Sodium in PDB 3agg: X-Ray Analysis of Lysozyme in the Absence of Arg

All present enzymatic activity of X-Ray Analysis of Lysozyme in the Absence of Arg:
3.2.1.17;

The structure of X-Ray Analysis of Lysozyme in the Absence of Arg, PDB code: 3agg was solved by L.Ito, K.Shiraki, K.Hasegawa, S.Baba, T.Kumasaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.31 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.609, 78.609, 37.289, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.8

The structure of X-Ray Analysis of Lysozyme in the Absence of Arg also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

The binding sites of Sodium atom in the X-Ray Analysis of Lysozyme in the Absence of Arg (pdb code 3agg). 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 X-Ray Analysis of Lysozyme in the Absence of Arg, PDB code: 3agg:

Sodium binding site 1 out of 1 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na139 b:11.3 occ:1.00 O G:SER60 2.4 9.8 1.0 O G:HOH209 2.4 11.2 1.0 O G:HOH173 2.4 9.1 1.0 O G:ARG73 2.4 12.1 1.0 O G:CYS64 2.5 8.9 1.0 OG G:SER72 2.5 13.6 1.0 CB G:SER72 3.2 14.1 1.0 C G:ARG73 3.5 12.1 1.0 C G:SER60 3.5 10.7 1.0 C G:CYS64 3.6 8.1 1.0 CA G:ASN65 3.9 8.7 1.0 N G:ARG73 4.0 13.9 1.0 C G:SER72 4.1 14.7 1.0 CA G:SER60 4.1 8.7 1.0 N G:ASN65 4.2 8.0 1.0 CB G:SER60 4.3 9.0 1.0 CA G:ARG73 4.3 13.1 1.0 CA G:SER72 4.3 14.6 1.0 N G:ASN74 4.4 11.8 1.0 N G:CYS64 4.4 8.0 1.0 CA G:ASN74 4.6 10.8 1.0 C G:ARG61 4.6 13.2 1.0 N G:ASP66 4.6 7.8 1.0 N G:ARG61 4.6 11.7 1.0 O G:ARG61 4.6 13.5 1.0 OD1 G:ASN65 4.6 10.7 1.0 O G:SER72 4.6 14.7 1.0 CA G:CYS64 4.7 8.7 1.0 CL G:CL131 4.7 13.1 1.0 CB G:THR69 4.7 10.9 1.0 O G:HOH274 4.7 26.6 1.0 CB G:ASN74 4.7 10.9 1.0 C G:ASN65 4.8 8.3 1.0 CB G:ASN65 4.8 7.3 1.0 CA G:ARG61 4.8 13.4 1.0 N G:TRP62 4.9 12.1 1.0 O G:HOH251 5.0 19.1 1.0

L.Ito, K.Shiraki, T.Matsuura, M.Okumura, K.Hasegawa, S.Baba, H.Yamaguchi, T.Kumasaka. High-Resolution X-Ray Analysis Reveals Binding of Arginine to Aromatic Residues of Lysozyme Surface: Implication of Suppression of Protein Aggregation By Arginine Protein Eng.Des.Sel. V. 24 269 2011.
ISSN: ISSN 1741-0126
PubMed: 21084280
DOI: 10.1093/PROTEIN/GZQ101