Sodium in PDB 4dc4: Lysozyme Trimer

All present enzymatic activity of Lysozyme Trimer:
3.2.1.17;

The structure of Lysozyme Trimer, PDB code: 4dc4 was solved by P.Sharma, Ashish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.91 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.472, 92.350, 114.239, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 30

The structure of Lysozyme Trimer also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Lysozyme Trimer (pdb code 4dc4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Lysozyme Trimer, PDB code: 4dc4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Lysozyme Trimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:29.6 occ:1.00 O A:CYS76 4.0 29.5 1.0 CB A:ASN93 4.0 19.8 1.0 CB A:CYS76 4.3 34.7 1.0 N A:CYS94 4.3 19.2 1.0 C A:ASN93 4.4 19.2 1.0 CG2 A:ILE78 4.4 34.5 1.0 O A:ASN93 4.5 27.1 1.0 CA A:CYS94 4.6 23.5 1.0 O B:ARG112 4.6 30.1 1.0 OD1 B:ASN113 4.7 28.1 1.0 CA A:CYS76 4.8 27.0 1.0 SG A:CYS76 4.8 27.1 1.0 C A:CYS76 4.8 31.2 1.0 CA A:ASN93 4.9 24.7 1.0 CB A:CYS94 4.9 28.3 1.0

Sodium binding site 2 out of 3 in the Lysozyme Trimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:17.0 occ:1.00 OD1 A:ASN65 3.5 21.8 1.0 N A:GLY67 3.5 22.1 1.0 OG A:SER72 3.5 29.1 1.0 O A:THR69 3.5 31.1 1.0 OD1 A:ASP66 3.6 23.5 1.0 N A:THR69 3.6 26.3 1.0 CG A:ASN65 3.7 21.0 1.0 CB A:THR69 3.8 24.9 1.0 N A:ASP66 3.8 26.4 1.0 CA A:ASN65 3.9 25.7 1.0 N A:ARG68 3.9 27.0 1.0 CB A:ASN65 4.0 22.4 1.0 CA A:GLY67 4.0 21.7 1.0 CA A:THR69 4.0 27.6 1.0 C A:THR69 4.1 29.4 1.0 OG1 A:THR69 4.1 23.6 1.0 C A:GLY67 4.2 26.7 1.0 ND2 A:ASN65 4.3 21.6 1.0 C A:ASN65 4.3 27.1 1.0 CB A:SER72 4.3 31.0 1.0 O A:HOH304 4.5 15.0 1.0 C A:ASP66 4.6 22.2 1.0 C A:ARG68 4.7 25.0 1.0 CG A:ASP66 4.7 21.5 1.0 CA A:ASP66 4.8 26.2 1.0 O A:SER60 4.9 27.8 1.0 O A:CYS64 4.9 21.5 1.0 CA A:ARG68 4.9 22.0 1.0

Sodium binding site 3 out of 3 in the Lysozyme Trimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lysozyme Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:26.9 occ:1.00 OG B:SER72 3.2 22.3 1.0 O B:HOH304 3.2 15.4 1.0 OD1 B:ASP66 3.3 17.4 1.0 OD1 B:ASN65 3.3 18.4 1.0 O B:SER60 3.4 27.1 1.0 O B:CYS64 3.4 15.4 1.0 N B:ASP66 3.4 19.3 1.0 CA B:ASN65 3.8 19.4 1.0 CB B:THR69 3.9 24.9 1.0 CB B:SER60 3.9 27.4 1.0 N B:GLY67 4.0 20.7 1.0 OG1 B:THR69 4.0 25.8 1.0 O B:THR69 4.0 22.4 1.0 CG B:ASP66 4.1 18.8 1.0 C B:ASN65 4.1 23.0 1.0 O B:ARG73 4.3 22.3 1.0 C B:SER60 4.3 26.8 1.0 CG B:ASN65 4.3 17.3 1.0 OG B:SER60 4.3 19.4 1.0 CB B:SER72 4.3 23.2 1.0 C B:CYS64 4.4 16.8 1.0 CA B:ASP66 4.4 16.1 1.0 N B:THR69 4.4 25.6 1.0 CA B:SER60 4.5 30.2 1.0 CB B:ASN65 4.5 13.7 1.0 CA B:THR69 4.6 28.3 1.0 N B:ASN65 4.6 16.2 1.0 C B:ASP66 4.7 17.8 1.0 CB B:ASP66 4.7 20.8 1.0 OD2 B:ASP66 4.8 19.2 1.0 C B:THR69 4.8 24.7 1.0 CA B:GLY67 4.9 13.8 1.0 CG2 B:THR69 4.9 21.0 1.0 N B:ARG68 5.0 22.4 1.0

P.Sharma, N.Verma, P.K.Singh, S.Korpole, Ashish. Characterization of Heat Induced Spherulites of Lysozyme Reveals New Insight on Amyloid Initiation Sci Rep V. 6 22475 2016.
ISSN: ESSN 2045-2322
PubMed: 26926993
DOI: 10.1038/SREP22475