Sodium in PDB 2d4i: Monoclinic Hen Egg-White Lysozyme Crystallized at PH4.5 Form Heavy Water Solution

All present enzymatic activity of Monoclinic Hen Egg-White Lysozyme Crystallized at PH4.5 Form Heavy Water Solution:
3.2.1.17;

The structure of Monoclinic Hen Egg-White Lysozyme Crystallized at PH4.5 Form Heavy Water Solution, PDB code: 2d4i 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)	17.20 / 1.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.008, 62.915, 60.494, 90.00, 90.55, 90.00
R / Rfree (%)	13.7 / 17.5

The binding sites of Sodium atom in the Monoclinic Hen Egg-White Lysozyme Crystallized at PH4.5 Form Heavy Water Solution (pdb code 2d4i). 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 Monoclinic Hen Egg-White Lysozyme Crystallized at PH4.5 Form Heavy Water Solution, PDB code: 2d4i:

Sodium binding site 1 out of 1 in the Monoclinic Hen Egg-White Lysozyme Crystallized at PH4.5 Form Heavy Water Solution


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 PH4.5 Form Heavy Water Solution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:20.1 occ:0.50 O B:DOD408 1.6 22.3 0.5 OG B:SER272 2.2 31.9 0.5 O B:SER260 2.3 19.6 1.0 O B:ARG273 2.4 21.4 0.5 O2 B:NO3405 2.4 18.4 0.5 O1 B:NO3405 2.4 31.7 0.5 O B:CYS264 2.4 16.9 1.0 O B:DOD409 2.5 24.3 0.5 O B:DOD407 2.6 25.5 0.5 CB B:SER272 2.7 29.0 0.5 N B:NO3405 2.8 25.9 0.5 CA B:SER272 3.1 25.8 0.5 C B:ARG273 3.5 19.3 0.5 C B:CYS264 3.5 16.1 1.0 C B:SER260 3.5 18.4 1.0 N B:ARG273 3.6 23.1 0.5 C B:SER272 3.8 22.6 0.5 N B:ARG273 3.9 17.2 0.5 O B:ARG261 4.0 24.7 1.0 CA B:ASN265 4.0 16.7 1.0 O3 B:NO3405 4.0 33.5 0.5 C B:ARG261 4.1 20.9 1.0 N B:ASN274 4.1 13.3 0.5 CA B:ARG273 4.1 21.2 0.5 N B:ASN265 4.2 16.1 1.0 CA B:SER260 4.3 16.7 1.0 C B:SER272 4.3 25.9 0.5 N B:SER272 4.4 27.6 0.5 N B:CYS264 4.4 15.0 1.0 O B:DOD410 4.4 26.5 0.5 CA B:ARG261 4.4 21.1 1.0 N B:ARG261 4.4 19.4 1.0 CB B:THR269 4.5 20.6 1.0 CA B:ASN274 4.5 14.6 0.5 CB B:SER260 4.5 18.9 1.0 N B:ASN274 4.6 20.5 0.5 N B:TRP262 4.6 17.5 1.0 CA B:CYS264 4.6 14.9 1.0 CB B:ARG273 4.6 21.1 0.5 CA B:SER272 4.6 28.0 0.5 CA B:ASN274 4.7 17.6 0.5 CB B:ASN274 4.8 17.1 0.5 N B:ASP266 4.8 18.0 1.0 O B:SER272 4.8 26.0 0.5 C B:TRP262 4.8 16.5 1.0 N B:TRP263 4.9 15.0 1.0 CB B:ASN265 4.9 19.0 1.0 C B:ASN265 4.9 16.9 1.0 CG2 B:THR269 4.9 24.7 1.0 CB B:ASN274 5.0 18.8 0.5

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