 53.8 1.0

Chlorine binding site 6 out of 12 in 8gih

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Chlorine binding site 6 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:52.4
occ:1.00
 N C:ALA137 3.5 59.5 1.0
CB C:ALA137 3.9 64.9 1.0
O C:PRO135 3.9 63.5 1.0
CA C:ASN136 4.2 51.4 1.0
CA C:ALA137 4.3 63.4 1.0
C C:ASN136 4.4 54.4 1.0
CH2 C:TRP125 4.6 36.6 1.0
CZ2 C:TRP125 4.7 34.0 1.0
C C:PRO135 4.9 60.0 1.0
OD1 C:ASN136 4.9 62.0 1.0

Chlorine binding site 7 out of 12 in 8gih

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Chlorine binding site 7 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:79.2
occ:1.00
 N D:ASP40 3.3 71.1 1.0
N D:ARG39 3.4 59.8 1.0
O D:LEU37 3.7 63.3 1.0
CB D:ASP40 3.7 84.0 1.0
C D:TYR38 3.8 65.2 1.0
CG D:ASP40 3.9 91.0 1.0
C D:LEU37 4.0 61.5 1.0
N D:TYR38 4.0 59.1 1.0
CA D:TYR38 4.0 62.6 1.0
CA D:ARG39 4.1 62.7 1.0
OD1 D:ASP40 4.1 93.9 1.0
CA D:ASP40 4.1 75.9 1.0
CB D:ARG39 4.2 64.2 1.0
C D:ARG39 4.2 73.3 1.0
OD2 D:ASP40 4.3 89.6 1.0
O D:ALA35 4.4 60.1 1.0
O D:ALA36 4.6 73.2 1.0
O D:TYR38 4.6 58.1 1.0
N D:ALA41 5.0 74.2 1.0
CA D:LEU37 5.0 61.0 1.0

Chlorine binding site 8 out of 12 in 8gih

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Chlorine binding site 8 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:56.5
occ:1.00
 O E:ARG133 3.6 62.3 1.0
N D:ALA137 3.9 63.9 1.0
O D:PRO135 4.0 57.1 1.0
CB D:ALA137 4.1 67.9 1.0
CD E:PRO135 4.5 59.6 1.0
C E:ARG133 4.5 49.5 1.0
CH2 D:TRP125 4.5 56.8 1.0
O E:ALA131 4.6 81.4 1.0
CA D:ASN136 4.6 58.1 1.0
CA D:ALA137 4.7 63.3 1.0
N E:PRO135 4.8 59.7 1.0
CZ2 D:TRP125 4.8 62.2 1.0
C D:ASN136 4.8 62.7 1.0
CA E:PRO134 4.9 55.7 1.0
O E:PRO130 4.9 75.7 1.0

Chlorine binding site 9 out of 12 in 8gih

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Chlorine binding site 9 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:80.2
occ:1.00
 N E:ASP40 3.4 71.8 1.0
CG E:ASP40 3.7 92.3 1.0
N E:ARG39 3.7 69.5 1.0
CB E:ASP40 3.7 79.4 1.0
OD1 E:ASP40 3.9 93.8 1.0
O E:LEU37 4.1 74.4 1.0
OD2 E:ASP40 4.1 95.3 1.0
CA E:ASP40 4.2 68.3 1.0
CB E:ARG39 4.2 70.0 1.0
CA E:ARG39 4.3 67.2 1.0
C E:TYR38 4.3 66.9 1.0
C E:ARG39 4.4 67.4 1.0
C E:LEU37 4.4 67.5 1.0
O E:ALA35 4.4 47.3 1.0
N E:TYR38 4.4 55.1 1.0
O E:ALA36 4.5 51.3 1.0
CA E:TYR38 4.5 54.9 1.0

Chlorine binding site 10 out of 12 in 8gih

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Chlorine binding site 10 out of 12 in the Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of Hepatitis B Virus Capsid Y132A Mutant in Complex with Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:67.5
occ:1.00
 N E:ALA137 3.8 60.8 1.0
CB E:ALA137 3.8 56.5 1.0
O E:PRO135 4.0 56.0 1.0
CH2 E:TRP125 4.4 62.9 1.0
CA E:ALA137 4.5 59.3 1.0
CZ2 E:TRP125 4.6 65.5 1.0
CA E:ASN136 4.7 59.6 1.0
C E:ASN136 4.7 57.9 1.0

Reference:

S.D.Kuduk, L.G.Deratt, B.Stoops, P.Shaffer, A.M.Lam, C.Espiritu, R.Vogel, V.Lau, O.A.Flores, G.D.Hartman. Diazepinone Hbv Capsid Assembly Modulators. Bioorg Med Chem Lett V. 72 28823 2022.
ISSN: ESSN 1464-3405
PubMed: 35644301
DOI: 10.1016/J.BMCL.2022.128823
Page generated: Tue Apr 25 19:25:01 2023

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