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Zinc 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:

Chlorine (Cl) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of A 60 Nm Small Molecule Bound to A Hot Spot on Il-2, PDB code: 1py2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1py2

Go back to Zinc Binding Sites List in 1py2
Zinc binding site 1 out of 3 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 Zinc with other atoms in the Zn 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
B:Zn601

b:0.5
occ:1.00
OD1 B:ASP20 2.3 42.8 1.0
NE2 B:HIS16 2.3 48.1 1.0
OD2 B:ASP20 3.0 41.4 1.0
CG B:ASP20 3.0 41.6 1.0
CD2 B:HIS16 3.1 47.5 1.0
CE1 B:HIS16 3.4 48.2 1.0
CG B:HIS16 4.3 46.9 1.0
ND1 B:HIS16 4.4 47.7 1.0
CB B:ASP20 4.5 39.8 1.0
O B:HIS16 4.8 45.1 1.0
CD1 B:LEU85 4.8 59.9 1.0

Zinc binding site 2 out of 3 in 1py2

Go back to Zinc Binding Sites List in 1py2
Zinc binding site 2 out of 3 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 Zinc with other atoms in the Zn 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
C:Zn701

b:0.2
occ:1.00
NE2 C:HIS16 2.2 61.0 1.0
CE1 C:HIS16 3.0 60.9 1.0
CD2 C:HIS16 3.3 59.5 1.0
ND1 C:HIS16 4.2 59.6 1.0
OD1 C:ASP20 4.4 49.1 1.0
CG C:HIS16 4.4 58.1 1.0
ND2 C:ASN88 4.4 65.0 1.0

Zinc binding site 3 out of 3 in 1py2

Go back to Zinc Binding Sites List in 1py2
Zinc binding site 3 out of 3 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 Zinc with other atoms in the Zn 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:Zn801

b:0.5
occ:1.00
OE1 B:GLU15 2.7 62.4 1.0
OE2 B:GLU15 2.7 61.7 1.0
CD B:GLU15 3.1 60.6 1.0
CG B:GLU15 4.6 57.1 1.0
NE2 B:GLN11 4.7 66.3 1.0
O C:SER130 4.9 70.1 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: Wed Dec 16 03:01:23 2020

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