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Yttrium in PDB 1r6q: Clpns with Fragments

Protein crystallography data

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

Yttrium Binding Sites:

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 1r6q

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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 1r6q

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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 1r6q

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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 1r6q

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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 1r6q

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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 1r6q

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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

Reference:

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
Page generated: Wed Dec 16 02:40:48 2020

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