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Chlorine in PDB 3ur9: 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor

Enzymatic activity of 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor

All present enzymatic activity of 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor:
3.4.22.66;

Protein crystallography data

The structure of 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor, PDB code: 3ur9 was solved by S.Lovell, K.P.Battaile, Y.Kim, K.C.Tiew, S.R.Mandadapu, K.R.Alliston, W.C.Groutas, K.O.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.68 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.649, 66.865, 125.109, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor (pdb code 3ur9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor, PDB code: 3ur9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3ur9

Go back to Chlorine Binding Sites List in 3ur9
Chlorine binding site 1 out of 4 in the 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:13.4
occ:1.00
 CL B:CL201 2.8 12.8 1.0
O B:HOH305 3.1 21.4 1.0
NZ A:LYS88 3.2 12.8 1.0
CA A:SER7 3.6 12.9 1.0
O B:HOH370 3.6 25.8 1.0
N A:SER7 3.7 12.3 1.0
C A:TRP6 3.8 11.3 1.0
O A:TRP6 3.8 10.9 1.0
CE A:LYS88 3.8 13.2 1.0
CB A:TRP6 4.1 13.0 1.0
CB A:SER7 4.1 12.3 1.0
CD2 B:LEU94 4.1 16.9 1.0
CE B:LYS88 4.5 13.3 1.0
O A:PRO3 4.5 15.0 1.0
O A:HOH344 4.6 29.2 1.0
CD1 B:LEU94 4.6 24.8 1.0
CA A:TRP6 4.6 10.4 1.0
NZ B:LYS88 4.6 12.3 1.0
CG B:LEU94 4.8 19.4 1.0
C A:SER7 4.8 12.1 1.0
O B:HOH313 4.8 24.2 1.0
O A:HOH333 4.9 24.8 1.0

Chlorine binding site 2 out of 4 in 3ur9

Go back to Chlorine Binding Sites List in 3ur9
Chlorine binding site 2 out of 4 in the 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:25.1
occ:1.00
 NH2 A:ARG147 3.3 27.3 1.0
CG A:PRO78 3.6 22.9 1.0
CD A:PRO78 3.7 17.8 1.0
NE A:ARG147 3.8 34.5 1.0
NE2 A:HIS145 3.9 20.1 1.0
CZ A:ARG147 4.1 26.4 1.0
CD2 A:HIS145 4.7 15.0 1.0
CE1 A:HIS145 4.8 16.3 1.0
CB A:PRO78 4.8 22.6 1.0
O A:HOH312 5.0 20.4 1.0

Chlorine binding site 3 out of 4 in 3ur9

Go back to Chlorine Binding Sites List in 3ur9
Chlorine binding site 3 out of 4 in the 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:12.8
occ:1.00
 CL A:CL201 2.8 13.4 1.0
O A:HOH311 3.1 21.2 1.0
NZ B:LYS88 3.3 12.3 1.0
O B:HOH370 3.4 25.8 1.0
CA B:SER7 3.6 11.3 1.0
N B:SER7 3.7 11.6 1.0
CE B:LYS88 3.8 13.3 1.0
C B:TRP6 3.9 12.8 1.0
O B:TRP6 3.9 11.7 1.0
CB B:SER7 4.0 12.1 1.0
CB B:TRP6 4.1 13.4 1.0
CD2 A:LEU94 4.1 17.4 1.0
O B:PRO3 4.5 15.3 1.0
CD1 A:LEU94 4.5 26.8 1.0
CE A:LYS88 4.5 13.2 1.0
NZ A:LYS88 4.6 12.8 1.0
CA B:TRP6 4.6 12.7 1.0
CG A:LEU94 4.7 19.3 1.0
C B:SER7 4.8 11.1 1.0
O B:HOH301 4.9 19.8 1.0
O A:HOH336 4.9 23.8 1.0

Chlorine binding site 4 out of 4 in 3ur9

Go back to Chlorine Binding Sites List in 3ur9
Chlorine binding site 4 out of 4 in the 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 1.65A Resolution Structure of Norwalk Virus Protease Containing A Covalently Bound Dipeptidyl Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:14.8
occ:1.00
 O B:HOH304 3.3 22.9 1.0
NE B:ARG8 3.3 18.4 1.0
CG2 B:THR4 3.3 16.1 0.5
NH2 B:ARG8 3.4 20.5 1.0
OG1 B:THR4 3.4 18.9 0.5
N B:LEU5 3.7 14.3 1.0
CB B:THR4 3.7 18.5 0.5
CZ B:ARG8 3.8 21.2 1.0
CA B:LEU5 3.9 13.9 1.0
C B:THR4 3.9 16.4 1.0
CB B:THR4 4.0 17.3 0.5
CB B:LEU5 4.2 18.0 1.0
O B:THR4 4.2 15.3 1.0
CD B:ARG8 4.5 16.1 1.0
CA B:THR4 4.5 16.3 0.5
CA B:THR4 4.6 16.1 0.5
CD1 B:LEU5 4.7 24.9 1.0
OG1 B:THR69 4.7 45.0 1.0
OG1 B:THR4 4.9 18.1 0.5

Reference:

Y.Kim, S.Lovell, K.C.Tiew, S.R.Mandadapu, K.R.Alliston, K.P.Battaile, W.C.Groutas, K.O.Chang. Broad-Spectrum Antivirals Against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses. J.Virol. V. 86 11754 2012.
ISSN: ISSN 0022-538X
PubMed: 22915796
DOI: 10.1128/JVI.01348-12
Page generated: Sat Dec 12 10:15:49 2020

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