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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 4ngw:

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

Ytterbium Binding Sites:

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 4ngw

Go back to Ytterbium Binding Sites List in 4ngw
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 4ngw

Go back to Ytterbium Binding Sites List in 4ngw
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 4ngw

Go back to Ytterbium Binding Sites List in 4ngw
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

Reference:

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
Page generated: Wed Dec 16 02:41:59 2020

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