Sodium in PDB 5v7e: T4 Lysozyme Y18YMCL

All present enzymatic activity of T4 Lysozyme Y18YMCL:
3.2.1.17;

The structure of T4 Lysozyme Y18YMCL, PDB code: 5v7e was solved by A.-C.C.Carlsson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.98 / 1.36
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.610, 59.610, 95.120, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 20.5

The structure of T4 Lysozyme Y18YMCL also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the T4 Lysozyme Y18YMCL (pdb code 5v7e). 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 Y18YMCL, PDB code: 5v7e:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the T4 Lysozyme Y18YMCL


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of T4 Lysozyme Y18YMCL within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:16.6 occ:1.00 O A:HOH420 3.0 15.9 1.0 O A:HOH593 3.0 27.2 1.0 NZ A:LYS135 3.0 28.4 0.8 ND2 A:ASN132 3.1 14.0 1.0 CE A:LYS135 3.6 23.9 0.2 CB A:ASN132 3.7 9.5 1.0 CE A:LYS135 3.7 23.9 0.8 CA A:ASN132 3.7 8.5 1.0 CD A:LYS135 3.9 22.3 0.8 CG A:ASN132 3.9 12.9 1.0 CD A:LYS135 4.1 21.4 0.2 N A:ASN132 4.1 7.4 1.0 CG1 A:VAL131 4.1 13.5 1.0 CE A:MET120 4.5 11.7 0.7 O A:HOH527 4.5 30.4 1.0 C A:VAL131 4.6 10.3 1.0 O A:HOH628 4.6 43.5 1.0 O A:GLU128 4.8 10.3 1.0 O A:VAL131 4.8 11.8 1.0 CB A:VAL131 4.9 11.8 1.0 NZ A:LYS135 4.9 20.9 0.2 O A:HOH621 4.9 21.3 1.0 CE A:MET120 5.0 13.7 0.3

Sodium binding site 2 out of 3 in the T4 Lysozyme Y18YMCL


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of T4 Lysozyme Y18YMCL within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:35.4 occ:1.00 O A:HOH337 3.1 30.1 1.0 CA A:ALA160 3.6 12.7 1.0 N A:ALA160 3.9 13.4 1.0 O A:ASP159 3.9 17.8 1.0 CB A:ALA160 3.9 11.4 1.0 C A:ASP159 4.0 14.6 1.0 CG2 A:THR151 4.0 15.0 1.0 O A:HOH369 4.3 28.7 1.0 O A:HOH587 4.3 23.3 1.0 O A:HOH506 4.3 43.6 1.0 CB A:ASP159 4.4 18.3 1.0 O A:HOH609 4.5 40.6 1.0 O A:HOH404 4.6 16.9 1.0 OG1 A:THR151 4.6 16.5 1.0 CB A:THR151 4.8 11.9 1.0 CA A:ASP159 4.9 13.6 1.0 C A:ALA160 4.9 13.2 1.0

Sodium binding site 3 out of 3 in the T4 Lysozyme Y18YMCL


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of T4 Lysozyme Y18YMCL within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:12.5 occ:1.00 N A:ARG145 3.2 8.1 1.0 N A:ASN144 3.3 9.3 1.0 O A:HOH533 3.4 30.3 1.0 C A:THR142 3.4 8.4 1.0 CA A:THR142 3.5 8.6 1.0 CB A:THR142 3.6 8.2 1.0 N A:PRO143 3.7 7.8 1.0 CB A:ASN144 3.8 10.7 1.0 O A:THR142 3.8 8.2 1.0 CA A:ASN144 3.8 9.7 1.0 CB A:ARG145 3.9 9.9 1.0 C A:ASN144 4.0 8.3 1.0 CD A:PRO143 4.2 9.1 1.0 CA A:ARG145 4.2 7.6 1.0 C A:PRO143 4.2 8.8 1.0 CG2 A:THR142 4.3 10.2 1.0 CA A:PRO143 4.6 7.8 1.0 CG A:ASN144 4.8 12.9 1.0 OG1 A:THR142 4.8 9.4 1.0 O A:HOH376 4.8 16.2 1.0 N A:THR142 4.9 7.6 1.0 CG A:PRO143 4.9 8.8 1.0

A.C.Carlsson, M.R.Scholfield, R.K.Rowe, M.C.Ford, A.T.Alexander, R.A.Mehl, P.S.Ho. Increasing Enzyme Stability and Activity Through Hydrogen Bond-Enhanced Halogen Bonds. Biochemistry V. 57 4135 2018.
ISSN: ISSN 1520-4995
PubMed: 29921126
DOI: 10.1021/ACS.BIOCHEM.8B00603