Sodium in PDB 7xe6: T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7

All present enzymatic activity of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7:
3.2.1.17;

The structure of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7, PDB code: 7xe6 was solved by T.Tamada, T.Hiromoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.52 / 1.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.999, 59.999, 97.101, 90, 90, 120
R / Rfree (%)	14.8 / 16.8

The binding sites of Sodium atom in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7 (pdb code 7xe6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7, PDB code: 7xe6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:9.1 occ:1.00 OE2 A:GLU45 3.0 13.8 0.2 NZ A:LYS48 3.1 12.1 1.0 CE A:LYS48 3.5 12.1 1.0 CD A:LYS48 3.7 10.6 1.0 CB A:CYS44 4.0 11.7 1.0 CD A:GLU45 4.0 12.6 0.2 O A:CYS44 4.1 10.7 1.0 C A:CYS44 4.1 10.0 1.0 OE1 A:GLU45 4.3 10.8 0.8 N A:GLU45 4.3 10.1 1.0 CD A:GLU45 4.4 10.5 0.8 CA A:GLU45 4.5 10.3 0.2 CA A:GLU45 4.5 10.1 0.8 CB A:LYS48 4.6 10.2 1.0 OE2 A:GLU45 4.6 12.4 0.8 CA A:CYS44 4.7 10.9 1.0 OE1 A:GLU45 4.7 12.7 0.2 CG A:LYS48 4.8 10.5 1.0 CG A:GLU45 4.8 11.3 0.2 CG A:GLU45 4.9 10.2 0.8

Sodium binding site 2 out of 3 in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:14.6 occ:1.00 OE1 A:GLU128 1.8 14.0 0.4 CD A:GLU128 2.6 13.4 0.4 OE2 A:GLU128 3.0 14.2 0.4 N A:ASP127 3.2 9.4 1.0 N A:TRP126 3.4 8.7 1.0 C A:ARG125 3.4 8.4 1.0 N A:GLU128 3.4 9.2 1.0 CB A:ASP127 3.6 10.2 1.0 CA A:ARG125 3.7 9.0 1.0 CA A:ASP127 3.8 9.8 1.0 CG A:GLU128 3.9 11.8 0.6 O A:ARG125 3.9 8.9 1.0 CG A:GLU128 3.9 12.2 0.4 CB A:ARG125 4.1 9.9 1.0 C A:TRP126 4.1 8.7 1.0 C A:ASP127 4.1 9.1 1.0 OE2 A:GLU128 4.2 15.4 0.6 CA A:TRP126 4.3 8.7 1.0 CB A:GLU128 4.3 10.1 0.6 CB A:GLU128 4.3 10.5 0.4 CA A:GLU128 4.5 9.4 0.6 CA A:GLU128 4.5 9.5 0.4 CG A:ASP127 4.5 10.5 1.0 CD A:GLU128 4.5 13.6 0.6 O A:HOH301 4.5 21.9 1.0 O A:HOH443 4.6 11.8 1.0 OD1 A:ASP127 4.8 11.2 1.0 CG A:ARG125 4.9 10.5 1.0

Sodium binding site 3 out of 3 in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, PH7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:48.4 occ:1.00 NH1 A:ARG80 2.5 40.4 1.0 CB A:ARG80 2.7 26.0 1.0 OE1 A:GLU108 2.7 21.2 0.4 OE2 A:GLU108 2.9 22.4 0.4 OE2 A:GLU108 2.9 21.4 0.6 O A:GLY77 2.9 24.0 1.0 CD A:GLU108 3.0 21.4 0.4 C A:ARG80 3.1 20.3 1.0 OE1 A:GLU108 3.2 21.5 0.6 CD A:GLU108 3.3 20.6 0.6 N A:ASN81 3.4 18.3 1.0 CA A:ARG80 3.4 22.3 1.0 O A:ARG80 3.4 21.8 1.0 CZ A:ARG80 3.5 39.8 1.0 C A:GLY77 3.7 21.9 1.0 CA A:GLY77 3.8 23.5 1.0 CA A:ASN81 3.9 16.6 1.0 O A:HOH302 3.9 36.9 1.0 N A:ARG80 4.0 20.6 1.0 CG A:ARG80 4.0 30.8 1.0 CB A:ASN81 4.0 16.7 1.0 NE A:ARG80 4.2 37.8 1.0 NH2 A:ARG80 4.3 40.2 1.0 CD A:ARG80 4.3 34.6 1.0 CG A:GLU108 4.4 19.9 0.4 CG A:GLU108 4.5 18.8 0.6 O A:ARG76 4.5 24.6 1.0 ND2 A:ASN81 4.9 17.4 1.0 N A:GLY77 5.0 23.7 1.0 CG A:ASN81 5.0 16.6 1.0

T.Hiromoto, T.Ikura, E.Honjo, M.Blaber, R.Kuroki, T.Tamada. Creation of Cross-Linked Crystals with Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions. Front Mol Biosci V. 9 08394 2022.
ISSN: ESSN 2296-889X
PubMed: 35755825
DOI: 10.3389/FMOLB.2022.908394