Ytterbium in PDB 4ngw: Dialyzed Hew Lysozyme Batch Crystallized in 0.5 M YBCL3 and Collected at 100 K

All present enzymatic activity of Dialyzed Hew Lysozyme Batch Crystallized in 0.5 M YBCL3 and Collected at 100 K:
3.2.1.17;

The structure of Dialyzed Hew Lysozyme Batch Crystallized in 0.5 M YBCL3 and Collected at 100 K, PDB code: 4ngw 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)	55.62 / 1.37
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.665, 78.665, 37.129, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 18.8

The structure of Dialyzed Hew Lysozyme Batch Crystallized in 0.5 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 0.5 M YBCL3 and Collected at 100 K (pdb code 4ngw). 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 0.5 M YBCL3 and Collected at 100 K, PDB code: 4ngw:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in the Dialyzed Hew Lysozyme Batch Crystallized in 0.5 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 0.5 M YBCL3 and Collected at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb201 b:34.9 occ:0.55 OD2 A:ASP52 2.0 16.6 1.0 O A:HOH301 2.2 28.1 0.8 O A:HOH304 2.2 34.5 0.9 O A:HOH302 2.3 29.1 1.0 O A:HOH303 2.3 27.6 1.0 OD1 A:ASN46 2.4 24.6 1.0 CG A:ASP52 3.1 14.9 1.0 CG A:ASN46 3.6 20.0 1.0 OD1 A:ASP52 3.8 17.4 1.0 CB A:ASP52 4.0 13.2 1.0 ND2 A:ASN46 4.2 16.4 1.0 O A:HOH362 4.4 18.1 0.9 O A:HOH363 4.5 23.3 0.9 O A:HOH414 4.6 37.7 1.0 OE1 A:GLN57 4.8 13.1 1.0 CB A:ASN46 4.9 18.7 1.0 O A:HOH375 5.0 29.7 0.9

Ytterbium binding site 2 out of 3 in the Dialyzed Hew Lysozyme Batch Crystallized in 0.5 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 0.5 M YBCL3 and Collected at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb202 b:0.3 occ:0.62 OXT A:LEU129 2.2 65.5 1.0 O A:LEU129 2.2 71.1 1.0 O A:HOH305 2.4 0.9 0.8 C A:LEU129 2.6 56.3 1.0 CA A:LEU129 4.2 47.1 1.0 CB A:LEU129 4.9 44.6 1.0

Ytterbium binding site 3 out of 3 in the Dialyzed Hew Lysozyme Batch Crystallized in 0.5 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 0.5 M YBCL3 and Collected at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb203 b:57.1 occ:0.34 O A:HOH423 2.2 62.5 1.0 O A:HOH306 2.2 56.3 0.9 OD2 A:ASP87 2.2 36.2 1.0 O A:HOH403 3.4 40.0 0.8 CG A:ASP87 3.4 27.4 1.0 CB A:ASP87 4.1 23.8 1.0 OD1 A:ASP87 4.4 24.0 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