Chlorine in PDB 5b07: Lysozyme (Denatured By Dcl and Refolded)

All present enzymatic activity of Lysozyme (Denatured By Dcl and Refolded):
3.2.1.17;

The structure of Lysozyme (Denatured By Dcl and Refolded), PDB code: 5b07 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 (Denatured By Dcl and Refolded) also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

The binding sites of Chlorine atom in the Lysozyme (Denatured By Dcl and Refolded) (pdb code 5b07). 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 (Denatured By Dcl and Refolded), PDB code: 5b07:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme (Denatured By Dcl and Refolded) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2013 b:17.5 occ:1.00 OH A:TYR23 3.1 14.2 1.0 NA A:NA2009 3.3 22.5 1.0 CZ A:TYR23 3.7 13.6 1.0 CE2 A:TYR23 3.7 12.5 1.0 C1 A:EDO2002 4.1 33.4 1.0 CA A:GLY104 4.2 15.2 1.0 O A:ARG21 4.6 16.0 1.0 C2 A:EDO2002 4.6 41.4 1.0 N A:GLY104 4.7 14.1 1.0 CE1 A:TYR23 4.9 13.4 1.0 CD2 A:TYR23 5.0 12.0 1.0

Chlorine binding site 2 out of 4 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme (Denatured By Dcl and Refolded) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2014 b:18.2 occ:1.00 O A:HOH2146 3.1 12.6 1.0 O A:HOH2208 3.1 28.1 1.0 N A:THR69 3.2 15.7 1.0 O A:THR69 3.3 16.4 1.0 O A:HOH2217 3.4 28.0 1.0 O A:HOH2124 3.5 28.6 1.0 N A:ARG68 3.5 15.2 1.0 C A:GLY67 3.5 16.4 1.0 CA A:GLY67 3.6 15.6 1.0 N A:GLY67 3.7 15.9 1.0 OG A:SER72 3.7 18.6 1.0 C A:THR69 3.7 17.0 1.0 OD1 A:ASN65 3.7 17.9 1.0 CA A:THR69 3.8 15.8 1.0 NA A:NA2011 4.0 25.3 1.0 CB A:THR69 4.2 17.1 1.0 C A:ARG68 4.2 17.1 1.0 OD1 A:ASP66 4.2 13.2 1.0 O A:GLY67 4.2 17.1 1.0 CA A:ARG68 4.3 16.6 1.0 N A:PRO70 4.6 18.3 1.0 O A:HOH2101 4.7 8.3 1.0 OG1 A:THR69 4.7 15.3 1.0 C A:ASP66 4.7 14.9 1.0 O A:HOH2163 4.8 22.5 0.5 N A:ASP66 4.9 13.1 1.0 CG A:ASN65 4.9 17.4 1.0 CB A:SER72 4.9 17.0 1.0

Chlorine binding site 3 out of 4 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme (Denatured By Dcl and Refolded) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2015 b:21.0 occ:1.00 O A:HOH2200 2.8 35.8 1.0 OG A:SER24 3.0 18.0 1.0 N A:GLY26 3.1 14.6 1.0 CA A:GLY26 3.5 15.3 1.0 CB A:SER24 3.5 17.3 1.0 CA A:GLN121 3.6 19.7 1.0 CD1 A:ILE124 3.9 26.4 1.0 N A:GLN121 4.0 18.2 1.0 CB A:GLN121 4.0 25.9 1.0 N A:LEU25 4.3 16.6 1.0 CG1 A:ILE124 4.3 21.2 1.0 O A:VAL120 4.3 17.2 1.0 CG2 A:VAL120 4.3 18.3 1.0 C A:VAL120 4.3 16.4 1.0 C A:LEU25 4.3 16.3 1.0 CG A:GLN121 4.4 31.1 1.0 C A:SER24 4.4 16.8 1.0 C A:GLY26 4.5 14.5 1.0 CA A:SER24 4.5 15.4 1.0 N A:ASN27 4.7 12.2 1.0 CA A:LEU25 4.7 15.7 1.0 C A:GLN121 4.8 17.3 1.0 O A:SER24 4.8 14.8 1.0

Chlorine binding site 4 out of 4 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme (Denatured By Dcl and Refolded) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2016 b:27.2 occ:1.00 NZ A:LYS33 3.4 23.9 1.0 CE2 A:PHE38 3.7 17.7 1.0 CZ3 A:TRP123 3.9 16.2 1.0 O A:HOH2151 4.0 44.3 1.0 CE A:LYS33 4.0 21.1 1.0 CD A:ARG5 4.2 22.1 1.0 CD A:LYS33 4.2 17.0 1.0 CB A:ARG5 4.3 18.6 1.0 CZ A:PHE38 4.4 15.0 1.0 O A:HOH2199 4.6 35.4 1.0 CD2 A:PHE38 4.7 16.7 1.0 CG A:ARG5 4.7 18.5 1.0 NE A:ARG5 4.7 21.6 1.0 CE3 A:TRP123 4.7 17.0 1.0 CH2 A:TRP123 4.8 18.4 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