Chlorine in PDB 5kxm: Hen Egg White Lysozyme at 100K, Data Set 3

All present enzymatic activity of Hen Egg White Lysozyme at 100K, Data Set 3:
3.2.1.17;

The structure of Hen Egg White Lysozyme at 100K, Data Set 3, PDB code: 5kxm was solved by S.Russi, A.Gonzalez, L.R.Kenner, D.A.Keedy, J.S.Fraser, H.Van Den Bedem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.20 / 1.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.289, 77.289, 37.205, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18

The structure of Hen Egg White Lysozyme at 100K, Data Set 3 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Hen Egg White Lysozyme at 100K, Data Set 3 (pdb code 5kxm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Hen Egg White Lysozyme at 100K, Data Set 3, PDB code: 5kxm:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Hen Egg White Lysozyme at 100K, Data Set 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hen Egg White Lysozyme at 100K, Data Set 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:11.0 occ:1.00 OH A:TYR23 2.8 7.8 0.3 OH A:TYR23 2.9 9.2 0.1 OH A:TYR23 3.0 7.8 0.6 O A:HOH364 3.2 10.7 1.0 O A:HOH401 3.3 27.1 1.0 CZ A:TYR23 3.5 7.5 0.3 CZ A:TYR23 3.6 9.1 0.1 CE2 A:TYR23 3.6 7.4 0.3 CZ A:TYR23 3.6 7.0 0.6 CE2 A:TYR23 3.7 6.7 0.6 CE2 A:TYR23 3.7 9.0 0.1 CA A:GLY104 4.2 7.6 1.0 O A:ARG21 4.5 10.8 1.0 CE1 A:TYR23 4.7 7.3 0.3 CE1 A:TYR23 4.8 9.0 0.1 N A:GLY104 4.8 7.8 1.0 CE1 A:TYR23 4.8 6.8 0.6 CD2 A:TYR23 4.8 7.3 0.3 CD2 A:TYR23 4.9 9.0 0.1 CD2 A:TYR23 4.9 6.9 0.6

Chlorine binding site 2 out of 3 in the Hen Egg White Lysozyme at 100K, Data Set 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hen Egg White Lysozyme at 100K, Data Set 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:11.3 occ:1.00 O A:HOH440 3.1 17.6 1.0 O A:HOH339 3.1 8.8 1.0 N A:THR69 3.1 8.5 0.5 O A:THR69 3.2 10.4 0.3 N A:THR69 3.2 11.4 0.3 O A:THR69 3.2 10.9 0.2 N A:THR69 3.2 10.7 0.2 O A:HOH402 3.3 15.0 1.0 O A:THR69 3.5 9.6 0.5 O A:HOH360 3.5 21.6 1.0 C A:GLY67 3.5 9.7 1.0 N A:ARG68 3.5 9.8 0.5 N A:ARG68 3.5 8.9 0.5 OG A:SER72 3.5 11.4 1.0 CA A:GLY67 3.5 9.2 1.0 C A:THR69 3.6 10.8 0.3 C A:THR69 3.6 10.9 0.2 N A:GLY67 3.7 8.5 1.0 C A:THR69 3.7 9.3 0.5 OD1 A:ASN65 3.7 8.4 0.8 CA A:THR69 3.8 11.2 0.3 CA A:THR69 3.8 9.1 0.5 CA A:THR69 3.8 11.1 0.2 O A:HOH384 4.0 11.1 1.0 O A:GLY67 4.1 11.3 1.0 OD1 A:ASP66 4.2 7.7 0.2 CB A:THR69 4.2 8.8 0.5 CB A:THR69 4.2 10.8 0.3 CB A:THR69 4.2 11.4 0.2 C A:ARG68 4.2 11.7 0.5 C A:ARG68 4.2 10.4 0.5 OD1 A:ASP66 4.2 7.3 0.8 CA A:ARG68 4.3 11.2 0.5 CA A:ARG68 4.3 9.4 0.5 OD1 A:ASN65 4.3 9.3 0.2 N A:PRO70 4.5 11.3 1.0 O A:HOH434 4.6 30.9 1.0 NA A:NA201 4.7 10.1 1.0 C A:ASP66 4.7 8.5 0.2 OG1 A:THR69 4.7 10.6 0.3 C A:ASP66 4.8 8.0 0.8 CB A:SER72 4.8 11.6 1.0 OG1 A:THR69 4.8 7.8 0.5 OG1 A:THR69 4.8 11.1 0.2 O A:HOH371 4.9 14.2 0.5 N A:ASP66 4.9 8.2 0.2 N A:ASP66 4.9 6.9 0.8 CG A:ASN65 4.9 8.5 0.8

Chlorine binding site 3 out of 3 in the Hen Egg White Lysozyme at 100K, Data Set 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hen Egg White Lysozyme at 100K, Data Set 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:33.1 occ:1.00 N A:GLY26 3.0 7.6 1.0 OG A:SER24 3.3 9.7 0.1 OG A:SER24 3.3 10.8 0.3 CD1 A:ILE124 3.5 12.8 0.5 CA A:GLY26 3.5 8.2 1.0 CB A:SER24 3.6 9.4 0.1 CB A:SER24 3.6 10.1 0.3 OG A:SER24 3.6 9.8 0.6 CB A:SER24 3.7 9.6 0.6 CD1 A:ILE124 3.7 12.8 0.2 CG1 A:ILE124 3.8 13.6 0.3 N A:LEU25 3.9 8.5 1.0 CA A:GLN121 4.0 14.6 1.0 CG1 A:ILE124 4.1 12.2 0.5 CG1 A:ILE124 4.1 12.3 0.2 C A:LEU25 4.1 7.7 1.0 CB A:GLN121 4.2 16.7 0.5 C A:SER24 4.2 8.6 0.6 CG A:GLN121 4.2 18.2 0.5 CB A:GLN121 4.3 17.1 0.5 C A:SER24 4.3 8.7 0.1 CD1 A:ILE124 4.3 14.1 0.3 C A:SER24 4.3 8.7 0.3 CA A:LEU25 4.3 8.6 1.0 O A:HOH390 4.4 12.0 0.5 CB A:LEU25 4.5 8.7 0.4 N A:GLN121 4.5 12.3 1.0 CB A:LEU25 4.5 9.0 0.6 CA A:SER24 4.5 9.0 0.1 CA A:SER24 4.6 9.1 0.3 O A:VAL120 4.6 10.5 1.0 CA A:SER24 4.6 8.9 0.6 CG2 A:ILE124 4.6 12.2 0.2 CG2 A:VAL120 4.7 12.0 0.5 C A:VAL120 4.7 10.5 1.0 C A:GLY26 4.7 7.6 1.0 O A:SER24 4.7 8.5 0.6 N A:ASN27 4.9 7.2 1.0 CG2 A:ILE124 4.9 11.4 0.5 O A:SER24 5.0 8.8 0.1 O A:SER24 5.0 8.9 0.3

S.Russi, A.Gonzalez, L.R.Kenner, D.A.Keedy, J.S.Fraser, H.Van Den Bedem. Conformational Variation of Proteins at Room Temperature Is Not Dominated By Radiation Damage. J Synchrotron Radiat V. 24 73 2017.
ISSN: ESSN 1600-5775
PubMed: 28009548
DOI: 10.1107/S1600577516017343