Magnesium in PDB 9lty: Crystal Structure of C-Terminal Stable Fragment of the Shaft Pilin Ebpc From Enterococcus Faecalis

The structure of Crystal Structure of C-Terminal Stable Fragment of the Shaft Pilin Ebpc From Enterococcus Faecalis, PDB code: 9lty was solved by V.Sharma, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	125.63 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.542, 47.6, 125.682, 91.68, 90.18, 89.87
R / Rfree (%)	22.3 / 24.8

The structure of Crystal Structure of C-Terminal Stable Fragment of the Shaft Pilin Ebpc From Enterococcus Faecalis also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of C-Terminal Stable Fragment of the Shaft Pilin Ebpc From Enterococcus Faecalis (pdb code 9lty). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of C-Terminal Stable Fragment of the Shaft Pilin Ebpc From Enterococcus Faecalis, PDB code: 9lty:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of C-Terminal Stable Fragment of the Shaft Pilin Ebpc From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of C-Terminal Stable Fragment of the Shaft Pilin Ebpc From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:26.7 occ:1.00 O A:HOH888 2.0 24.8 1.0 O A:THR463 2.0 29.3 1.0 OG1 A:THR463 2.0 34.3 1.0 O A:HOH818 2.0 25.6 1.0 O A:HOH906 2.0 24.2 1.0 OD1 A:ASP461 2.1 31.6 1.0 C A:THR463 2.8 30.9 1.0 CG A:ASP461 2.9 31.1 1.0 CB A:THR463 3.0 35.9 1.0 OD2 A:ASP461 3.2 30.4 1.0 CA A:THR463 3.2 34.6 1.0 N A:THR463 3.5 34.7 1.0 N A:PRO464 4.0 30.9 1.0 O A:HOH932 4.1 34.9 1.0 O A:HOH884 4.1 36.3 1.0 CG2 A:THR463 4.3 39.6 1.0 CB A:ASP461 4.3 30.5 1.0 CA A:PRO464 4.5 29.1 1.0 NZ A:LYS323 4.5 50.5 1.0 C A:PRO464 4.6 28.9 1.0 O A:HOH802 4.7 33.4 1.0 CD A:LYS323 4.8 48.2 1.0 O A:HOH905 4.8 30.9 1.0 C A:GLN462 4.8 35.8 1.0 N A:GLN462 4.9 35.1 1.0 O A:PRO464 4.9 28.7 1.0 N A:PRO465 5.0 29.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of C-Terminal Stable Fragment of the Shaft Pilin Ebpc From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of C-Terminal Stable Fragment of the Shaft Pilin Ebpc From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:27.9 occ:1.00 O B:HOH859 2.0 25.7 1.0 OG1 B:THR463 2.0 37.4 1.0 O B:THR463 2.0 31.3 1.0 O B:HOH898 2.0 22.3 1.0 O B:HOH822 2.0 26.0 1.0 OD1 B:ASP461 2.1 32.6 1.0 C B:THR463 2.8 33.6 1.0 CB B:THR463 3.0 38.5 1.0 CG B:ASP461 3.0 31.7 1.0 OD2 B:ASP461 3.2 32.0 1.0 CA B:THR463 3.2 36.5 1.0 N B:THR463 3.5 36.3 1.0 N B:PRO464 4.0 33.0 1.0 CG2 B:THR463 4.3 41.0 1.0 O B:HOH881 4.3 43.7 1.0 O B:HOH856 4.3 33.5 1.0 CB B:ASP461 4.4 29.6 1.0 NZ B:LYS323 4.4 52.7 1.0 CA B:PRO464 4.5 31.7 1.0 C B:PRO464 4.7 30.4 1.0 C B:GLN462 4.8 36.2 1.0 CD B:LYS323 4.8 51.2 1.0 O B:HOH875 4.8 33.8 1.0 N B:GLN462 4.9 35.5 1.0 O B:PRO464 5.0 28.2 1.0 N B:PRO465 5.0 30.3 1.0

V.Sharma, V.Krishnan. Structural Basis of Ebp Pilus Shaft Formation and Anchoring in Vancomycin-Resistant Enterococci. Febs J. 2025.
ISSN: ISSN 1742-464X
PubMed: 40608565
DOI: 10.1111/FEBS.70173