Sodium in PDB 5xpf: High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme

All present enzymatic activity of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme:
3.2.1.17;

The structure of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme, PDB code: 5xpf was solved by T.Hiromoto, R.Kuroki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.58 / 1.04
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.839, 59.839, 95.828, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 19.3

The structure of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme (pdb code 5xpf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme, PDB code: 5xpf:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:18.9 occ:0.69 O A:HOH471 2.5 22.7 1.0 OH A:TYR25 2.5 18.7 0.6 O A:HOH432 2.6 26.8 1.0 O A:PRO37 2.6 24.0 1.0 OH A:TYR25 2.8 18.5 0.5 CZ A:TYR25 3.7 16.3 0.6 C A:PRO37 3.7 20.3 1.0 CZ A:TYR25 3.7 15.4 0.5 O A:HOH466 3.8 32.6 1.0 CE2 A:TYR25 3.9 15.5 0.5 CE2 A:TYR25 4.1 15.5 0.6 CA A:PRO37 4.2 21.6 1.0 O A:HOH303 4.2 30.7 1.0 CB A:PRO37 4.4 25.5 1.0 NZ A:LYS19 4.4 17.0 1.0 CE A:LYS19 4.7 16.1 1.0 N A:LEU39 4.8 19.0 1.0 CE1 A:TYR25 4.8 15.2 0.6 N A:SER38 4.8 20.3 1.0 O A:HOH328 4.9 25.4 1.0 CE1 A:TYR25 4.9 15.6 0.5

Sodium binding site 2 out of 3 in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:12.4 occ:0.70 O A:HOH480 2.5 31.2 1.0 O A:HOH403 2.7 17.1 0.6 O A:GLY30 2.8 12.7 1.0 O A:PHE104 2.8 12.3 1.0 O A:HOH443 3.0 21.2 0.5 O A:HOH452 3.1 23.4 1.0 CE1 A:PHE104 3.3 12.9 1.0 CD1 A:PHE104 3.4 12.1 1.0 O A:HOH403 3.9 16.5 0.4 C A:PHE104 3.9 11.1 1.0 C A:GLY30 4.0 11.4 1.0 CZ A:PHE104 4.1 12.7 1.0 CG A:PHE104 4.2 10.8 1.0 O A:HOH443 4.2 18.5 0.5 O A:HOH414 4.4 39.7 1.0 N A:LEU32 4.6 12.4 1.0 CE2 A:PHE104 4.7 12.3 1.0 CA A:PHE104 4.7 11.0 1.0 CA A:GLN105 4.7 11.2 1.0 N A:GLN105 4.8 11.1 1.0 CA A:GLY30 4.8 12.2 1.0 CD2 A:PHE104 4.8 11.7 1.0 OE1 A:GLU11 4.8 15.8 1.0 N A:HIS31 4.9 11.5 1.0 CA A:HIS31 4.9 11.2 1.0 NE2 A:HIS26 5.0 14.8 1.0

Sodium binding site 3 out of 3 in the High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Resolution X-Ray Structure of the T26H Mutant of T4 Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:20.3 occ:0.53 O A:HOH418 2.3 17.7 0.5 O A:HOH418 2.4 19.8 0.5 O A:HOH408 2.4 18.0 0.4 O A:HOH386 2.5 19.2 1.0 O A:GLU11 2.6 14.5 1.0 O A:HOH483 2.8 34.4 1.0 C A:GLU11 3.4 12.8 1.0 O A:HOH408 3.5 23.2 0.6 O A:HOH513 3.8 45.4 1.0 CA A:GLU11 3.8 12.2 1.0 O A:HOH459 4.1 27.9 1.0 O A:HOH396 4.2 15.4 1.0 OE2 A:GLU11 4.2 15.8 1.0 O A:ASP10 4.3 13.8 1.0 N A:GLY12 4.4 12.4 1.0 CE1 A:TYR18 4.5 14.1 1.0 OH A:TYR18 4.6 14.2 1.0 CB A:GLU11 4.7 12.6 1.0 CA A:GLY12 4.8 13.2 1.0 CZ A:TYR18 4.9 12.8 1.0 N A:GLU11 4.9 11.7 1.0 C A:ASP10 5.0 11.3 1.0

T.Hiromoto, F.Meilleur, R.Shimizu, C.Shibazaki, M.Adachi, T.Tamada, R.Kuroki. Neutron Structure of the T26H Mutant of T4 Phage Lysozyme Provides Insight Into the Catalytic Activity of the Mutant Enzyme and How It Differs From That of Wild Type. Protein Sci. V. 26 1953 2017.
ISSN: ESSN 1469-896X
PubMed: 28707339
DOI: 10.1002/PRO.3230