Sodium in PDB 1v7t: Triclinic Lysozyme with Low Solvent Content Obtained By Phase Transition

All present enzymatic activity of Triclinic Lysozyme with Low Solvent Content Obtained By Phase Transition:
3.2.1.17;

The structure of Triclinic Lysozyme with Low Solvent Content Obtained By Phase Transition, PDB code: 1v7t 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)	39.94 / 1.13
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.930, 39.970, 42.390, 88.00, 95.44, 90.58
R / Rfree (%)	11.9 / 16.2

The binding sites of Sodium atom in the Triclinic Lysozyme with Low Solvent Content Obtained By Phase Transition (pdb code 1v7t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Triclinic Lysozyme with Low Solvent Content Obtained By Phase Transition, PDB code: 1v7t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Triclinic Lysozyme with Low Solvent Content Obtained By Phase Transition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Triclinic Lysozyme with Low Solvent Content Obtained By Phase Transition within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:12.2 occ:1.00 O A:SER60 2.2 9.3 1.0 O A:ARG73 2.3 10.8 1.0 O2 A:NO3401 2.4 13.7 1.0 O A:CYS64 2.4 7.9 1.0 O1 A:NO3401 2.6 12.0 1.0 O A:HOH407 2.6 13.4 1.0 N A:NO3401 2.9 14.0 1.0 C A:SER60 3.4 9.1 1.0 C A:ARG73 3.4 10.1 1.0 C A:CYS64 3.5 6.7 1.0 N A:ARG73 3.7 12.3 1.0 CA A:ASN65 4.0 6.6 1.0 CB A:THR69 4.1 9.8 1.0 CA A:SER60 4.1 7.8 1.0 O3 A:NO3401 4.1 16.1 1.0 CA A:ARG73 4.1 10.1 1.0 C A:SER72 4.1 12.5 1.0 O A:ARG61 4.2 11.8 1.0 N A:ASN65 4.2 6.2 1.0 C A:ARG61 4.2 9.0 1.0 CB A:SER60 4.3 7.4 1.0 N A:CYS64 4.4 6.9 1.0 N A:ARG61 4.4 9.2 1.0 CA A:SER72 4.4 10.5 1.0 CA A:ARG61 4.4 9.8 1.0 N A:ASN74 4.5 7.2 1.0 CG2 A:THR69 4.5 10.4 1.0 OG1 A:THR69 4.6 9.3 1.0 CA A:CYS64 4.6 7.0 1.0 N A:TRP62 4.7 8.4 1.0 O A:SER72 4.7 14.6 1.0 N A:ASP66 4.7 7.0 1.0 CA A:ASN74 4.8 7.0 1.0 CB A:ARG73 4.8 13.2 0.5 O A:HOH425 4.9 13.6 1.0 CB A:ARG73 4.9 12.9 0.6 C A:ASN65 4.9 6.3 1.0 N A:TRP63 4.9 7.2 1.0 N A:SER72 4.9 11.0 1.0 O A:THR69 5.0 11.8 1.0 C A:TRP62 5.0 7.3 1.0 OG A:SER60 5.0 8.1 1.0 CB A:ASN65 5.0 7.4 1.0

Sodium binding site 2 out of 2 in the Triclinic Lysozyme with Low Solvent Content Obtained By Phase Transition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Triclinic Lysozyme with Low Solvent Content Obtained By Phase Transition within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:16.8 occ:1.00 O B:SER260 2.2 12.6 1.0 O B:CYS264 2.4 11.9 1.0 O B:HOH410 2.4 17.8 1.0 O B:HOH409 2.4 13.9 1.0 O B:ARG273 2.4 15.7 1.0 OG B:SER272 2.4 17.2 1.0 CB B:SER272 3.2 17.6 1.0 C B:SER260 3.4 11.9 1.0 C B:ARG273 3.5 14.5 1.0 C B:CYS264 3.5 9.7 1.0 CA B:ASN265 3.9 10.0 1.0 N B:ARG273 4.0 16.7 1.0 CA B:SER260 4.1 9.6 1.0 N B:ASN265 4.1 10.1 1.0 C B:SER272 4.3 19.2 1.0 O3 B:NO3402 4.3 24.3 1.0 CB B:SER260 4.3 9.9 1.0 N B:ASN274 4.3 13.2 1.0 C B:ARG261 4.3 11.4 1.0 CA B:SER272 4.4 16.6 1.0 CA B:ARG273 4.4 19.9 1.0 O1 B:NO3402 4.4 20.4 1.0 N B:ARG261 4.4 12.0 1.0 O B:ARG261 4.4 14.7 1.0 N B:CYS264 4.5 8.9 1.0 CA B:ASN274 4.5 11.2 1.0 CA B:ARG261 4.6 11.6 1.0 CA B:CYS264 4.6 9.4 1.0 N B:TRP262 4.7 10.9 1.0 CB B:ASN274 4.7 12.3 1.0 OD1 B:ASN265 4.7 21.0 1.0 CB B:THR269 4.7 12.1 1.0 N B:ASP266 4.7 9.9 1.0 CB B:ASN265 4.7 17.5 1.0 N B:NO3402 4.8 21.6 1.0 O B:SER272 4.8 22.8 1.0 N B:TRP263 4.9 9.7 1.0 C B:ASN265 4.9 10.1 1.0 C B:TRP262 4.9 9.2 1.0

K.Harata, T.Akiba. Phase Transition of Triclinic Hen Egg-White Lysozyme Crystal Associated with Sodium Binding. Acta Crystallogr.,Sect.D V. 60 630 2004.
ISSN: ISSN 0907-4449
PubMed: 15039550
DOI: 10.1107/S0907444904001805