Magnesium in PDB 8h09: Structure of the Thermolabile Hemolysin From Vibrio Alginolyticus (Apo Form)

The structure of Structure of the Thermolabile Hemolysin From Vibrio Alginolyticus (Apo Form), PDB code: 8h09 was solved by Q.Ma, C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.78 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.932, 71.238, 83.645, 90, 101.32, 90
R / Rfree (%)	18 / 20.4

The binding sites of Magnesium atom in the Structure of the Thermolabile Hemolysin From Vibrio Alginolyticus (Apo Form) (pdb code 8h09). 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 Thermolabile Hemolysin From Vibrio Alginolyticus (Apo Form), PDB code: 8h09:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Thermolabile Hemolysin From Vibrio Alginolyticus (Apo Form)


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 Thermolabile Hemolysin From Vibrio Alginolyticus (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:47.3 occ:1.00 OD1 A:ASP263 2.0 30.8 1.0 O A:HOH658 2.1 42.5 1.0 O A:HOH640 2.1 41.5 1.0 O A:HOH708 2.2 50.1 1.0 CG A:ASP263 3.1 33.6 1.0 OD2 A:ASP263 3.7 38.3 1.0 OE1 A:GLU266 4.1 39.6 1.0 N A:ASP263 4.2 26.1 1.0 CA A:ASP263 4.2 24.9 1.0 O A:GLU259 4.3 27.6 1.0 CB A:ASP263 4.3 26.2 1.0 CB A:ALA262 4.5 26.5 1.0 C A:ALA262 4.6 29.0 1.0 NH1 A:ARG255 4.6 47.0 1.0 O A:ALA262 5.0 29.1 1.0

Magnesium binding site 2 out of 2 in the Structure of the Thermolabile Hemolysin From Vibrio Alginolyticus (Apo Form)


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 Thermolabile Hemolysin From Vibrio Alginolyticus (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg507 b:35.6 occ:1.00 OD1 B:ASP263 1.9 32.1 1.0 O B:HOH647 2.0 34.8 1.0 O B:HOH640 2.0 33.9 1.0 OE2 B:GLU208 2.0 39.1 1.0 O B:HOH667 2.1 35.4 1.0 CG B:ASP263 3.0 31.4 1.0 CD B:GLU208 3.2 58.6 1.0 OD2 B:ASP263 3.5 31.6 1.0 CG B:GLU208 3.8 45.9 1.0 O B:HOH629 4.1 36.6 1.0 O B:GLU259 4.1 28.7 1.0 OE1 B:GLU266 4.2 47.1 1.0 OE1 B:GLU208 4.2 44.7 1.0 CB B:ASP263 4.2 26.0 1.0 N B:ASP263 4.3 26.3 1.0 CA B:ASP263 4.3 25.7 1.0 NH1 B:ARG255 4.4 33.9 1.0 CB B:ALA262 4.8 27.9 1.0 C B:ALA262 4.8 30.5 1.0

C.Wang, C.Liu, X.Zhu, Q.Peng, Q.Ma. Catalytic Site Flexibility Facilitates the Substrate and Catalytic Promiscuity of Vibrio Dual Lipase/Transferase. Nat Commun V. 14 4795 2023.
ISSN: ESSN 2041-1723
PubMed: 37558668
DOI: 10.1038/S41467-023-40455-Y