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Yttrium in PDB 1r6o: Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps

Protein crystallography data

The structure of Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps, PDB code: 1r6o 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 / 2.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.436, 87.436, 212.955, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 20.5

Other elements in 1r6o:

The structure of Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps (pdb code 1r6o). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 6 binding sites of Yttrium where determined in the Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps, PDB code: 1r6o:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6;

Yttrium binding site 1 out of 6 in 1r6o

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Yttrium binding site 1 out of 6 in the Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y412

b:69.4
occ:1.00
Y1 A:YBT412 0.0 69.4 1.0
O A:HOH417 2.0 53.8 1.0
O5 A:YBT412 2.3 71.0 1.0
O1 A:YBT412 2.3 75.8 1.0
O4 A:YBT412 2.3 76.9 1.0
O2 A:YBT412 2.4 79.6 1.0
OE1 A:GLU45 2.4 31.8 1.0
OE1 A:GLU42 2.5 32.1 1.0
OE2 A:GLU42 2.9 34.2 1.0
N1 A:YBT412 2.9 75.3 1.0
CD A:GLU42 3.1 34.3 1.0
C8 A:YBT412 3.2 77.7 1.0
C6 A:YBT412 3.3 76.5 1.0
C2 A:YBT412 3.3 79.0 1.0
C1 A:YBT412 3.3 79.3 1.0
C3 A:YBT412 3.3 79.4 1.0
CD A:GLU45 3.5 34.7 1.0
C7 A:YBT412 3.5 78.7 1.0
C5 A:YBT412 3.7 76.1 1.0
OE2 A:GLU45 3.9 36.4 1.0
CG A:GLU42 4.5 27.4 1.0
NE A:ARG41 4.7 36.4 1.0
CG A:GLU45 4.8 32.5 1.0
C4 A:YBT412 4.8 86.5 1.0
CB A:GLU45 4.9 25.9 1.0

Yttrium binding site 2 out of 6 in 1r6o

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Yttrium binding site 2 out of 6 in the Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y413

b:73.4
occ:1.00
Y1 A:YBT413 0.0 73.4 1.0
O2 A:YBT413 2.3 77.9 1.0
O1 A:YBT413 2.3 81.7 1.0
O5 A:YBT413 2.4 76.4 1.0
O4 A:YBT413 2.4 80.3 1.0
OE2 D:GLU56 2.4 36.2 1.0
OE2 A:GLU7 2.7 42.4 1.0
OE1 A:GLU7 2.7 40.3 1.0
O A:HOH445 2.7 65.2 1.0
N1 A:YBT413 2.9 79.3 1.0
CD A:GLU7 3.1 40.0 1.0
C8 A:YBT413 3.3 76.2 1.0
C1 A:YBT413 3.3 83.9 1.0
C2 A:YBT413 3.3 80.5 1.0
C3 A:YBT413 3.3 83.7 1.0
C6 A:YBT413 3.3 79.9 1.0
CD D:GLU56 3.5 27.8 1.0
C7 A:YBT413 3.6 75.8 1.0
C5 A:YBT413 3.7 82.1 1.0
OE1 D:GLU56 3.9 30.4 1.0
O D:HOH483 4.0 56.6 1.0
O A:HOH488 4.2 60.6 1.0
O C:HOH128 4.5 57.3 1.0
OD2 C:ASP11 4.5 92.0 1.0
CG A:GLU7 4.5 35.8 1.0
O A:HOH459 4.7 60.3 1.0
C4 A:YBT413 4.8 91.0 1.0
OD1 C:ASP11 4.8 88.0 1.0
CG D:GLU56 4.8 27.2 1.0

Yttrium binding site 3 out of 6 in 1r6o

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Yttrium binding site 3 out of 6 in the Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y413

b:50.0
occ:1.00
Y1 B:YBT413 0.0 50.0 1.0
OE2 B:GLU102 2.3 36.9 1.0
O1 B:YBT413 2.3 55.4 1.0
O5 B:YBT413 2.3 51.5 1.0
O2 B:YBT413 2.4 52.4 1.0
O4 B:YBT413 2.4 58.7 1.0
OD1 B:ASN3 2.4 26.4 1.0
N1 B:YBT413 2.8 52.7 1.0
C1 B:YBT413 3.2 59.8 1.0
C8 B:YBT413 3.3 54.4 1.0
C6 B:YBT413 3.3 53.3 1.0
C2 B:YBT413 3.3 58.1 1.0
CD B:GLU102 3.3 43.2 1.0
C3 B:YBT413 3.3 52.2 1.0
CG B:ASN3 3.5 26.7 1.0
C7 B:YBT413 3.5 48.6 1.0
C5 B:YBT413 3.6 53.6 1.0
OE1 B:GLU102 3.8 47.8 1.0
ND2 B:ASN3 4.2 31.5 1.0
O B:HOH445 4.2 60.4 1.0
CB B:ASN3 4.5 25.6 1.0
CG B:GLU102 4.5 38.9 1.0
N B:GLN4 4.6 23.1 1.0
OE1 B:GLU5 4.6 40.4 1.0
CA B:ASN3 4.6 25.9 1.0
O B:HOH455 4.6 54.2 1.0
C4 B:YBT413 4.8 64.9 1.0
CG B:GLN4 4.8 31.1 1.0

Yttrium binding site 4 out of 6 in 1r6o

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Yttrium binding site 4 out of 6 in the Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y414

b:62.5
occ:1.00
Y1 B:YBT414 0.0 62.5 1.0
O4 B:YBT414 2.3 70.8 1.0
O1 B:YBT414 2.3 74.2 1.0
O B:HOH419 2.3 52.3 1.0
O5 B:YBT414 2.3 69.7 1.0
O2 B:YBT414 2.4 76.8 1.0
OE1 B:GLU42 2.4 30.3 1.0
OE1 B:GLU45 2.5 31.2 1.0
OE2 B:GLU42 2.9 24.9 1.0
N1 B:YBT414 2.9 71.3 1.0
CD B:GLU42 3.0 30.5 1.0
C6 B:YBT414 3.2 73.3 1.0
C8 B:YBT414 3.3 72.2 1.0
C1 B:YBT414 3.3 76.5 1.0
C2 B:YBT414 3.3 76.6 1.0
C3 B:YBT414 3.3 73.2 1.0
CD B:GLU45 3.5 28.5 1.0
C7 B:YBT414 3.5 71.4 1.0
C5 B:YBT414 3.7 71.3 1.0
OE2 B:GLU45 3.9 31.7 1.0
CG B:GLU42 4.5 24.3 1.0
O B:HOH481 4.5 71.6 1.0
O B:HOH486 4.5 49.0 1.0
O B:HOH464 4.6 69.0 1.0
O B:HOH438 4.6 63.2 1.0
NE B:ARG41 4.7 34.6 1.0
CG B:GLU45 4.8 30.2 1.0
C4 B:YBT414 4.8 80.6 1.0
NH2 B:ARG41 4.9 30.8 1.0
CB B:GLU45 4.9 26.2 1.0

Yttrium binding site 5 out of 6 in 1r6o

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Yttrium binding site 5 out of 6 in the Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Y413

b:79.7
occ:1.00
ND1 D:HIS66 2.2 27.4 1.0
O D:HOH462 2.7 53.3 1.0
CG D:HIS66 3.1 25.5 1.0
CE1 D:HIS66 3.2 25.6 1.0
CB D:HIS66 3.4 27.2 1.0
OE2 A:GLU19 3.7 26.2 1.0
CA D:HIS66 4.0 27.7 1.0
OD1 D:ASN34 4.1 26.5 1.0
CD2 D:HIS66 4.2 27.5 1.0
NE2 D:HIS66 4.2 25.5 1.0
OE1 A:GLU19 4.2 34.4 1.0
CD A:GLU19 4.2 27.8 1.0

Yttrium binding site 6 out of 6 in 1r6o

Go back to Yttrium Binding Sites List in 1r6o
Yttrium binding site 6 out of 6 in the Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 6 of Atp-Dependent Clp Protease Atp-Binding Subunit Clpa/Atp-Dependent Clp Protease Adaptor Protein Clps within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Y414

b:0.5
occ:1.00
OD1 D:ASP9 2.3 0.2 1.0
OD1 D:ASP11 2.3 0.9 1.0
CG D:ASP9 3.4 0.6 1.0
CG D:ASP11 3.5 0.9 1.0
OD2 D:ASP9 3.9 0.0 1.0
OD2 D:ASP11 4.0 0.3 1.0
O D:ASP11 4.1 0.6 1.0
N D:ASP11 4.4 0.3 1.0
CB D:ASP9 4.6 0.4 1.0
CA D:ASP9 4.6 0.5 1.0
CB D:ASP11 4.7 0.2 1.0
CA D:ASP11 4.8 0.1 1.0
C D:ASP11 4.9 0.3 1.0
N D:PHE10 4.9 0.6 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 02:40:47 2020

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