Sodium in PDB 5kim: Pseudo T4 Lysozyme Mutant - Y88PHE-I

All present enzymatic activity of Pseudo T4 Lysozyme Mutant - Y88PHE-I:
3.2.1.17;

The structure of Pseudo T4 Lysozyme Mutant - Y88PHE-I, PDB code: 5kim was solved by M.R.Scholfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.37 / 1.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.283, 60.283, 96.197, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 18.4

The structure of Pseudo T4 Lysozyme Mutant - Y88PHE-I also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Sodium atom in the Pseudo T4 Lysozyme Mutant - Y88PHE-I (pdb code 5kim). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pseudo T4 Lysozyme Mutant - Y88PHE-I, PDB code: 5kim:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pseudo T4 Lysozyme Mutant - Y88PHE-I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pseudo T4 Lysozyme Mutant - Y88PHE-I within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:15.9 occ:1.00 OE1 A:GLN105 2.8 8.9 1.0 OD1 A:ASN101 2.8 9.3 1.0 CA A:MET102 3.3 8.1 1.0 NE A:ARG145 3.4 12.0 1.0 CZ2 A:TRP138 3.5 9.7 1.0 N A:MET102 3.5 8.2 1.0 O A:ASN101 3.6 7.9 1.0 NE1 A:TRP138 3.6 9.6 1.0 C A:ASN101 3.6 8.0 1.0 CG2 A:VAL149 3.7 8.6 1.0 CE2 A:TRP138 3.8 8.7 1.0 CG A:MET102 3.8 11.0 1.0 CG A:ASN101 3.9 8.3 1.0 CB A:GLN105 3.9 8.2 1.0 CD A:GLN105 3.9 10.0 1.0 CD A:ARG145 4.0 15.4 1.0 CZ A:ARG145 4.0 10.3 1.0 CB A:MET102 4.1 8.5 1.0 NH2 A:ARG145 4.2 9.0 1.0 CB A:ASN101 4.4 8.3 1.0 CG1 A:VAL149 4.4 9.5 1.0 CB A:VAL149 4.4 7.8 1.0 C A:MET102 4.5 8.6 1.0 CE A:MET106 4.5 11.7 0.5 CG A:GLN105 4.5 9.8 1.0 CH2 A:TRP138 4.6 10.8 1.0 CA A:ASN101 4.6 7.9 1.0 O A:MET102 4.6 9.7 1.0 CD1 A:TRP138 4.8 9.7 1.0 ND2 A:ASN101 4.9 7.9 1.0

Sodium binding site 2 out of 2 in the Pseudo T4 Lysozyme Mutant - Y88PHE-I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pseudo T4 Lysozyme Mutant - Y88PHE-I within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:10.6 occ:1.00 O A:HOH321 2.4 22.1 1.0 O A:HOH607 3.0 34.5 1.0 CE A:LYS124 3.4 10.7 0.6 NZ A:LYS124 3.4 9.6 0.4 CE A:LYS124 3.8 10.4 0.4 O A:HOH391 3.9 21.4 1.0 CD A:LYS124 4.3 9.9 0.6 CD A:LYS124 4.3 10.0 0.4 NZ A:LYS124 4.5 9.9 0.6 O A:HOH471 4.9 22.1 1.0 O A:SER90 5.0 9.4 1.0

M.R.Scholfield, M.C.Ford, A.C.Carlsson, H.Butta, R.A.Mehl, P.S.Ho. Structure-Energy Relationships of Halogen Bonds in Proteins. Biochemistry V. 56 2794 2017.
ISSN: ISSN 1520-4995
PubMed: 28345933
DOI: 10.1021/ACS.BIOCHEM.7B00022