Ytterbium in PDB 4ngy: Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K

All present enzymatic activity of Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K:
3.2.1.17;

The structure of Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K, PDB code: 4ngy was solved by P.Benas, L.Legrand, M.Ries-Kautt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.63 / 1.35
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.666, 78.666, 37.151, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.6

The structure of Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Ytterbium atom in the Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K (pdb code 4ngy). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 3 binding sites of Ytterbium where determined in the Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K, PDB code: 4ngy:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in the Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb201 b:33.6 occ:0.75 O A:HOH301 2.0 19.1 1.0 O A:HOH305 2.1 35.3 1.0 O A:HOH304 2.1 34.6 0.9 O A:HOH302 2.2 21.9 1.0 OD2 A:ASP52 2.2 19.9 1.0 O A:HOH303 2.4 20.0 1.0 OD1 A:ASN46 2.7 22.4 1.0 CG A:ASP52 3.2 17.4 1.0 CG A:ASN46 3.9 17.5 1.0 OD1 A:ASP52 3.9 17.4 1.0 CB A:ASP52 4.0 14.7 1.0 O A:HOH435 4.3 47.6 0.9 ND2 A:ASN46 4.4 17.7 1.0 O A:HOH366 4.5 21.1 1.0 O A:HOH372 4.6 21.2 0.9 O A:HOH391 4.8 26.1 1.0 OE1 A:GLN57 4.8 14.6 1.0

Ytterbium binding site 2 out of 3 in the Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb202 b:43.3 occ:0.72 O A:HOH306 2.1 26.6 0.7 OXT A:LEU129 2.4 59.4 1.0 O A:LEU129 3.1 51.9 1.0 C A:LEU129 3.2 61.2 1.0 CE A:LYS13 4.6 36.6 1.0 CA A:LEU129 4.7 52.1 1.0

Ytterbium binding site 3 out of 3 in the Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Dialyzed Hew Lysozyme Batch Crystallized in 0.75 M YBCL3 and Collected at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb203 b:53.0 occ:0.42 O A:HOH310 2.1 41.1 0.8 O A:HOH309 2.1 47.8 0.9 O A:HOH308 2.1 55.7 1.0 O A:HOH307 2.1 38.0 1.0 OD2 A:ASP87 2.5 33.9 1.0 CG A:ASP87 3.7 26.3 1.0 CB A:ASP87 4.3 23.2 1.0 O A:HOH424 4.6 32.2 0.8 OD1 A:ASP87 4.6 23.3 1.0

P.Benas, N.Auzeil, L.Legrand, F.Brachet, A.Regazzetti, M.Ries-Kautt. Weak Protein-Cationic Co-Ion Interactions Addressed By X-Ray Crystallography and Mass Spectrometry. Acta Crystallogr.,Sect.D V. 70 2217 2014.
ISSN: ISSN 0907-4449
PubMed: 25084340
DOI: 10.1107/S1399004714011304