Ytterbium in PDB 1ytt: Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K

The structure of Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K, PDB code: 1ytt was solved by F.T.Burling, W.I.Weis, K.M.Flaherty, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.508, 72.216, 45.035, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 20.6

The binding sites of Ytterbium atom in the Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K (pdb code 1ytt). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 4 binding sites of Ytterbium where determined in the Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K, PDB code: 1ytt:
Jump to Ytterbium binding site number: 1; 2; 3; 4;

Ytterbium binding site 1 out of 4 in the Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb1 b:7.1 occ:1.00 OD1 A:ASP194 2.4 8.3 1.0 OD1 A:ASP188 2.4 7.4 1.0 OE1 A:GLU165 2.4 4.0 1.0 O A:GLU193 2.4 2.7 1.0 O A:HOH222 2.4 5.5 1.0 OD2 A:ASP161 2.4 6.3 1.0 OE2 A:GLU165 2.5 4.7 1.0 OD1 A:ASP161 2.6 4.0 1.0 CD A:GLU165 2.7 3.9 1.0 CG A:ASP161 2.9 4.8 1.0 CG A:ASP188 3.3 7.2 1.0 C A:GLU193 3.4 4.4 1.0 CG A:ASP194 3.5 8.9 1.0 CA A:ASP194 3.8 3.0 1.0 N A:ASP194 4.0 3.1 1.0 CB A:ASP188 4.0 8.1 1.0 OD2 A:ASP188 4.0 9.2 1.0 CB A:ASP194 4.1 5.8 1.0 N A:GLU193 4.2 4.9 1.0 CG A:GLU165 4.3 4.2 1.0 CB A:ASP161 4.4 4.1 1.0 CA A:GLU193 4.4 3.7 1.0 CA A:ASP188 4.5 7.9 1.0 OD2 A:ASP194 4.5 9.5 1.0 O A:HOH225 4.5 9.8 1.0 CZ A:PHE168 4.6 6.1 1.0 O A:ASP161 4.6 4.0 1.0 OD2 A:ASP206 4.6 6.2 1.0 N A:GLY166 4.7 5.6 1.0 O A:HOH227 4.9 12.1 1.0 CA A:GLU165 4.9 6.3 1.0

Ytterbium binding site 2 out of 4 in the Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb2 b:12.2 occ:1.00 OD1 A:ASN187 2.3 9.3 1.0 OE1 A:GLU193 2.3 7.2 1.0 OD1 A:ASP206 2.3 5.1 1.0 O A:HOH232 2.3 17.8 1.0 O A:ASP206 2.4 2.7 1.0 OE1 A:GLU185 2.4 17.6 1.0 OD1 A:ASN205 2.4 13.9 1.0 CD A:GLU193 3.3 6.6 1.0 CD A:GLU185 3.3 19.0 1.0 CG A:ASN187 3.4 10.1 1.0 CG A:ASP206 3.4 7.0 1.0 CG A:ASN205 3.5 11.9 1.0 C A:ASP206 3.5 4.0 1.0 OE2 A:GLU193 3.6 8.5 1.0 OE2 A:GLU185 3.7 23.3 1.0 N A:ASP206 3.7 5.2 1.0 ND2 A:ASN205 4.0 15.7 1.0 ND2 A:ASN187 4.0 10.3 1.0 CA A:ASP206 4.1 3.8 1.0 OD2 A:ASP206 4.1 6.2 1.0 N A:ASN187 4.2 9.5 1.0 CB A:ASP206 4.3 5.7 1.0 O A:HOH284 4.4 56.6 1.0 CB A:ASN187 4.6 9.4 1.0 C A:ASN205 4.6 5.2 1.0 CG A:GLU193 4.6 4.3 1.0 CG A:GLU185 4.6 15.6 1.0 N A:ILE207 4.6 3.6 1.0 CB A:HIS189 4.6 13.5 1.0 N A:ASP188 4.7 8.6 1.0 CA A:ASN187 4.7 9.9 1.0 CB A:ASN205 4.8 9.5 1.0 CB A:GLU193 4.8 3.7 1.0 N A:HIS189 4.8 9.1 1.0 O A:HOH302 4.9 23.6 1.0 CA A:ASN205 4.9 7.2 1.0 CA A:ILE207 5.0 4.0 1.0

Ytterbium binding site 3 out of 4 in the Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K within 5.0Å range: probe atom residue distance (Å) B Occ B:Yb1 b:13.6 occ:1.00 O B:HOH282 2.1 14.3 1.0 OD1 B:ASP194 2.3 16.5 1.0 OD2 B:ASP161 2.4 12.9 1.0 O B:GLU193 2.4 11.8 1.0 OE1 B:GLU165 2.4 12.7 1.0 OD1 B:ASP188 2.4 16.9 1.0 OE2 B:GLU165 2.5 12.6 1.0 OD1 B:ASP161 2.6 9.1 1.0 CD B:GLU165 2.8 13.4 1.0 CG B:ASP161 2.8 11.0 1.0 C B:GLU193 3.3 11.8 1.0 CG B:ASP188 3.4 18.6 1.0 CG B:ASP194 3.4 13.9 1.0 CA B:ASP194 3.8 10.5 1.0 N B:ASP194 3.9 11.1 1.0 CB B:ASP188 4.0 18.0 1.0 CB B:ASP194 4.1 12.3 1.0 N B:GLU193 4.2 18.1 1.0 OD2 B:ASP188 4.2 18.6 1.0 CB B:ASP161 4.3 8.4 1.0 CG B:GLU165 4.3 13.4 1.0 OD2 B:ASP194 4.4 16.7 1.0 CA B:GLU193 4.4 14.3 1.0 CZ B:PHE168 4.4 9.0 1.0 O B:HOH272 4.5 54.9 1.0 O B:HOH231 4.5 16.0 1.0 OD2 B:ASP206 4.5 10.8 1.0 CA B:ASP188 4.6 19.1 1.0 N B:GLY166 4.6 14.7 1.0 O B:ASP161 4.6 10.1 1.0 CE1 B:PHE168 4.9 10.3 1.0 CB B:GLU193 5.0 13.5 1.0

Ytterbium binding site 4 out of 4 in the Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Yb Substituted Subtilisin Fragment of Mannose Binding Protein-A (Sub- Mbp-A), Mad Structure at 110K within 5.0Å range: probe atom residue distance (Å) B Occ B:Yb2 b:15.8 occ:1.00 OD1 B:ASP206 2.3 7.8 1.0 OE1 B:GLU193 2.3 13.8 1.0 OD1 B:ASN205 2.3 16.8 1.0 O B:HOH283 2.4 16.1 1.0 OE1 B:GLU185 2.4 20.6 1.0 O B:HOH227 2.4 18.5 1.0 OD1 B:ASN187 2.5 19.7 1.0 O B:ASP206 2.5 12.2 1.0 CD B:GLU193 3.3 13.9 1.0 CG B:ASP206 3.4 12.7 1.0 CG B:ASN205 3.4 14.2 1.0 CD B:GLU185 3.5 21.2 1.0 C B:ASP206 3.6 11.5 1.0 CG B:ASN187 3.6 19.9 1.0 N B:ASP206 3.7 10.8 1.0 OE2 B:GLU193 3.7 14.3 1.0 OE2 B:GLU185 3.9 23.4 1.0 ND2 B:ASN205 3.9 17.7 1.0 CA B:ASP206 4.1 11.6 1.0 OD2 B:ASP206 4.2 10.8 1.0 ND2 B:ASN187 4.2 21.2 1.0 N B:ASN187 4.2 17.3 1.0 CB B:ASP206 4.3 9.2 1.0 C B:ASN205 4.5 10.4 1.0 CG B:GLU193 4.6 15.1 1.0 CG B:GLU185 4.7 18.6 1.0 CB B:ASN205 4.7 13.8 1.0 N B:ILE207 4.7 11.0 1.0 CB B:ASN187 4.7 19.6 1.0 CB B:HIS189 4.8 22.7 1.0 N B:ASP188 4.8 18.6 1.0 CB B:GLU193 4.8 13.5 1.0 N B:HIS189 4.8 20.7 1.0 CA B:ASN205 4.8 11.4 1.0 CA B:ASN187 4.8 18.4 1.0

F.T.Burling, W.I.Weis, K.M.Flaherty, A.T.Brunger. Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases. Science V. 271 72 1996.
ISSN: ISSN 0036-8075
PubMed: 8539602