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Ytterbium in PDB 4ngv: Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3

Enzymatic activity of Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3

All present enzymatic activity of Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3:
3.2.1.17;

Protein crystallography data

The structure of Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3, PDB code: 4ngv 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) 55.79 / 1.64
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.906, 78.906, 37.699, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 18.6

Other elements in 4ngv:

The structure of Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3 (pdb code 4ngv). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 4 binding sites of Ytterbium where determined in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3, PDB code: 4ngv:
Jump to Ytterbium binding site number: 1; 2; 3; 4;

Ytterbium binding site 1 out of 4 in 4ngv

Go back to Ytterbium Binding Sites List in 4ngv
Ytterbium binding site 1 out of 4 in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3


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 Batch Crystallized in 0.5 M YBCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb201

b:39.8
occ:0.22
 YB A:YB201 0.0 39.8 0.2
YB A:YB201 2.1 28.4 0.7
O A:HOH304 2.3 24.6 1.0
O A:HOH303 2.4 36.1 1.0
YB A:YB203 2.5 20.0 0.1
OD2 A:ASP52 2.5 21.9 1.0
O A:HOH307 2.8 38.7 1.0
O A:HOH301 3.0 31.1 1.0
CG A:ASP52 3.7 15.8 1.0
O A:HOH311 3.8 35.2 1.0
O A:HOH302 3.9 30.7 1.0
OE1 A:GLU35 4.1 18.2 1.0
OD1 A:ASN46 4.2 26.4 1.0
CB A:ASP52 4.5 12.9 1.0
OD1 A:ASP52 4.5 14.7 1.0
O A:HOH336 4.5 29.8 1.0
O A:HOH305 4.6 29.4 1.0
OE1 A:GLN57 4.7 12.5 1.0
CB A:GLN57 4.9 11.3 1.0

Ytterbium binding site 2 out of 4 in 4ngv

Go back to Ytterbium Binding Sites List in 4ngv
Ytterbium binding site 2 out of 4 in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3


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 Batch Crystallized in 0.5 M YBCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb201

b:28.4
occ:0.67
 YB A:YB201 0.0 28.4 0.7
YB A:YB201 2.1 39.8 0.2
OD2 A:ASP52 2.1 21.9 1.0
OD1 A:ASN46 2.3 26.4 1.0
O A:HOH301 2.4 31.1 1.0
O A:HOH303 2.7 36.1 1.0
O A:HOH307 2.7 38.7 1.0
O A:HOH302 2.7 30.7 1.0
CG A:ASP52 3.2 15.8 1.0
CG A:ASN46 3.3 22.2 1.0
OD1 A:ASP52 3.7 14.7 1.0
ND2 A:ASN46 3.8 21.8 1.0
O A:HOH304 3.9 24.6 1.0
CB A:ASP52 4.4 12.9 1.0
CB A:ASN46 4.4 20.1 1.0
YB A:YB203 4.5 20.0 0.1
O A:HOH351 4.8 34.3 1.0

Ytterbium binding site 3 out of 4 in 4ngv

Go back to Ytterbium Binding Sites List in 4ngv
Ytterbium binding site 3 out of 4 in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3


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 Batch Crystallized in 0.5 M YBCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb202

b:37.0
occ:0.39
 O A:HOH309 2.3 41.6 0.9
O A:HOH308 2.3 33.8 1.0
OXT A:LEU129 2.4 45.7 1.0
O A:LEU129 3.2 52.2 1.0
C A:LEU129 3.2 48.9 1.0
NZ A:LYS13 3.5 36.6 0.5
NZ A:LYS13 4.2 30.9 0.5
CE A:LYS13 4.5 33.4 0.5
CA A:LEU129 4.7 46.2 1.0
CE A:LYS13 4.9 29.0 0.5

Ytterbium binding site 4 out of 4 in 4ngv

Go back to Ytterbium Binding Sites List in 4ngv
Ytterbium binding site 4 out of 4 in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Previously De-Ionized Hew Lysozyme Batch Crystallized in 0.5 M YBCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb203

b:20.0
occ:0.10
 O A:HOH304 2.2 24.6 1.0
YB A:YB201 2.5 39.8 0.2
O A:HOH305 2.7 29.4 1.0
OE1 A:GLU35 2.7 18.2 1.0
O A:HOH306 2.8 30.5 0.9
O A:HOH311 3.4 35.2 1.0
CD A:GLU35 3.8 15.4 1.0
O A:HOH303 4.3 36.1 1.0
OE2 A:GLU35 4.3 17.7 1.0
O A:GLU35 4.5 11.9 1.0
O A:HOH307 4.5 38.7 1.0
YB A:YB201 4.5 28.4 0.7
O A:HOH301 4.6 31.1 1.0
CA A:GLU35 4.6 11.6 1.0
OE1 A:GLN57 4.7 12.5 1.0
CG A:GLN57 4.7 10.9 1.0
OD2 A:ASP52 4.7 21.9 1.0
CB A:GLN57 4.8 11.3 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 21:12:29 2024

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