Chlorine in PDB 6d9i: Pekin Duck Egg Lysozyme Isoform II (Del-II)

All present enzymatic activity of Pekin Duck Egg Lysozyme Isoform II (Del-II):
3.2.1.17;

The structure of Pekin Duck Egg Lysozyme Isoform II (Del-II), PDB code: 6d9i was solved by D.B.Langley, D.Christ, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.99 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.340, 55.130, 69.029, 90.00, 95.95, 90.00
R / Rfree (%)	15.5 / 18.6

The structure of Pekin Duck Egg Lysozyme Isoform II (Del-II) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the Pekin Duck Egg Lysozyme Isoform II (Del-II) (pdb code 6d9i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Pekin Duck Egg Lysozyme Isoform II (Del-II), PDB code: 6d9i:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Pekin Duck Egg Lysozyme Isoform II (Del-II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pekin Duck Egg Lysozyme Isoform II (Del-II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:15.7 occ:1.00 OG A:SER24 3.1 12.6 1.0 O A:HOH406 3.1 24.7 1.0 N A:GLY26 3.2 6.7 1.0 CB A:SER24 3.5 10.0 1.0 CA A:GLY26 3.5 6.7 1.0 CA A:SER121 3.6 10.2 1.0 CB A:SER121 3.9 12.5 1.0 N A:SER121 4.0 9.8 1.0 N A:LEU25 4.1 7.3 1.0 CD1 A:ILE124 4.3 18.4 1.0 C A:SER24 4.3 8.2 1.0 C A:VAL120 4.3 8.4 1.0 O A:VAL120 4.3 9.4 1.0 C A:LEU25 4.3 7.3 1.0 CG2 A:VAL120 4.4 9.4 1.0 CA A:SER24 4.5 8.0 1.0 C A:GLY26 4.6 7.3 1.0 CA A:LEU25 4.6 7.0 1.0 O A:SER24 4.7 8.3 1.0 CG1 A:ILE124 4.7 16.0 1.0 N A:ASN27 4.7 7.0 1.0 O A:HOH302 4.7 13.6 0.5 C A:SER121 4.8 10.1 1.0 CB A:LEU25 4.9 7.1 1.0 O A:SER121 5.0 10.7 1.0 O A:HOH450 5.0 33.3 1.0 O A:HOH378 5.0 23.4 1.0

Chlorine binding site 2 out of 5 in the Pekin Duck Egg Lysozyme Isoform II (Del-II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pekin Duck Egg Lysozyme Isoform II (Del-II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:18.2 occ:1.00 O A:HOH411 2.8 14.3 1.0 O A:HOH356 2.9 9.0 1.0 O A:HOH377 3.3 14.5 1.0 CD A:LYS96 3.7 8.0 1.0 CG A:ARG93 4.1 8.6 1.0 NH1 A:ARG93 4.2 14.9 1.0 CA A:ARG93 4.3 8.1 1.0 NZ A:LYS96 4.3 10.5 1.0 CB A:ARG93 4.5 7.7 1.0 CB A:LYS96 4.5 7.1 1.0 CE A:LYS96 4.7 8.5 1.0 O A:ARG93 4.7 8.0 1.0 CG A:LYS96 4.7 7.7 1.0 O A:HOH427 4.8 29.1 1.0 O A:HOH418 4.9 11.4 1.0

Chlorine binding site 3 out of 5 in the Pekin Duck Egg Lysozyme Isoform II (Del-II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pekin Duck Egg Lysozyme Isoform II (Del-II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:17.0 occ:1.00 O B:HOH335 3.0 16.6 1.0 CA B:ALA110 3.6 8.5 1.0 CB B:ASN113 3.8 13.7 1.0 O B:VAL109 3.8 9.2 1.0 CG1 B:VAL109 3.9 12.3 1.0 CG B:ARG114 3.9 9.9 1.0 N B:ALA110 4.0 8.8 1.0 C B:VAL109 4.0 9.6 1.0 CB B:ALA110 4.1 8.6 1.0 CD B:ARG114 4.2 10.2 1.0 O B:HOH389 4.2 20.9 1.0 ND2 B:ASN113 4.4 12.0 1.0 CG B:ASN113 4.5 12.8 1.0 C B:ALA110 4.7 9.6 1.0 O B:HOH330 4.7 14.2 1.0 O B:ALA110 4.8 10.5 1.0 CB B:VAL109 4.8 11.2 1.0 CA B:ASN113 4.9 12.9 1.0

Chlorine binding site 4 out of 5 in the Pekin Duck Egg Lysozyme Isoform II (Del-II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pekin Duck Egg Lysozyme Isoform II (Del-II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:14.0 occ:1.00 O B:HOH379 3.1 10.1 1.0 O B:HOH342 3.2 14.5 1.0 ND2 B:ASN33 3.4 10.0 1.0 CE1 B:TYR34 3.7 10.0 1.0 CD1 B:TYR34 4.1 9.1 1.0 OD1 B:ASN33 4.2 11.8 1.0 CG B:ASN33 4.2 10.9 1.0 O B:HOH331 4.5 22.2 1.0 CZ B:TYR34 4.6 10.0 1.0 OH B:TYR34 4.8 11.9 1.0 O B:HOH378 4.9 14.5 1.0 O B:HOH314 5.0 17.3 1.0

Chlorine binding site 5 out of 5 in the Pekin Duck Egg Lysozyme Isoform II (Del-II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pekin Duck Egg Lysozyme Isoform II (Del-II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl204 b:15.1 occ:1.00 OG B:SER24 2.9 12.7 1.0 N B:GLY26 3.2 7.5 1.0 O B:HOH392 3.2 22.5 1.0 CB B:SER24 3.4 10.2 1.0 CA B:GLY26 3.5 7.2 1.0 CA B:SER121 3.6 10.2 1.0 CB B:SER121 4.0 12.0 1.0 N B:SER121 4.0 9.4 1.0 N B:LEU25 4.1 7.8 1.0 CD1 B:ILE124 4.1 16.4 1.0 C B:SER24 4.3 8.1 1.0 CG2 B:VAL120 4.3 12.3 1.0 C B:LEU25 4.3 7.6 1.0 O B:VAL120 4.4 8.7 1.0 C B:VAL120 4.4 8.0 1.0 CA B:SER24 4.5 8.5 1.0 C B:GLY26 4.6 6.6 1.0 CG1 B:ILE124 4.6 13.7 1.0 N B:ASN27 4.7 6.9 1.0 CA B:LEU25 4.7 7.7 1.0 O B:SER24 4.7 9.4 1.0 C B:SER121 4.8 10.6 1.0 O B:SER121 5.0 11.9 1.0 CB B:LEU25 5.0 8.0 1.0

D.B.Langley, D.Christ. Crystal Structure of Duck Egg Lysozyme Isoform II (Del-II). Bmc Struct. Biol. V. 18 10 2018.
ISSN: ESSN 1472-6807
PubMed: 30134879
DOI: 10.1186/S12900-018-0090-7