Sodium in PDB 6lfh: X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme

All present enzymatic activity of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme:
3.2.1.17;

The structure of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme, PDB code: 6lfh was solved by A.Kar, A.Das, K.Mandal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.61 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	32.950, 56.410, 61.220, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.6

The structure of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme (pdb code 6lfh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme, PDB code: 6lfh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ X:Na207 b:23.0 occ:1.00 O X:HOH433 2.3 30.6 1.0 O X:HOH384 2.4 17.1 1.0 O X:PRO103 2.4 18.2 1.0 O X:HOH325 2.4 17.0 1.0 O X:ASP102 2.8 20.6 1.0 C X:PRO103 3.0 19.0 1.0 CA X:PRO103 3.4 17.1 1.0 N X:GLY105 3.6 15.8 1.0 C X:ASP102 3.7 20.5 1.0 N X:PRO103 4.0 18.5 1.0 CA X:GLY105 4.0 15.0 1.0 N X:GLN104 4.1 15.3 1.0 O X:VAL100 4.1 14.9 1.0 C X:GLN104 4.2 15.7 1.0 NH1 X:ARG21 4.3 11.1 0.5 CA X:GLN104 4.7 15.1 1.0 O X:ARG101 4.8 20.0 1.0 CB X:PRO103 4.8 21.0 1.0 C X:ARG101 4.9 17.3 1.0 O X:GLN104 4.9 16.3 1.0 CA X:ASP102 5.0 19.0 1.0

Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ X:Na208 b:22.2 occ:1.00 O X:HIS78 2.2 20.4 1.0 O X:HOH426 2.4 23.5 1.0 O X:HOH412 2.6 26.2 1.0 C X:HIS78 3.3 18.9 1.0 ND1 X:HIS78 3.9 26.1 1.0 CA X:LEU79 4.1 13.7 1.0 N X:LEU79 4.1 13.8 1.0 CD2 X:LEU79 4.2 18.7 1.0 CB X:HIS78 4.3 20.3 1.0 CA X:HIS78 4.4 22.1 1.0 O X:HOH380 4.5 18.9 1.0 CG X:HIS78 4.5 25.4 1.0 CG X:LEU79 4.9 22.4 1.0 CE1 X:HIS78 5.0 29.5 1.0 CB X:LEU79 5.0 20.1 1.0

A.Kar, J.Mannuthodikayil, S.Singh, A.Biswas, P.Dubey, A.Das, K.Mandal. Efficient Chemical Protein Synthesis Using Fmoc-Masked N-Terminal Cysteine in Peptide Thioester Segments. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32333711
DOI: 10.1002/ANIE.202000491