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: Sat Dec 12 12:27:32 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy