Atomistry » Yttrium » PDB 1dde-3ph5 » 2r3c
Atomistry »
  Yttrium »
    PDB 1dde-3ph5 »
      2r3c »

Yttrium in PDB 2r3c: Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1

Protein crystallography data

The structure of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1, PDB code: 2r3c was solved by A.P.Vandemark, B.Welch, A.Heroux, C.P.Hill, M.S.Kay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.73
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 46.843, 46.843, 137.079, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 23

Other elements in 2r3c:

The structure of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 (pdb code 2r3c). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 5 binding sites of Yttrium where determined in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1, PDB code: 2r3c:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5;

Yttrium binding site 1 out of 5 in 2r3c

Go back to Yttrium Binding Sites List in 2r3c
Yttrium binding site 1 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y501

b:28.4
occ:1.00
O C:HOH113 2.3 26.6 1.0
OE2 C:DGL9 2.4 27.7 1.0
OE2 A:GLU10 2.4 17.9 1.0
OE1 A:GLU10 2.5 22.6 1.0
O C:HOH107 2.5 28.5 1.0
OE1 C:DGL9 2.5 26.0 1.0
O A:HOH633 2.5 30.2 1.0
OD2 A:ASP7 2.8 29.9 1.0
CD A:GLU10 2.8 19.0 1.0
CD C:DGL9 2.8 26.0 1.0
CG A:ASP7 3.9 30.9 1.0
CG C:DGL9 4.3 26.7 1.0
CG A:GLU10 4.3 18.9 1.0
O A:HOH637 4.6 30.7 1.0
OD1 A:ASP7 4.6 33.6 1.0
O C:HOH119 4.7 29.6 1.0
O A:HOH616 4.7 42.8 1.0
CA A:ASP7 4.8 26.6 1.0
CB A:ASP7 4.9 27.9 1.0

Yttrium binding site 2 out of 5 in 2r3c

Go back to Yttrium Binding Sites List in 2r3c
Yttrium binding site 2 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y502

b:22.6
occ:0.33
OE1 A:GLN16 3.4 25.2 1.0
CG A:GLN16 3.8 21.7 1.0
CD A:GLN16 4.0 22.2 1.0
CD1 A:ILE19 4.2 19.6 1.0
CB A:GLN16 4.4 19.2 1.0
CA A:GLN16 4.5 19.1 1.0

Yttrium binding site 3 out of 5 in 2r3c

Go back to Yttrium Binding Sites List in 2r3c
Yttrium binding site 3 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y101

b:35.3
occ:1.00
OD1 B:ASP7 2.1 42.2 1.0
OE2 D:DGL9 2.3 23.5 1.0
O B:HOH222 2.3 29.6 1.0
OE1 D:DGL9 2.4 20.6 1.0
OE1 B:GLU10 2.4 36.3 1.0
O B:HOH206 2.5 27.3 1.0
CD D:DGL9 2.7 21.6 1.0
O D:HOH112 2.7 25.8 1.0
OE2 B:GLU10 2.7 36.1 1.0
CD B:GLU10 2.9 35.9 1.0
CG B:ASP7 3.3 44.0 1.0
OD2 B:ASP7 3.9 45.7 1.0
CG D:DGL9 4.2 22.4 1.0
O B:HOH275 4.3 41.4 1.0
O B:HOH218 4.4 28.3 1.0
CB B:ASP7 4.4 43.2 1.0
CG B:GLU10 4.4 32.3 1.0
CA B:ASP7 4.5 42.4 1.0
O D:HOH116 4.5 19.6 1.0
O B:HOH235 4.6 43.0 1.0

Yttrium binding site 4 out of 5 in 2r3c

Go back to Yttrium Binding Sites List in 2r3c
Yttrium binding site 4 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y102

b:25.6
occ:0.33
NE2 B:GLN16 3.2 22.7 1.0
CG B:GLN16 3.6 22.2 1.0
CD B:GLN16 3.9 22.7 1.0
CB B:GLN16 4.1 20.3 1.0
CD1 B:ILE19 4.4 19.4 1.0
CA B:GLN16 4.4 20.2 1.0

Yttrium binding site 5 out of 5 in 2r3c

Go back to Yttrium Binding Sites List in 2r3c
Yttrium binding site 5 out of 5 in the Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Structure of the GP41 N-Peptide in Complex with the Hiv Entry Inhibitor PIE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y103

b:32.4
occ:0.33
OG1 B:THR33 2.8 21.8 1.0
CB B:THR33 3.3 20.1 1.0
CD1 B:LEU30 3.6 20.5 1.0
CG2 B:THR33 3.7 20.2 1.0
CA B:THR33 4.8 20.4 1.0
O B:LEU30 5.0 23.4 1.0

Reference:

B.D.Welch, A.P.Vandemark, A.Heroux, C.P.Hill, M.S.Kay. Potent D-Peptide Inhibitors of Hiv-1 Entry Proc.Natl.Acad.Sci.Usa V. 104 16828 2007.
ISSN: ISSN 0027-8424
PubMed: 17942675
DOI: 10.1073/PNAS.0708109104
Page generated: Wed Dec 16 02:40:51 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy