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Ytterbium in PDB 4ngz: Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K

Enzymatic activity of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K

All present enzymatic activity of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K:
3.2.1.17;

Protein crystallography data

The structure of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K, PDB code: 4ngz 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) 55.57 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.589, 78.589, 37.017, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.5

Other elements in 4ngz:

The structure of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K (pdb code 4ngz). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 3 binding sites of Ytterbium where determined in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K, PDB code: 4ngz:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in 4ngz

Go back to Ytterbium Binding Sites List in 4ngz
Ytterbium binding site 1 out of 3 in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb201

b:31.7
occ:0.79
 O A:HOH303 2.1 21.9 1.0
OD2 A:ASP52 2.1 15.9 1.0
O A:HOH301 2.2 20.6 1.0
O A:HOH304 2.2 22.5 0.7
O A:HOH305 2.2 30.1 1.0
O A:HOH302 2.3 15.7 1.0
OD1 A:ASN46 3.3 18.8 1.0
CG A:ASP52 3.3 18.7 1.0
O A:HOH370 3.8 22.4 0.8
O A:HOH422 3.9 31.8 0.9
OD1 A:ASP52 4.1 17.9 1.0
CB A:ASP52 4.2 14.2 1.0
O A:HOH361 4.2 30.3 0.9
CG A:ASN46 4.4 21.3 1.0
O A:HOH423 4.7 40.2 1.0
OE1 A:GLN57 4.7 16.1 1.0
OE1 A:GLU35 4.8 13.4 1.0
O A:HOH366 4.8 26.2 1.0
ND2 A:ASN46 4.9 18.8 1.0
O A:HOH371 4.9 23.9 1.0
CB A:GLN57 5.0 13.8 1.0

Ytterbium binding site 2 out of 3 in 4ngz

Go back to Ytterbium Binding Sites List in 4ngz
Ytterbium binding site 2 out of 3 in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb202

b:50.5
occ:0.46
 O A:HOH306 2.2 27.0 0.5
O A:HOH307 2.2 29.9 0.7
OXT A:LEU129 2.3 43.7 0.5
OXT A:LEU129 2.3 53.9 0.5
O A:LEU129 3.0 49.9 0.5
O A:LEU129 3.0 61.1 0.5
C A:LEU129 3.0 46.2 0.5
C A:LEU129 3.1 53.3 0.5
CA A:LEU129 4.5 42.5 0.5
CA A:LEU129 4.6 48.1 0.5
CE A:LYS13 4.8 33.1 1.0

Ytterbium binding site 3 out of 3 in 4ngz

Go back to Ytterbium Binding Sites List in 4ngz
Ytterbium binding site 3 out of 3 in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb203

b:35.3
occ:0.67
 O A:HOH308 2.2 36.9 1.0
OD2 A:ASP101 2.2 30.9 1.0
O A:HOH310 2.2 40.7 1.0
O A:HOH309 2.2 28.8 1.0
O A:HOH312 2.2 44.8 1.0
O A:HOH311 2.2 37.7 1.0
O A:HOH381 2.2 45.4 1.0
OD1 A:ASP101 2.7 32.1 1.0
CG A:ASP101 2.8 27.7 1.0
CB A:ASP101 4.3 26.1 1.0
O A:ASP101 4.3 22.1 1.0
O A:HOH429 4.9 43.6 1.0
O A:HOH355 4.9 30.6 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: Sat Oct 12 21:14:28 2024

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