Yttrium in PDB 1mbx: Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound

The structure of Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound, PDB code: 1mbx was solved by F.Guo, L.Esser, S.K.Singh, M.R.Maurizi, D.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.54 / 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 (%)	20.8 / 23.1

The structure of Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound also contains other interesting chemical elements:

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

The binding sites of Yttrium atom in the Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound (pdb code 1mbx). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 5 binding sites of Yttrium where determined in the Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound, PDB code: 1mbx:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5;

Yttrium binding site 1 out of 5 in the Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Y211 b:69.6 occ:1.00 Y1 A:YBT211 0.0 69.6 1.0 O A:HOH215 2.3 53.5 1.0 O4 A:YBT211 2.3 69.8 1.0 O5 A:YBT211 2.3 69.9 1.0 O2 A:YBT211 2.4 70.8 1.0 O1 A:YBT211 2.4 70.0 1.0 OE1 A:GLU45 2.4 55.4 1.0 OE1 A:GLU42 2.6 56.6 1.0 N1 A:YBT211 2.7 70.2 1.0 OE2 A:GLU42 2.9 57.6 1.0 CD A:GLU42 3.1 56.5 1.0 C6 A:YBT211 3.3 69.6 1.0 C8 A:YBT211 3.3 70.5 1.0 C1 A:YBT211 3.3 70.7 1.0 C3 A:YBT211 3.4 70.6 1.0 C2 A:YBT211 3.4 70.5 1.0 CD A:GLU45 3.4 54.2 1.0 C7 A:YBT211 3.4 70.5 1.0 C5 A:YBT211 3.5 69.6 1.0 OE2 A:GLU45 3.7 55.2 1.0 CG A:GLU42 4.6 50.5 1.0 CG A:GLU45 4.7 52.2 1.0 O A:HOH258 4.8 55.7 1.0 O A:HOH253 4.8 67.3 1.0 NE A:ARG41 4.8 49.6 1.0 C4 A:YBT211 4.9 72.4 1.0 CB A:GLU45 4.9 50.2 1.0

Yttrium binding site 2 out of 5 in the Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Y212 b:73.4 occ:1.00 Y1 A:YBT212 0.0 73.4 1.0 O2 A:YBT212 2.4 74.9 1.0 O5 A:YBT212 2.4 75.6 1.0 O4 A:YBT212 2.4 75.9 1.0 O1 A:YBT212 2.4 76.0 1.0 N1 A:YBT212 2.7 75.5 1.0 OE1 A:GLU7 2.7 58.0 1.0 OE2 D:GLU56 2.8 60.7 1.0 O D:HOH140 2.8 57.0 1.0 OE2 A:GLU7 2.9 56.9 1.0 CD A:GLU7 3.0 55.4 1.0 C8 A:YBT212 3.3 75.4 1.0 C6 A:YBT212 3.3 74.8 1.0 C1 A:YBT212 3.4 76.9 1.0 C3 A:YBT212 3.4 76.2 1.0 C2 A:YBT212 3.4 75.9 1.0 C7 A:YBT212 3.4 74.2 1.0 CD D:GLU56 3.5 54.6 1.0 C5 A:YBT212 3.5 75.0 1.0 OE1 D:GLU56 3.6 54.1 1.0 CG A:GLU7 4.4 52.7 1.0 CG D:GLU56 4.9 51.6 1.0 C4 A:YBT212 4.9 79.3 1.0

Yttrium binding site 3 out of 5 in the Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Y212 b:45.6 occ:1.00 Y1 B:YBT212 0.0 45.6 1.0 O2 B:YBT212 2.3 45.9 1.0 O5 B:YBT212 2.4 47.9 1.0 O4 B:YBT212 2.4 47.4 1.0 O1 B:YBT212 2.4 47.5 1.0 OD1 B:ASN3 2.4 42.9 1.0 OE2 B:GLU102 2.4 53.6 1.0 N1 B:YBT212 2.7 47.2 1.0 CD B:GLU102 3.2 54.6 1.0 C6 B:YBT212 3.3 47.0 1.0 C1 B:YBT212 3.3 49.6 1.0 C8 B:YBT212 3.3 48.4 1.0 C3 B:YBT212 3.3 47.9 1.0 C2 B:YBT212 3.4 48.2 1.0 C7 B:YBT212 3.4 47.0 1.0 OE1 B:GLU102 3.5 58.5 1.0 C5 B:YBT212 3.5 47.9 1.0 CG B:ASN3 3.5 41.9 1.0 O B:HOH250 4.2 59.7 1.0 ND2 B:ASN3 4.3 43.3 1.0 CG B:GLU102 4.4 54.1 1.0 CB B:ASN3 4.5 39.4 1.0 N B:GLN4 4.6 40.1 1.0 CA B:ASN3 4.6 41.1 1.0 O B:HOH262 4.6 45.5 1.0 OE1 B:GLU5 4.7 53.9 1.0 C4 B:YBT212 4.8 51.9 1.0 CG B:GLN4 4.9 46.9 1.0

Yttrium binding site 4 out of 5 in the Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Y213 b:63.1 occ:1.00 Y1 B:YBT213 0.0 63.1 1.0 O4 B:YBT213 2.3 63.9 1.0 O5 B:YBT213 2.3 64.0 1.0 O1 B:YBT213 2.4 63.9 1.0 O2 B:YBT213 2.4 65.8 1.0 O B:HOH218 2.4 54.2 1.0 OE1 B:GLU42 2.5 47.7 1.0 OE1 B:GLU45 2.6 44.1 1.0 N1 B:YBT213 2.7 64.2 1.0 OE2 B:GLU42 2.9 43.9 1.0 CD B:GLU42 3.1 45.9 1.0 C6 B:YBT213 3.3 64.4 1.0 C8 B:YBT213 3.3 64.5 1.0 C1 B:YBT213 3.4 65.0 1.0 C2 B:YBT213 3.4 64.6 1.0 C7 B:YBT213 3.4 63.9 1.0 C3 B:YBT213 3.4 64.8 1.0 C5 B:YBT213 3.5 63.4 1.0 CD B:GLU45 3.5 45.7 1.0 OE2 B:GLU45 3.8 46.7 1.0 CG B:GLU42 4.6 42.0 1.0 O B:HOH272 4.6 65.1 1.0 NE B:ARG41 4.7 44.9 1.0 O B:HOH241 4.8 64.5 1.0 CG B:GLU45 4.8 44.1 1.0 NH2 B:ARG41 4.8 47.8 1.0 C4 B:YBT213 4.9 66.9 1.0 CB B:GLU45 4.9 44.4 1.0 CA B:GLU42 5.0 40.9 1.0

Yttrium binding site 5 out of 5 in the Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Crystal Structure Analysis of Clpsn with Transition Metal Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Y107 b:75.9 occ:1.00 Y1 D:YBT107 0.0 75.9 1.0 ND1 D:HIS66 2.2 49.8 1.0 O2 D:YBT107 2.3 75.4 1.0 O5 D:YBT107 2.3 74.9 1.0 O4 D:YBT107 2.4 75.3 1.0 O1 D:YBT107 2.4 76.1 1.0 N1 D:YBT107 2.6 76.0 1.0 CG D:HIS66 3.0 48.9 1.0 CB D:HIS66 3.2 46.5 1.0 CE1 D:HIS66 3.2 48.9 1.0 C6 D:YBT107 3.3 75.8 1.0 C8 D:YBT107 3.3 75.7 1.0 C1 D:YBT107 3.3 77.1 1.0 C3 D:YBT107 3.4 75.8 1.0 C2 D:YBT107 3.4 77.0 1.0 C7 D:YBT107 3.4 76.0 1.0 C5 D:YBT107 3.5 76.3 1.0 OE2 A:GLU19 3.9 56.8 1.0 CA D:HIS66 3.9 46.3 1.0 CD2 D:HIS66 4.1 50.4 1.0 OE1 A:GLU19 4.2 54.5 1.0 OD1 D:ASN34 4.2 42.0 1.0 NE2 D:HIS66 4.2 51.0 1.0 CD A:GLU19 4.2 57.1 1.0 C4 D:YBT107 4.9 77.5 1.0 C D:HIS66 4.9 46.9 1.0 N D:HIS66 5.0 43.8 1.0

F.Guo, L.Esser, S.K.Singh, M.R.Maurizi, D.Xia. Crystal Structure of the Heterodimeric Complex of the Adaptor, Clps, with the N-Domain of the Aaa+ Chaperone, Clpa J.Biol.Chem. V. 277 46753 2002.
ISSN: ISSN 0021-9258
PubMed: 12235156
DOI: 10.1074/JBC.M208104200