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Sodium in PDB 6f2j: Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate

Enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate

All present enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate, PDB code: 6f2j was solved by S.Engilberge, F.Riobe, S.Di Pietro, E.Girard, E.Dumont, O.Maury, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.84 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.915, 77.915, 37.738, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 17.9

Other elements in 6f2j:

The structure of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate also contains other interesting chemical elements:

Terbium (Tb) 3 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate (pdb code 6f2j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate, PDB code: 6f2j:

Sodium binding site 1 out of 1 in 6f2j

Go back to Sodium Binding Sites List in 6f2j
Sodium binding site 1 out of 1 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:14.3
occ:1.00
O A:SER60 2.3 13.3 1.0
O A:CYS64 2.4 11.6 1.0
O A:HOH419 2.5 16.9 1.0
O A:ARG73 2.5 16.6 1.0
OG A:SER72 2.5 17.1 1.0
O A:HOH374 2.5 14.6 1.0
HB2 A:SER72 2.9 17.4 1.0
HA A:ASN65 3.0 10.5 1.0
HG A:SER72 3.2 17.1 1.0
CB A:SER72 3.3 17.8 1.0
HB2 A:SER60 3.4 13.8 1.0
C A:SER60 3.5 12.5 1.0
C A:CYS64 3.5 11.1 1.0
C A:ARG73 3.5 17.8 1.0
HB A:THR69 3.7 15.3 1.0
HA A:SER60 3.7 8.5 1.0
H A:ASP66 3.9 9.6 1.0
HB2 A:ASN74 3.9 16.9 1.0
H A:CYS64 3.9 13.3 1.0
CA A:ASN65 3.9 10.8 1.0
N A:ARG73 4.0 17.8 1.0
HB3 A:SER72 4.0 17.7 1.0
CA A:SER60 4.0 10.8 1.0
HA A:ASN74 4.1 13.9 1.0
H A:ARG73 4.1 17.5 1.0
C A:SER72 4.1 19.6 1.0
N A:ASN65 4.1 11.4 1.0
CB A:SER60 4.2 11.8 1.0
CA A:SER72 4.3 17.6 1.0
CA A:ARG73 4.4 18.0 1.0
N A:ASN74 4.4 15.2 1.0
N A:CYS64 4.5 11.9 1.0
O A:HOH383 4.5 31.4 1.0
O A:SER72 4.6 21.7 1.0
CA A:ASN74 4.6 15.4 1.0
HB2 A:ASN65 4.6 14.3 1.0
N A:ARG61 4.6 13.7 1.0
CA A:CYS64 4.6 10.7 1.0
C A:ARG61 4.6 16.0 1.0
N A:ASP66 4.6 11.4 1.0
HA A:ARG61 4.7 16.2 1.0
O A:ARG61 4.7 15.9 1.0
OD1 A:ASN65 4.7 15.9 1.0
CB A:THR69 4.7 15.6 1.0
CL A:CL203 4.7 20.4 1.0
CB A:ASN74 4.7 17.1 1.0
HG21 A:THR69 4.8 11.6 1.0
C A:ASN65 4.8 11.9 1.0
CB A:ASN65 4.9 14.5 1.0
HA A:ARG73 4.9 17.8 1.0
N A:TRP62 4.9 14.3 1.0
HG A:SER60 4.9 14.1 1.0
HG1 A:THR69 4.9 13.7 1.0
CA A:ARG61 4.9 15.4 1.0
H A:TRP63 4.9 11.3 1.0
HB3 A:SER60 4.9 12.2 1.0
O A:THR69 5.0 18.1 1.0

Reference:

S.Engilberge, F.Riobe, T.Wagner, S.Di Pietro, C.Breyton, B.Franzetti, S.Shima, E.Girard, E.Dumont, O.Maury. Unveiling the Binding Modes of the Crystallophore, A Terbium-Based Nucleating and Phasing Molecular Agent For Protein Crystallography. Chemistry V. 24 9739 2018.
ISSN: ISSN 1521-3765
PubMed: 29806881
DOI: 10.1002/CHEM.201802172
Page generated: Tue Dec 15 12:14:22 2020

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