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Chlorine in PDB 1py2: Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2

Protein crystallography data

The structure of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2, PDB code: 1py2 was solved by C.D.Thanos, M.Randal, J.A.Wells, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.982, 52.448, 89.469, 90.00, 106.34, 90.00
R / Rfree (%) 27.1 / 32

Other elements in 1py2:

The structure of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 (pdb code 1py2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2, PDB code: 1py2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 1py2

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Chlorine binding site 1 out of 8 in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:55.6
occ:1.00
 CL8 A:FRH201 0.0 55.6 1.0
C21 A:FRH201 1.8 60.0 1.0
C16 A:FRH201 2.7 63.6 1.0
C24 A:FRH201 2.8 62.3 1.0
C13 A:FRH201 3.1 58.4 1.0
CL9 A:FRH201 3.1 63.3 1.0
C11 A:FRH201 3.2 54.4 1.0
CB A:LEU72 3.8 62.3 1.0
CG2 A:VAL69 3.8 49.2 1.0
C30 A:FRH201 4.0 69.7 1.0
C10 A:FRH201 4.1 70.0 1.0
CD1 A:LEU72 4.1 60.8 1.0
CA A:MET39 4.2 56.8 1.0
O A:ARG38 4.2 61.4 1.0
N7 A:FRH201 4.3 60.1 1.0
C23 A:FRH201 4.3 53.7 1.0
CG A:MET39 4.3 56.1 1.0
O A:VAL69 4.4 50.8 1.0
CD2 A:PHE42 4.5 44.9 1.0
CG A:LEU72 4.6 62.4 1.0
C33 A:FRH201 4.6 73.3 1.0
C A:ARG38 4.7 61.9 1.0
N A:MET39 4.8 59.9 1.0
CB A:PHE42 4.8 45.7 1.0
CB A:MET39 4.8 57.0 1.0
C A:LEU72 4.8 64.8 1.0
CA A:VAL69 4.8 49.1 1.0
O A:LEU72 4.9 68.2 1.0
CB A:VAL69 4.9 48.1 1.0
N3 A:FRH201 4.9 58.0 1.0
O A:MET39 4.9 53.2 1.0
CA A:LEU72 4.9 63.2 1.0
C A:MET39 5.0 55.0 1.0

Chlorine binding site 2 out of 8 in 1py2

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Chlorine binding site 2 out of 8 in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:63.3
occ:1.00
 CL9 A:FRH201 0.0 63.3 1.0
C16 A:FRH201 1.8 63.6 1.0
C30 A:FRH201 2.8 69.7 1.0
C21 A:FRH201 2.8 60.0 1.0
O43 A:FRH201 3.0 74.0 1.0
CL8 A:FRH201 3.1 55.6 1.0
CG A:MET39 3.6 56.1 1.0
CB A:ALA73 3.8 63.3 1.0
CB A:MET39 3.9 57.0 1.0
CA A:ALA73 3.9 64.8 1.0
CA A:MET39 4.0 56.8 1.0
C33 A:FRH201 4.1 73.3 1.0
C24 A:FRH201 4.1 62.3 1.0
O A:LEU72 4.1 68.2 1.0
N A:MET39 4.1 59.9 1.0
C35 A:FRH201 4.2 79.9 1.0
O A:LYS35 4.2 65.8 1.0
N A:ALA73 4.3 63.5 1.0
C A:LEU72 4.4 64.8 1.0
CE A:LYS35 4.4 66.4 1.0
C A:ARG38 4.6 61.9 1.0
C10 A:FRH201 4.6 70.0 1.0
SD A:MET39 4.7 56.1 1.0
CG A:LYS35 4.7 69.2 1.0
CB A:ARG38 4.8 66.8 1.0
O A:ARG38 4.8 61.4 1.0
O A:VAL69 4.9 50.8 1.0
CE A:MET39 5.0 55.0 1.0

Chlorine binding site 3 out of 8 in 1py2

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Chlorine binding site 3 out of 8 in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:63.2
occ:1.00
 CL8 B:FRH301 0.0 63.2 1.0
C21 B:FRH301 1.8 64.8 1.0
C16 B:FRH301 2.8 69.9 1.0
C24 B:FRH301 2.8 63.5 1.0
C13 B:FRH301 3.1 60.1 1.0
C11 B:FRH301 3.1 56.8 1.0
CL9 B:FRH301 3.2 75.9 1.0
CG2 B:VAL69 3.7 48.0 1.0
CA B:MET39 3.9 50.5 1.0
CD1 B:LEU72 3.9 53.8 1.0
O B:ARG38 3.9 55.0 1.0
CB B:LEU72 4.0 56.4 1.0
C30 B:FRH301 4.1 72.7 1.0
C10 B:FRH301 4.1 68.0 1.0
CG B:MET39 4.3 51.5 1.0
C23 B:FRH301 4.3 57.4 1.0
CD2 B:PHE42 4.3 44.4 1.0
N7 B:FRH301 4.3 62.5 1.0
O B:VAL69 4.5 50.3 1.0
CB B:MET39 4.5 51.1 1.0
C B:ARG38 4.5 54.9 1.0
N B:MET39 4.6 52.8 1.0
O B:MET39 4.6 48.2 1.0
CG B:LEU72 4.6 55.7 1.0
C33 B:FRH301 4.6 71.5 1.0
CB B:PHE42 4.6 44.0 1.0
C B:MET39 4.7 49.1 1.0
CB B:VAL69 4.7 47.8 1.0
CA B:VAL69 4.8 49.0 1.0
N3 B:FRH301 4.9 62.0 1.0
CG B:PHE42 4.9 43.7 1.0

Chlorine binding site 4 out of 8 in 1py2

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Chlorine binding site 4 out of 8 in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:75.9
occ:1.00
 CL9 B:FRH301 0.0 75.9 1.0
C16 B:FRH301 1.8 69.9 1.0
C30 B:FRH301 2.7 72.7 1.0
C21 B:FRH301 2.8 64.8 1.0
O43 B:FRH301 2.9 78.9 1.0
CL8 B:FRH301 3.2 63.2 1.0
CG B:MET39 3.6 51.5 1.0
CB B:MET39 3.6 51.1 1.0
CB B:ALA73 3.6 62.9 1.0
CA B:ALA73 3.7 64.7 1.0
CA B:MET39 3.9 50.5 1.0
N B:ALA73 4.0 62.8 1.0
O B:LEU72 4.0 63.6 1.0
C33 B:FRH301 4.1 71.5 1.0
C24 B:FRH301 4.1 63.5 1.0
C B:LEU72 4.1 61.8 1.0
N B:MET39 4.2 52.8 1.0
C35 B:FRH301 4.3 82.6 1.0
O B:LYS35 4.4 55.7 1.0
C10 B:FRH301 4.6 68.0 1.0
O B:VAL69 4.6 50.3 1.0
CB B:LEU72 4.6 56.4 1.0
C B:ARG38 4.7 54.9 1.0
SD B:MET39 4.7 52.4 1.0
O B:ARG38 4.9 55.0 1.0

Chlorine binding site 5 out of 8 in 1py2

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Chlorine binding site 5 out of 8 in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:0.9
occ:1.00
 CL8 C:FRH401 0.0 0.9 1.0
C21 C:FRH401 1.8 1.0 1.0
C16 C:FRH401 2.8 0.8 1.0
C24 C:FRH401 2.8 0.9 1.0
C13 C:FRH401 3.1 0.5 1.0
OG1 C:THR41 3.1 61.8 1.0
N C:MET39 3.1 66.6 1.0
C11 C:FRH401 3.2 0.7 1.0
CL9 C:FRH401 3.2 0.4 1.0
CA C:MET39 3.5 62.2 1.0
CB C:ARG38 4.0 74.2 1.0
C30 C:FRH401 4.1 1.0 1.0
C10 C:FRH401 4.1 0.9 1.0
N7 C:FRH401 4.1 0.4 1.0
C C:ARG38 4.2 69.8 1.0
CD2 C:LEU72 4.2 65.7 1.0
C23 C:FRH401 4.3 0.3 1.0
CD C:ARG38 4.3 78.8 1.0
C C:MET39 4.3 60.2 1.0
CB C:THR41 4.4 61.6 1.0
N C:PHE42 4.5 55.4 1.0
CA C:ARG38 4.5 72.8 1.0
NE C:ARG38 4.5 80.7 1.0
C33 C:FRH401 4.6 0.4 1.0
CB C:PHE42 4.7 52.9 1.0
O C:MET39 4.7 59.5 1.0
N3 C:FRH401 4.7 0.1 1.0
CB C:MET39 4.7 61.3 1.0
CG C:ARG38 4.8 77.8 1.0
N C:THR41 4.9 58.0 1.0

Chlorine binding site 6 out of 8 in 1py2

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Chlorine binding site 6 out of 8 in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:0.4
occ:1.00
 CL9 C:FRH401 0.0 0.4 1.0
C16 C:FRH401 1.8 0.8 1.0
C30 C:FRH401 2.8 1.0 1.0
C21 C:FRH401 2.8 1.0 1.0
O43 C:FRH401 3.0 0.8 1.0
CL8 C:FRH401 3.2 0.9 1.0
N C:MET39 3.3 66.6 1.0
C39 C:FRH401 3.5 0.8 1.0
CA C:MET39 3.6 62.2 1.0
CB C:ARG38 3.7 74.2 1.0
CB C:MET39 3.8 61.3 1.0
C33 C:FRH401 4.1 0.4 1.0
C24 C:FRH401 4.1 0.9 1.0
C C:ARG38 4.1 69.8 1.0
C35 C:FRH401 4.1 0.1 1.0
C18 C:FRH401 4.1 0.3 1.0
CG C:MET39 4.3 59.8 1.0
CB C:ALA73 4.4 71.8 1.0
C12 C:FRH401 4.4 0.5 1.0
CA C:ARG38 4.5 72.8 1.0
C10 C:FRH401 4.6 0.9 1.0
CB C:LEU72 4.6 65.2 1.0
O C:LEU72 4.7 69.5 1.0
CG C:ARG38 4.8 77.8 1.0
C C:LEU72 4.9 68.1 1.0
O C:ARG38 4.9 70.3 1.0
CD2 C:LEU72 4.9 65.7 1.0
CG C:LEU72 4.9 66.9 1.0

Chlorine binding site 7 out of 8 in 1py2

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Chlorine binding site 7 out of 8 in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:67.2
occ:1.00
 CL8 D:FRH501 0.0 67.2 1.0
C21 D:FRH501 1.8 71.2 1.0
C16 D:FRH501 2.7 75.8 1.0
C24 D:FRH501 2.8 71.2 1.0
CL9 D:FRH501 3.1 79.4 1.0
C13 D:FRH501 3.1 69.0 1.0
C11 D:FRH501 3.1 63.6 1.0
O D:ARG38 3.2 55.4 1.0
CA D:MET39 3.9 53.0 1.0
C D:ARG38 4.0 55.7 1.0
C30 D:FRH501 4.1 80.0 1.0
C10 D:FRH501 4.1 75.8 1.0
CG2 D:VAL69 4.2 47.6 1.0
C23 D:FRH501 4.2 65.2 1.0
N7 D:FRH501 4.3 75.2 1.0
N D:MET39 4.3 55.1 1.0
CD1 D:LEU72 4.3 52.1 1.0
O D:MET39 4.3 51.9 1.0
CB D:PHE42 4.4 44.7 1.0
CD2 D:PHE42 4.4 44.1 1.0
OG1 D:THR41 4.4 48.5 1.0
C D:MET39 4.5 52.4 1.0
C33 D:FRH501 4.6 79.8 1.0
N3 D:FRH501 4.8 72.8 1.0
CG D:PHE42 4.8 44.1 1.0
CB D:MET39 4.9 53.8 1.0
CB D:LEU72 4.9 52.5 1.0
N D:PHE42 4.9 47.1 1.0
CG D:MET39 5.0 54.0 1.0

Chlorine binding site 8 out of 8 in 1py2

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Chlorine binding site 8 out of 8 in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:79.4
occ:1.00
 CL9 D:FRH501 0.0 79.4 1.0
C16 D:FRH501 1.8 75.8 1.0
C21 D:FRH501 2.7 71.2 1.0
C30 D:FRH501 2.8 80.0 1.0
O43 D:FRH501 3.1 86.1 1.0
CL8 D:FRH501 3.1 67.2 1.0
C35 D:FRH501 3.3 94.0 1.0
SD D:MET39 3.5 56.2 1.0
CA D:MET39 4.0 53.0 1.0
C24 D:FRH501 4.0 71.2 1.0
CB D:MET39 4.1 53.8 1.0
CG D:MET39 4.1 54.0 1.0
C33 D:FRH501 4.1 79.8 1.0
CA D:ALA73 4.1 59.2 1.0
N D:ALA73 4.2 56.9 1.0
CB D:ALA73 4.3 58.9 1.0
N D:MET39 4.3 55.1 1.0
C18 D:FRH501 4.4 0.4 1.0
C D:LEU72 4.5 55.5 1.0
O D:VAL69 4.6 48.5 1.0
C10 D:FRH501 4.6 75.8 1.0
O D:LEU72 4.6 56.5 1.0
O D:LYS35 4.6 54.8 1.0
CB D:LEU72 4.6 52.5 1.0
O D:ARG38 4.6 55.4 1.0
C D:ARG38 4.7 55.7 1.0
CG2 D:VAL69 4.8 47.6 1.0
CE D:MET39 4.8 55.5 1.0

Reference:

C.D.Thanos, M.Randal, J.A.Wells. Potent Small-Molecule Binding to A Dynamic Hot Spot on Il-2. J.Am.Chem.Soc. V. 125 15280 2003.
ISSN: ISSN 0002-7863
PubMed: 14664558
DOI: 10.1021/JA0382617
Page generated: Thu Jul 10 18:54:50 2025

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