Magnesium 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:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pekin Duck Egg Lysozyme Isoform II (Del-II), PDB code: 6d9i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pekin Duck Egg Lysozyme Isoform II (Del-II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg201 b:18.4 occ:1.00 O A:HOH407 1.9 23.8 1.0 O A:HOH444 2.0 23.7 1.0 O A:HOH409 2.0 34.5 1.0 O A:HOH322 2.2 22.4 1.0 OE1 A:GLU35 2.3 14.0 1.0 O A:HOH326 2.3 19.9 1.0 CD A:GLU35 3.4 10.7 1.0 OE2 A:GLU35 3.9 13.8 1.0 O A:GLU35 4.1 9.6 1.0 O A:HOH342 4.2 33.8 1.0 O A:HOH330 4.2 17.8 1.0 CG A:GLN57 4.4 7.8 1.0 CA A:GLU35 4.4 8.2 1.0 OE1 A:GLN57 4.4 8.5 1.0 CB A:GLN57 4.5 7.0 1.0 OD2 A:ASP52 4.5 18.5 1.0 O A:HOH422 4.5 29.4 1.0 CG A:GLU35 4.6 9.0 1.0 CB A:GLU35 4.7 8.0 1.0 C A:GLU35 4.7 8.7 1.0 CB A:ALA110 4.9 9.9 1.0 CD A:GLN57 4.9 7.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pekin Duck Egg Lysozyme Isoform II (Del-II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:16.8 occ:1.00 O B:HOH409 1.9 22.3 1.0 O B:HOH369 2.0 18.9 1.0 O B:HOH313 2.0 14.9 1.0 O B:HOH389 2.1 20.9 1.0 OE1 B:GLU35 2.2 12.9 1.0 O B:HOH323 2.2 21.6 1.0 CD B:GLU35 3.3 11.2 1.0 OE2 B:GLU35 3.9 12.1 1.0 O B:GLU35 4.2 9.3 1.0 O B:HOH330 4.2 14.2 1.0 O B:HOH334 4.4 16.1 1.0 CA B:GLU35 4.4 8.4 1.0 CG B:GLN57 4.5 8.5 1.0 O B:HOH397 4.5 27.1 1.0 OE1 B:GLN57 4.5 9.6 1.0 CB B:GLN57 4.5 8.3 1.0 CG B:GLU35 4.5 9.4 1.0 OD2 B:ASP52 4.6 20.9 1.0 CB B:GLU35 4.7 8.9 1.0 C B:GLU35 4.8 8.4 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