Magnesium in PDB 5ly8: Structure of the CBM2 Module of Lactobacillus Casei BL23 Phage J-1 Evolved Dit.

The structure of Structure of the CBM2 Module of Lactobacillus Casei BL23 Phage J-1 Evolved Dit., PDB code: 5ly8 was solved by C.Cambillau, S.Spinelli, M.-E.Dieterle, M.Piuri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.44 / 1.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.020, 63.670, 74.460, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 19.8

The binding sites of Magnesium atom in the Structure of the CBM2 Module of Lactobacillus Casei BL23 Phage J-1 Evolved Dit. (pdb code 5ly8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the CBM2 Module of Lactobacillus Casei BL23 Phage J-1 Evolved Dit., PDB code: 5ly8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the CBM2 Module of Lactobacillus Casei BL23 Phage J-1 Evolved Dit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the CBM2 Module of Lactobacillus Casei BL23 Phage J-1 Evolved Dit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:14.9 occ:1.00 O A:SER132 2.3 14.2 1.0 O A:GLU108 2.3 13.2 1.0 O A:ASN135 2.3 17.0 1.0 O A:ALA106 2.5 19.4 1.0 OD2 A:ASP130 2.5 19.2 1.0 OD1 A:ASP130 2.6 15.1 1.0 CG A:ASP130 2.8 13.6 1.0 O A:ASN105 2.9 19.8 1.0 C A:ALA106 3.4 18.6 1.0 C A:GLU108 3.5 13.3 1.0 C A:SER132 3.5 14.1 1.0 C A:ASN135 3.5 17.1 1.0 N A:GLU108 3.9 12.8 1.0 CA A:ALA106 3.9 17.4 1.0 O A:HOH445 4.0 23.1 1.0 C A:ASN105 4.1 22.2 1.0 CA A:ASP136 4.1 15.7 0.5 OG1 A:THR104 4.2 11.6 0.5 CA A:GLU108 4.2 11.5 1.0 CA A:ASP136 4.2 18.9 0.5 N A:ASN135 4.3 15.6 1.0 N A:ASP136 4.3 15.6 0.5 CB A:ASP130 4.3 12.9 1.0 N A:ASP136 4.3 17.8 0.5 CA A:ALA133 4.3 14.3 1.0 N A:ALA133 4.3 13.1 1.0 N A:ALA107 4.4 15.5 1.0 C A:ALA107 4.4 15.6 1.0 N A:SER132 4.5 13.3 1.0 N A:ALA106 4.5 17.0 1.0 CA A:SER132 4.5 13.2 1.0 CA A:ASN135 4.6 15.4 1.0 N A:VAL109 4.6 11.8 1.0 C A:ALA133 4.7 16.2 1.0 CG2 A:VAL109 4.7 14.2 1.0 N A:SER134 4.8 15.4 1.0 CA A:ALA107 4.8 15.1 1.0 CA A:VAL109 4.9 11.1 1.0 CB A:GLU108 4.9 12.3 1.0 CB A:ASP136 4.9 18.7 0.5 C A:ASP136 5.0 16.7 0.5 O A:ASP130 5.0 11.6 1.0 C A:ASP130 5.0 11.6 1.0

Magnesium binding site 2 out of 2 in the Structure of the CBM2 Module of Lactobacillus Casei BL23 Phage J-1 Evolved Dit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the CBM2 Module of Lactobacillus Casei BL23 Phage J-1 Evolved Dit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:14.2 occ:1.00 O A:GLY59 2.3 13.0 1.0 O A:GLN227 2.3 12.2 1.0 O A:ASP21 2.4 13.4 1.0 O A:HOH463 2.4 14.0 1.0 O A:HOH673 2.4 19.1 1.0 O A:HOH527 2.5 20.7 1.0 C A:GLY59 3.3 13.1 1.0 C A:ASP21 3.4 14.0 1.0 C A:GLN227 3.5 11.1 1.0 CA A:GLY59 3.8 11.4 1.0 CA A:ASP21 3.8 12.9 1.0 O A:HOH717 4.1 42.1 1.0 CB A:ASP21 4.1 14.8 1.0 CA A:GLN227 4.2 10.8 1.0 O A:HOH692 4.3 18.3 1.0 CB A:GLN227 4.5 12.7 1.0 N A:PHE22 4.5 12.9 1.0 O A:HOH431 4.5 18.8 1.0 N A:ILE60 4.5 12.1 1.0 N A:ASP228 4.6 11.1 1.0 OD1 A:ASP228 4.6 12.8 1.0 O A:HOH702 4.6 34.0 1.0 OD1 A:ASN23 4.6 19.7 1.0 CB A:PHE22 4.7 13.7 1.0 O A:HOH545 4.7 17.3 1.0 CD1 A:PHE22 4.7 13.4 1.0 CA A:ASP228 4.7 10.3 1.0 CB A:ASP228 4.8 11.9 1.0 CA A:PHE22 5.0 13.2 1.0

M.E.Dieterle, S.Spinelli, I.Sadovskaya, M.Piuri, C.Cambillau. Evolved Distal Tail Carbohydrate Binding Modules of Lactobacillus Phage J-1: A Novel Type of Anti-Receptor Widespread Among Lactic Acid Bacteria Phages. Mol. Microbiol. V. 104 608 2017.
ISSN: ESSN 1365-2958
PubMed: 28196397
DOI: 10.1111/MMI.13649