Chlorine in PDB 5b05: Lysozyme (Control Experiment)

All present enzymatic activity of Lysozyme (Control Experiment):
3.2.1.17;

The structure of Lysozyme (Control Experiment), PDB code: 5b05 was solved by A.Kita, Y.Morimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.73 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.816, 78.816, 36.800, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18.7

The structure of Lysozyme (Control Experiment) also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

The binding sites of Chlorine atom in the Lysozyme (Control Experiment) (pdb code 5b05). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Lysozyme (Control Experiment), PDB code: 5b05:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme (Control Experiment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2013 b:18.2 occ:1.00 OH A:TYR23 3.0 13.7 1.0 NA A:NA2009 3.3 23.3 1.0 CZ A:TYR23 3.7 13.8 1.0 CE2 A:TYR23 3.7 12.8 1.0 C1 A:EDO2002 4.1 33.3 1.0 CA A:GLY104 4.1 14.9 1.0 O A:ARG21 4.6 15.7 1.0 N A:GLY104 4.7 13.9 1.0 CE1 A:TYR23 4.9 13.1 1.0 CD2 A:TYR23 4.9 12.2 1.0

Chlorine binding site 2 out of 4 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme (Control Experiment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2014 b:19.5 occ:1.00 O A:HOH2206 3.1 29.9 1.0 O A:HOH2152 3.1 11.9 1.0 N A:THR69 3.1 17.1 1.0 O A:THR69 3.3 17.9 1.0 N A:ARG68 3.5 15.5 1.0 C A:GLY67 3.5 16.1 1.0 O A:HOH2214 3.5 25.8 1.0 O A:HOH2118 3.5 32.2 1.0 CA A:GLY67 3.6 15.2 1.0 N A:GLY67 3.7 16.0 1.0 C A:THR69 3.7 18.4 1.0 OD1 A:ASN65 3.7 18.6 1.0 OG A:SER72 3.7 21.1 1.0 CA A:THR69 3.8 17.3 1.0 NA A:NA2011 4.0 26.9 1.0 CB A:THR69 4.1 17.2 1.0 C A:ARG68 4.1 17.9 1.0 OD1 A:ASP66 4.2 13.7 1.0 O A:GLY67 4.2 20.2 1.0 CA A:ARG68 4.2 17.4 1.0 N A:PRO70 4.6 19.5 1.0 O A:HOH2101 4.7 11.2 1.0 OG1 A:THR69 4.7 16.0 1.0 C A:ASP66 4.7 14.5 1.0 O A:HOH2169 4.8 22.1 0.5 O A:HOH2163 4.8 44.0 1.0 CG A:ASN65 4.8 18.5 1.0 N A:ASP66 4.9 13.7 1.0 CB A:SER72 4.9 21.3 1.0

Chlorine binding site 3 out of 4 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme (Control Experiment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2015 b:21.9 occ:1.00 O A:HOH2199 2.8 34.9 1.0 OG A:SER24 3.0 18.5 1.0 N A:GLY26 3.2 15.3 1.0 CA A:GLY26 3.5 15.2 1.0 CB A:SER24 3.5 18.8 1.0 CA A:GLN121 3.6 19.9 1.0 CD1 A:ILE124 3.8 26.6 1.0 N A:GLN121 4.0 18.5 1.0 CB A:GLN121 4.0 25.2 1.0 CG1 A:ILE124 4.2 22.0 1.0 O A:VAL120 4.3 16.4 1.0 CG2 A:VAL120 4.3 16.7 1.0 C A:VAL120 4.3 16.4 1.0 N A:LEU25 4.3 16.7 1.0 CG A:GLN121 4.3 31.4 1.0 C A:LEU25 4.4 16.5 1.0 C A:SER24 4.4 17.3 1.0 C A:GLY26 4.5 14.0 1.0 CA A:SER24 4.5 16.2 1.0 N A:ASN27 4.6 12.2 1.0 CA A:LEU25 4.8 16.2 1.0 C A:GLN121 4.8 17.2 1.0 O A:SER24 4.9 14.7 1.0

Chlorine binding site 4 out of 4 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme (Control Experiment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2016 b:27.9 occ:1.00 NZ A:LYS33 3.5 24.3 1.0 CE2 A:PHE38 3.7 15.4 1.0 CZ3 A:TRP123 4.0 16.1 1.0 CE A:LYS33 4.1 21.0 1.0 O A:HOH2181 4.1 38.7 1.0 CD A:ARG5 4.1 22.5 1.0 CD A:LYS33 4.2 16.9 1.0 CB A:ARG5 4.3 19.4 1.0 CZ A:PHE38 4.4 13.6 1.0 O A:HOH2196 4.4 40.4 1.0 CD2 A:PHE38 4.6 15.9 1.0 CG A:ARG5 4.7 18.8 1.0 CE3 A:TRP123 4.7 16.1 1.0 NE A:ARG5 4.8 21.2 1.0 CH2 A:TRP123 4.9 16.7 1.0

A.Kita, Y.Morimoto. An Effective Deuterium Exchange Method For Neutron Crystal Structure Analysis with Unfolding-Refolding Processes Mol Biotechnol. V. 58 130 2016.
ISSN: ESSN 1559-0305
PubMed: 26718545
DOI: 10.1007/S12033-015-9908-8