Sodium in PDB 2d4k: Monoclinic Hen Egg-White Lysozyme Crystallized at 313K

All present enzymatic activity of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K:
3.2.1.17;

The structure of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K, PDB code: 2d4k was solved by K.Harata, T.Akiba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.70 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.217, 63.484, 59.189, 90.00, 92.93, 90.00
R / Rfree (%)	13.3 / 16.4

The structure of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K (pdb code 2d4k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K, PDB code: 2d4k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:21.8 occ:1.00 OG A:SER72 2.3 45.2 1.0 O A:SER60 2.3 18.6 1.0 O A:CYS64 2.3 19.8 1.0 O A:ARG73 2.4 27.8 1.0 O A:HOH403 2.6 17.4 0.5 O A:HOH402 2.7 43.8 1.0 CB A:SER72 3.2 45.2 1.0 C A:CYS64 3.4 18.4 1.0 C A:ARG73 3.4 25.4 1.0 C A:SER60 3.5 15.7 1.0 N A:ARG73 3.6 30.0 1.0 O A:ARG61 3.7 30.4 1.0 CA A:SER72 3.9 37.4 1.0 C A:ARG61 3.9 20.5 1.0 CL A:CL405 3.9 38.2 0.5 C A:SER72 4.0 33.2 1.0 CA A:ASN65 4.0 21.6 1.0 N A:ASN65 4.1 19.7 1.0 N A:CYS64 4.2 19.5 1.0 CA A:ARG73 4.2 28.9 1.0 CA A:SER60 4.3 13.9 1.0 CA A:ARG61 4.3 18.5 1.0 N A:ASN74 4.4 26.8 1.0 N A:ARG61 4.4 16.4 1.0 CA A:CYS64 4.4 17.3 1.0 N A:TRP62 4.4 20.1 1.0 CA A:ASN74 4.6 24.8 1.0 CB A:SER60 4.6 13.2 1.0 N A:TRP63 4.6 18.0 1.0 C A:TRP62 4.7 21.8 1.0 O A:HOH404 4.7 26.3 0.5 OD1 A:ASN65 4.7 45.3 1.0 CB A:ASN65 4.8 29.2 1.0 CB A:ASN74 4.9 27.1 1.0 O A:SER72 4.9 38.4 1.0 CA A:TRP62 4.9 21.3 1.0 CB A:THR69 4.9 18.5 1.0

Sodium binding site 2 out of 2 in the Monoclinic Hen Egg-White Lysozyme Crystallized at 313K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Monoclinic Hen Egg-White Lysozyme Crystallized at 313K within 5.0Å range: probe atom residue distance (Å) B Occ N:Na406 b:16.6 occ:1.00 O N:CYS264 2.3 15.2 1.0 O N:SER260 2.3 14.7 1.0 O N:ARG273 2.4 16.1 1.0 OG N:SER272 2.5 18.6 1.0 O N:HOH408 2.5 23.5 1.0 O N:HOH407 2.6 22.2 1.0 CB N:SER272 3.2 17.5 1.0 C N:CYS264 3.4 13.5 1.0 C N:ARG273 3.5 15.1 1.0 C N:SER260 3.5 13.0 1.0 N N:ARG273 3.8 17.1 1.0 CA N:ASN265 4.0 15.8 1.0 C N:SER272 4.1 16.1 1.0 N N:ASN265 4.1 15.0 1.0 CA N:SER260 4.2 12.5 1.0 CA N:SER272 4.3 17.1 1.0 CA N:ARG273 4.3 15.8 1.0 C N:ARG261 4.4 12.2 1.0 O N:ARG261 4.4 15.4 1.0 CB N:SER260 4.4 14.0 1.0 N N:CYS264 4.4 12.2 1.0 N N:ASN274 4.4 16.2 1.0 N N:ARG261 4.5 13.3 1.0 CA N:CYS264 4.5 12.2 1.0 O N:SER272 4.6 20.8 1.0 CA N:ASN274 4.6 14.8 1.0 CA N:ARG261 4.7 12.6 1.0 N N:ASP266 4.7 15.6 1.0 N N:TRP262 4.8 13.3 1.0 CL N:CL409 4.8 29.5 1.0 O N:HOH517 4.8 43.1 0.8 CB N:ASN274 4.8 15.6 1.0 OD1 N:ASN265 4.8 31.8 1.0 CB N:ASN265 4.9 20.0 1.0 CB N:THR269 4.9 20.0 1.0 C N:ASN265 4.9 14.9 1.0 N N:TRP263 5.0 12.0 1.0

K.Harata, T.Akiba. Structural Phase Transition of Monoclinic Crystals of Hen Egg-White Lysozyme Acta Crystallogr.,Sect.D V. 62 375 2006.
ISSN: ISSN 0907-4449
PubMed: 16552138
DOI: 10.1107/S0907444906001314