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Sodium in PDB 8pob: Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3

Enzymatic activity of Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3

All present enzymatic activity of Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3, PDB code: 8pob was solved by Z.Alsalman, E.Girard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.70 / 1.74
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.404, 77.404, 37.602, 90, 90, 90
R / Rfree (%) 18 / 22.8

Other elements in 8pob:

The structure of Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3 also contains other interesting chemical elements:

Terbium (Tb) 2 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3 (pdb code 8pob). 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 with 10 Mm TBXO4-SO3, PDB code: 8pob:

Sodium binding site 1 out of 1 in 8pob

Go back to Sodium Binding Sites List in 8pob
Sodium binding site 1 out of 1 in the Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3


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 with 10 Mm TBXO4-SO3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na210

b:28.0
occ:1.00
O A:SER60 2.3 28.7 1.0
O A:HOH360 2.4 29.8 1.0
OG A:SER72 2.4 37.8 1.0
O A:HOH349 2.5 26.2 1.0
O A:ARG73 2.5 31.0 1.0
O A:CYS64 2.6 32.7 1.0
HB2 A:SER72 2.8 49.1 1.0
HG A:SER72 3.0 45.2 1.0
HA A:ASN65 3.0 30.2 1.0
CB A:SER72 3.1 41.0 1.0
HB2 A:SER60 3.5 28.6 1.0
C A:SER60 3.5 27.7 1.0
C A:ARG73 3.5 31.3 1.0
C A:CYS64 3.7 28.4 1.0
HB A:THR69 3.7 29.5 1.0
HB3 A:SER72 3.8 49.1 1.0
H A:ASP66 3.9 34.6 1.0
CA A:ASN65 4.0 25.3 1.0
HA A:SER60 4.0 28.7 1.0
N A:ARG73 4.0 29.9 1.0
C A:SER72 4.1 41.7 1.0
H A:ARG73 4.1 35.7 1.0
H A:CYS64 4.1 35.3 1.0
HB2 A:ASN74 4.1 31.8 1.0
CA A:SER60 4.2 24.0 1.0
CA A:SER72 4.2 48.0 1.0
HA A:ASN74 4.2 31.4 1.0
CB A:SER60 4.2 23.9 1.0
N A:ASN65 4.3 27.4 1.0
CA A:ARG73 4.3 27.3 1.0
N A:ASN74 4.5 26.5 1.0
HB2 A:ASN65 4.5 33.2 1.0
C A:ARG61 4.5 25.0 1.0
O A:ARG61 4.6 30.7 1.0
OD1 A:ASN65 4.6 30.6 1.0
O A:HOH390 4.6 41.0 1.0
HA A:ARG61 4.6 31.2 1.0
CL A:CL204 4.6 34.6 1.0
N A:ARG61 4.6 28.1 1.0
CB A:THR69 4.6 24.7 1.0
N A:CYS64 4.6 29.6 1.0
O A:SER72 4.6 35.9 1.0
N A:ASP66 4.6 29.0 1.0
HA A:ARG73 4.7 32.6 1.0
HG23 A:THR69 4.7 43.1 1.0
CA A:ASN74 4.7 26.3 1.0
HG1 A:THR69 4.7 30.8 1.0
CB A:ASN65 4.8 27.8 1.0
HA A:SER72 4.8 57.4 1.0
CA A:CYS64 4.8 30.8 1.0
CA A:ARG61 4.8 26.1 1.0
N A:TRP62 4.8 27.6 1.0
C A:ASN65 4.9 26.8 1.0
O A:THR69 4.9 30.5 1.0
CB A:ASN74 4.9 26.6 1.0
HB3 A:SER60 4.9 28.6 1.0
O A:HOH389 4.9 35.9 1.0
H A:TRP63 4.9 29.8 1.0
H A:SER72 5.0 41.8 1.0

Reference:

A.Roux, Z.Alsalman, T.Jiang, J.C.Mulatier, D.Pitrat, E.Dumont, F.Riobe, N.Gillet, E.Girard, O.Maury. Influence of Chemical Modifications of the Crystallophore on Protein Nucleating Properties and Supramolecular Interactions Network. Chemistry 00900 2024.
ISSN: ISSN 0947-6539
PubMed: 38738452
DOI: 10.1002/CHEM.202400900
Page generated: Wed Oct 9 13:01:09 2024

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