Yttrium in PDB 1r6q: Clpns with Fragments

The structure of Clpns with Fragments, PDB code: 1r6q was solved by D.Xia, M.R.Maurizi, F.Guo, S.K.Singh, L.Esser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.35
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.913, 87.913, 209.420, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.3

The binding sites of Yttrium atom in the Clpns with Fragments (pdb code 1r6q). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 6 binding sites of Yttrium where determined in the Clpns with Fragments, PDB code: 1r6q:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6;

Yttrium binding site 1 out of 6 in the Clpns with Fragments


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Clpns with Fragments within 5.0Å range: probe atom residue distance (Å) B Occ A:Y144 b:65.8 occ:1.00 Y1 A:YBT144 0.0 65.8 1.0 O1 A:YBT144 2.3 72.1 1.0 O4 A:YBT144 2.3 71.8 1.0 O5 A:YBT144 2.3 69.6 1.0 O2 A:YBT144 2.4 76.6 1.0 OE1 A:GLU45 2.4 26.8 1.0 OE1 A:GLU42 2.5 32.8 1.0 OE2 A:GLU42 2.9 26.6 1.0 N1 A:YBT144 2.9 72.1 1.0 CD A:GLU42 3.1 27.4 1.0 C6 A:YBT144 3.2 71.4 1.0 C8 A:YBT144 3.2 72.9 1.0 C1 A:YBT144 3.3 74.3 1.0 C2 A:YBT144 3.3 76.9 1.0 C3 A:YBT144 3.3 73.3 1.0 CD A:GLU45 3.5 28.1 1.0 C7 A:YBT144 3.5 73.5 1.0 C5 A:YBT144 3.6 69.0 1.0 OE2 A:GLU45 3.8 26.8 1.0 O A:HOH183 4.5 58.2 1.0 CG A:GLU42 4.6 26.1 1.0 CG A:GLU45 4.8 23.2 1.0 C4 A:YBT144 4.8 81.5 1.0 NE A:ARG41 4.9 29.8 1.0 CB A:GLU45 4.9 19.1 1.0

Yttrium binding site 2 out of 6 in the Clpns with Fragments


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Clpns with Fragments within 5.0Å range: probe atom residue distance (Å) B Occ A:Y145 b:74.8 occ:0.70 Y1 A:YBT145 0.0 74.8 0.7 O2 A:YBT145 2.3 75.2 0.7 O5 A:YBT145 2.3 73.0 0.7 O1 A:YBT145 2.3 76.9 0.7 O4 A:YBT145 2.3 77.0 0.7 OE1 A:GLU7 2.5 52.1 1.0 N1 A:YBT145 2.9 78.4 0.7 CD A:GLU7 3.2 46.6 1.0 C8 A:YBT145 3.2 76.6 0.7 C1 A:YBT145 3.3 78.9 0.7 C2 A:YBT145 3.3 77.0 0.7 C6 A:YBT145 3.3 77.7 0.7 C3 A:YBT145 3.3 79.9 0.7 OE2 A:GLU7 3.3 55.2 1.0 OE2 D:GLU56 3.4 26.6 1.0 OE1 D:GLU56 3.4 44.4 1.0 C7 A:YBT145 3.5 76.7 0.7 C5 A:YBT145 3.7 79.6 0.7 CD D:GLU56 3.7 42.5 1.0 O A:HOH198 4.0 60.2 1.0 CG A:GLU7 4.5 37.2 1.0 Y C:Y1107 4.6 68.0 0.3 C4 A:YBT145 4.8 84.8 0.7 OD2 C:ASP11 5.0 94.6 1.0

Yttrium binding site 3 out of 6 in the Clpns with Fragments


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Clpns with Fragments within 5.0Å range: probe atom residue distance (Å) B Occ B:Y144 b:45.3 occ:1.00 Y1 B:YBT144 0.0 45.3 1.0 O1 B:YBT144 2.3 53.3 1.0 O5 B:YBT144 2.3 47.8 1.0 O4 B:YBT144 2.4 53.5 1.0 O2 B:YBT144 2.4 53.9 1.0 OD1 B:ASN3 2.4 24.5 1.0 OE2 B:GLU102 2.5 23.7 1.0 N1 B:YBT144 2.9 48.8 1.0 C8 B:YBT144 3.2 55.3 1.0 C6 B:YBT144 3.3 52.2 1.0 C1 B:YBT144 3.3 57.1 1.0 C2 B:YBT144 3.3 56.2 1.0 C3 B:YBT144 3.3 55.4 1.0 CD B:GLU102 3.5 37.5 1.0 CG B:ASN3 3.5 15.9 1.0 C7 B:YBT144 3.5 52.7 1.0 C5 B:YBT144 3.6 52.8 1.0 OE1 B:GLU102 3.8 35.7 1.0 O B:HOH175 4.1 50.3 1.0 ND2 B:ASN3 4.4 28.6 1.0 CB B:ASN3 4.4 12.8 1.0 CA B:ASN3 4.5 16.3 1.0 N B:GLN4 4.5 13.3 0.8 O B:HOH209 4.6 53.3 1.0 OE1 B:GLU5 4.6 37.3 0.8 C4 B:YBT144 4.8 68.7 1.0 CG B:GLN4 4.9 18.0 0.8 CG B:GLU102 4.9 31.5 1.0

Yttrium binding site 4 out of 6 in the Clpns with Fragments


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Clpns with Fragments within 5.0Å range: probe atom residue distance (Å) B Occ B:Y145 b:61.0 occ:1.00 Y1 B:YBT145 0.0 61.0 1.0 O5 B:YBT145 2.3 59.3 1.0 O1 B:YBT145 2.3 64.0 1.0 O4 B:YBT145 2.3 68.8 1.0 O2 B:YBT145 2.4 70.0 1.0 OE1 B:GLU45 2.5 31.7 1.0 OE1 B:GLU42 2.6 34.1 1.0 OE2 B:GLU42 2.9 22.4 1.0 N1 B:YBT145 2.9 62.5 1.0 CD B:GLU42 3.1 25.1 1.0 C6 B:YBT145 3.2 65.2 1.0 C8 B:YBT145 3.2 64.4 1.0 C1 B:YBT145 3.3 68.9 1.0 C2 B:YBT145 3.3 66.9 1.0 C3 B:YBT145 3.3 63.5 1.0 CD B:GLU45 3.5 23.3 1.0 C7 B:YBT145 3.5 64.6 1.0 C5 B:YBT145 3.6 64.1 1.0 OE2 B:GLU45 3.9 28.9 1.0 O B:HOH167 4.6 52.1 1.0 CG B:GLU42 4.6 18.9 1.0 CG B:GLU45 4.8 20.5 1.0 NE B:ARG41 4.8 24.9 1.0 C4 B:YBT145 4.8 76.9 1.0 CB B:GLU45 4.9 20.0 1.0 NH2 B:ARG41 5.0 25.5 1.0

Yttrium binding site 5 out of 6 in the Clpns with Fragments


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Clpns with Fragments within 5.0Å range: probe atom residue distance (Å) B Occ C:Y107 b:68.0 occ:0.30 OD1 C:ASP11 2.3 91.7 1.0 OD1 C:ASP9 2.7 97.2 1.0 OD2 C:ASP9 3.1 0.9 1.0 CG C:ASP9 3.3 98.5 1.0 CG C:ASP11 3.3 90.5 1.0 O1 A:YBT145 3.4 76.9 0.7 O5 A:YBT145 3.4 73.0 0.7 OD2 C:ASP11 3.5 94.6 1.0 C2 A:YBT145 3.8 77.0 0.7 C8 A:YBT145 4.2 76.6 0.7 C7 A:YBT145 4.4 76.7 0.7 Y1 A:YBT145 4.6 74.8 0.7 CB C:ASP11 4.7 92.3 1.0 N C:ASP11 4.7 89.7 1.0 CB C:ASP9 4.8 91.8 1.0 C C:ASP11 5.0 94.1 1.0 CA C:ASP11 5.0 92.3 1.0

Yttrium binding site 6 out of 6 in the Clpns with Fragments


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 6 of Clpns with Fragments within 5.0Å range: probe atom residue distance (Å) B Occ D:Y107 b:0.5 occ:1.00 OD1 D:ASP9 2.2 100.0 1.0 OD1 D:ASP11 2.8 0.2 1.0 CG D:ASP9 3.4 0.4 1.0 OD2 D:ASP9 3.8 98.7 1.0 CG D:ASP11 3.8 0.1 1.0 OD2 D:ASP11 4.1 0.6 1.0 CB D:ASP9 4.6 99.9 1.0 CA D:ASP9 4.7 99.9 1.0 N D:ASP11 4.8 0.9 1.0 N D:PHE10 4.9 0.5 1.0 C D:ASP11 5.0 0.3 1.0

D.Xia, L.Esser, S.K.Singh, F.Guo, M.R.Maurizi. Crystallographic Investigation of Peptide Binding Sites in the N-Domain of the Clpa Chaperone. J.Struct.Biol. V. 146 166 2004.
ISSN: ISSN 1047-8477
PubMed: 15037248
DOI: 10.1016/J.JSB.2003.11.025