Sodium in PDB 3fi5: Crystal Structure of T4 Lysozyme Mutant R96W

All present enzymatic activity of Crystal Structure of T4 Lysozyme Mutant R96W:
3.2.1.17;

The structure of Crystal Structure of T4 Lysozyme Mutant R96W, PDB code: 3fi5 was solved by B.H.M.Mooers, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.80 / 1.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.800, 56.110, 85.240, 90.00, 106.47, 90.00
R / Rfree (%)	19.4 / 26.1

The structure of Crystal Structure of T4 Lysozyme Mutant R96W also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of T4 Lysozyme Mutant R96W (pdb code 3fi5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of T4 Lysozyme Mutant R96W, PDB code: 3fi5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of T4 Lysozyme Mutant R96W


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of T4 Lysozyme Mutant R96W within 5.0Å range: probe atom residue distance (Å) B Occ A:Na513 b:31.1 occ:1.00 OE1 A:GLU11 2.9 17.3 1.0 O A:GLU11 2.9 17.2 1.0 OH A:TYR18 3.0 23.1 1.0 O A:HOH1429 3.1 24.3 1.0 NH2 A:ARG14 3.1 41.0 1.0 O A:HOH1393 3.2 29.9 1.0 O A:HOH1714 3.3 24.5 1.0 C A:GLU11 3.7 16.0 1.0 CA A:GLU11 3.7 15.2 1.0 CE1 A:TYR18 3.7 22.2 1.0 CZ A:TYR18 3.8 22.0 1.0 O A:HOH1994 3.9 28.5 1.0 CB A:GLU11 4.0 13.5 1.0 CD A:GLU11 4.0 15.4 1.0 CA A:GLY30 4.1 12.9 1.0 CZ A:ARG14 4.1 40.7 1.0 NH1 A:ARG14 4.1 42.7 1.0 N A:GLY30 4.2 12.9 1.0 CG A:GLU11 4.6 15.3 1.0 O A:HOH2321 4.7 45.8 1.0 O A:ASP10 4.8 14.5 1.0 N A:GLY12 4.9 15.8 1.0 CD1 A:TYR18 5.0 21.9 1.0 OE2 A:GLU11 5.0 14.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of T4 Lysozyme Mutant R96W


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of T4 Lysozyme Mutant R96W within 5.0Å range: probe atom residue distance (Å) B Occ B:Na512 b:35.6 occ:1.00 O B:HOH1226 2.8 27.1 1.0 O B:GLU11 2.9 20.7 1.0 OE1 B:GLU11 3.0 19.8 1.0 O B:HOH1174 3.6 25.4 1.0 CA B:GLU11 3.6 13.6 1.0 C B:GLU11 3.6 17.4 1.0 OH B:TYR18 3.8 24.1 1.0 CB B:GLU11 3.9 14.1 1.0 CD B:GLU11 3.9 16.7 1.0 CA B:GLY30 3.9 15.0 1.0 O B:HOH2222 4.2 36.4 1.0 N B:GLY30 4.2 14.2 1.0 CG B:GLU11 4.5 16.3 1.0 O B:HOH1781 4.7 47.7 1.0 O B:HOH1753 4.7 44.4 1.0 OE2 B:GLU11 4.8 17.3 1.0 O B:HOH2097 4.8 15.1 0.5 O B:ASP10 4.8 13.7 1.0 N B:GLY12 4.9 17.4 1.0 N B:GLU11 4.9 13.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of T4 Lysozyme Mutant R96W


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of T4 Lysozyme Mutant R96W within 5.0Å range: probe atom residue distance (Å) B Occ C:Na511 b:47.7 occ:1.00 O C:GLU11 2.9 29.6 1.0 O C:HOH1692 3.0 46.6 1.0 OE1 C:GLU11 3.0 32.6 1.0 O C:HOH1447 3.0 26.1 0.5 C C:GLU11 3.6 29.8 1.0 CA C:GLU11 3.7 27.6 1.0 O C:HOH1447 3.8 28.6 0.5 OH C:TYR18 3.9 30.8 1.0 CB C:GLU11 4.0 29.4 1.0 CD C:GLU11 4.1 33.0 1.0 O C:HOH1784 4.2 39.5 1.0 O C:HOH2075 4.2 40.7 1.0 CA C:GLY30 4.5 15.3 1.0 N C:GLY30 4.6 13.6 1.0 O C:ASP10 4.6 26.0 1.0 CG C:GLU11 4.7 32.1 1.0 O C:HOH1354 4.7 30.3 1.0 N C:GLY12 4.8 30.6 1.0 CZ C:TYR18 4.9 29.4 1.0 N C:GLU11 5.0 23.6 1.0

B.H.Mooers, W.A.Baase, J.W.Wray, B.W.Matthews. Contributions of All 20 Amino Acids at Site 96 to the Stability and Structure of T4 Lysozyme. Protein Sci. V. 18 871 2009.
ISSN: ISSN 0961-8368
PubMed: 19384988
DOI: 10.1002/PRO.94