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Chlorine in PDB 5t2p: Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)

Protein crystallography data

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01), PDB code: 5t2p was solved by Z.Zhou, Z.H.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.04 / 1.69
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.927, 68.048, 85.703, 68.49, 69.99, 83.49
R / Rfree (%) 18 / 20.8

Other elements in 5t2p:

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) also contains other interesting chemical elements:

Fluorine (F) 24 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) (pdb code 5t2p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01), PDB code: 5t2p:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5t2p

Go back to Chlorine Binding Sites List in 5t2p
Chlorine binding site 1 out of 5 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:64.2
occ:1.00
 O C:HOH355 3.4 41.0 1.0
N C:ASP40 3.4 34.3 1.0
N C:ARG39 3.6 31.7 1.0
CG C:ASP40 3.7 54.1 1.0
OD2 C:ASP40 3.8 50.9 1.0
CB C:ASP40 3.8 44.3 1.0
C C:TYR38 4.1 33.4 1.0
CB C:ARG39 4.1 39.9 1.0
O C:LEU37 4.2 34.3 1.0
CA C:ARG39 4.2 32.1 1.0
CA C:ASP40 4.2 37.2 1.0
O C:ALA35 4.3 34.4 1.0
C C:ARG39 4.3 31.6 1.0
N C:TYR38 4.3 31.6 1.0
OD1 C:ASP40 4.3 50.2 1.0
O C:ALA36 4.3 36.8 1.0
C C:LEU37 4.3 35.1 1.0
CA C:TYR38 4.4 29.5 1.0
O C:TYR38 4.8 29.3 1.0
C C:ALA36 5.0 32.0 1.0

Chlorine binding site 2 out of 5 in 5t2p

Go back to Chlorine Binding Sites List in 5t2p
Chlorine binding site 2 out of 5 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl202

b:64.8
occ:1.00
 O E:ARG133 3.2 42.1 1.0
N D:ALA137 3.3 40.1 1.0
CA D:ASN136 3.8 36.5 1.0
O D:PRO135 3.9 40.4 1.0
CB D:ALA137 3.9 47.0 1.0
C E:ARG133 4.0 41.4 1.0
C D:ASN136 4.1 29.9 1.0
CD E:PRO135 4.2 40.5 1.0
CA E:PRO134 4.2 46.4 1.0
CA D:ALA137 4.2 41.2 1.0
O D:HOH314 4.3 51.6 1.0
N E:PRO134 4.4 42.4 1.0
OD1 D:ASN136 4.5 44.9 1.0
CH2 D:TRP125 4.5 30.9 1.0
O E:ALA131 4.6 58.1 1.0
N E:PRO135 4.6 41.4 1.0
CB D:ASN136 4.6 39.1 1.0
C E:PRO134 4.7 37.1 1.0
C D:PRO135 4.7 37.9 1.0
O E:PRO130 4.8 54.2 1.0
N D:ASN136 4.8 35.7 1.0
CZ2 D:TRP125 4.8 28.0 1.0
N E:ARG133 4.8 43.0 1.0
C E:ALA132 5.0 43.6 1.0

Chlorine binding site 3 out of 5 in 5t2p

Go back to Chlorine Binding Sites List in 5t2p
Chlorine binding site 3 out of 5 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl203

b:56.8
occ:1.00
 N D:ASP40 3.3 30.2 1.0
O D:HOH374 3.3 36.2 1.0
N D:ARG39 3.6 24.9 1.0
CG D:ASP40 3.6 43.6 1.0
OD2 D:ASP40 3.7 48.8 1.0
CB D:ASP40 3.7 35.3 1.0
C D:TYR38 4.0 27.0 1.0
CA D:ASP40 4.1 30.6 1.0
OD1 D:ASP40 4.1 40.2 1.0
O D:HOH310 4.1 60.8 1.0
O D:LEU37 4.2 27.4 1.0
CA D:ARG39 4.2 27.1 1.0
C D:ARG39 4.2 26.6 1.0
CB D:ARG39 4.3 29.8 1.0
N D:TYR38 4.3 26.9 1.0
CA D:TYR38 4.3 24.3 1.0
C D:LEU37 4.4 28.4 1.0
O D:ALA36 4.4 30.2 1.0
O D:ALA35 4.5 27.0 1.0
O D:TYR38 4.8 25.5 1.0

Chlorine binding site 4 out of 5 in 5t2p

Go back to Chlorine Binding Sites List in 5t2p
Chlorine binding site 4 out of 5 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl202

b:62.6
occ:1.00
 O E:HOH349 3.3 42.3 1.0
OD2 E:ASP40 3.5 54.3 1.0
N E:ASP40 3.7 34.5 1.0
N E:ARG39 3.8 31.3 0.5
CG E:ASP40 3.8 47.9 1.0
N E:ARG39 3.8 31.2 0.5
CB E:ASP40 4.0 42.5 1.0
O E:LEU37 4.1 29.3 1.0
O E:HOH393 4.2 65.8 1.0
C E:LEU37 4.3 31.4 1.0
C E:TYR38 4.3 30.6 1.0
O E:ALA36 4.3 33.2 1.0
N E:TYR38 4.4 29.4 1.0
CA E:TYR38 4.5 24.9 1.0
CA E:ASP40 4.5 35.2 1.0
OD1 E:ASP40 4.5 45.2 1.0
CA E:ARG39 4.5 32.5 0.5
CA E:ARG39 4.6 32.5 0.5
CB E:ARG39 4.6 34.4 0.5
O E:ALA35 4.6 33.9 1.0
C E:ARG39 4.6 32.2 0.5
C E:ARG39 4.6 32.1 0.5
CB E:ARG39 4.7 34.6 0.5
NH1 E:ARG39 4.9 55.3 0.5
O E:HOH370 4.9 48.2 1.0

Chlorine binding site 5 out of 5 in 5t2p

Go back to Chlorine Binding Sites List in 5t2p
Chlorine binding site 5 out of 5 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl202

b:76.7
occ:1.00
 O F:HOH357 3.0 34.8 1.0
OD2 F:ASP40 3.5 66.8 1.0
CG F:ASP40 3.8 58.4 1.0
N F:ASP40 3.9 37.5 1.0
O F:LEU37 4.0 39.0 1.0
CB F:ASP40 4.0 51.7 1.0
N F:ARG39 4.1 34.8 1.0
C F:LEU37 4.3 32.9 1.0
O F:ALA36 4.3 40.2 1.0
OD1 F:ASP40 4.5 58.8 1.0
N F:TYR38 4.5 31.8 1.0
C F:TYR38 4.6 34.3 1.0
O F:HOH351 4.6 52.9 1.0
CA F:ASP40 4.6 44.2 1.0
CA F:TYR38 4.7 33.4 1.0
CA F:ARG39 4.9 42.1 1.0
O F:HOH365 4.9 49.6 1.0
C F:ARG39 4.9 41.0 1.0
CB F:ARG39 4.9 45.2 1.0
O F:ALA35 5.0 39.0 1.0

Reference:

Z.Zhou, T.Hu, X.Zhou, S.Wildum, F.Garcia-Alcalde, Z.H.Xu, D.Wu, Y.Mao, X.Tian, Y.Zhou, F.Shen, Z.Zhang, G.Tang, I.Najera, G.Yang, H.C.Shen, J.A.T.Young, N.Qin. Heteroaryldihydropyrimidine (Hap) and Sulfamoylbenzamide (Sba) Inhibit Hepatitis B Virus Replication By Different Molecular Mechanisms Sci Rep V. 7 42374 2017.
ISSN: ESSN 2045-2322
DOI: 10.1038/SREP42374
Page generated: Fri Jul 26 17:16:57 2024

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