Magnesium in PDB 8rlk: Structure of the Apo Form of Pib-1 in An Orthorombic Space Group

The structure of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group, PDB code: 8rlk was solved by F.J.Medrano, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.44 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.89, 101.452, 267.758, 90, 90, 90
R / Rfree (%)	19.1 / 23.5

The structure of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

The binding sites of Magnesium atom in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group (pdb code 8rlk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group, PDB code: 8rlk:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


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 Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.7 occ:1.00 O E:HOH622 1.9 41.7 1.0 O A:HOH699 2.0 39.3 1.0 O A:HOH664 2.0 36.1 1.0 O E:HOH677 2.1 36.8 1.0 O A:HOH620 2.2 39.5 1.0 O E:HOH699 2.3 35.7 1.0 OE1 E:GLN146 3.8 43.9 1.0 O E:HOH665 4.0 37.5 1.0 O A:ALA113 4.2 34.0 1.0 O A:VAL112 4.3 34.4 1.0 O A:GLY76 4.3 37.1 1.0 O A:HOH744 4.4 43.3 1.0 O A:HOH621 4.4 37.5 1.0 O E:HOH689 4.6 45.5 1.0 O A:VAL77 4.6 44.4 1.0 CD E:GLN146 4.7 39.7 1.0 CA A:ALA78 4.7 38.2 1.0 CB A:ALA75 4.8 38.3 1.0 C A:ALA113 4.9 35.8 1.0 N A:GLY76 4.9 35.8 1.0 O E:GLN146 5.0 37.2 1.0 CB A:ALA78 5.0 40.5 1.0

Magnesium binding site 2 out of 3 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


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 Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:38.4 occ:1.00 O B:HOH717 1.9 35.5 1.0 O B:HOH734 2.0 37.6 1.0 O B:HOH627 2.1 41.8 1.0 OE1 B:GLN146 3.8 40.9 1.0 O B:HOH643 4.0 33.5 1.0 OE2 B:GLU313 4.2 45.2 1.0 O B:HOH732 4.3 38.1 1.0 OE1 B:GLU313 4.4 51.0 1.0 CD B:GLN146 4.7 34.0 1.0 CD B:GLU313 4.7 50.7 1.0 O B:HOH698 4.8 44.0 1.0

Magnesium binding site 3 out of 3 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:41.7 occ:1.00 O C:HOH686 2.1 42.0 1.0 OD1 C:ASP306 2.3 34.7 1.0 O C:HOH634 2.4 45.6 1.0 NZ C:LYS69 2.4 45.0 1.0 O C:HOH602 2.5 47.2 1.0 CG C:ASP306 3.2 36.4 1.0 OD2 C:ASP306 3.4 40.3 1.0 CE C:LYS69 3.7 51.2 1.0 CG C:ARG71 4.5 40.4 1.0 CB C:ASP306 4.6 32.0 1.0 O C:MET262 4.7 39.3 1.0 CD C:LYS69 4.8 53.0 1.0 CB C:ARG71 4.9 40.7 1.0 CA C:ASP306 5.0 35.0 1.0 N C:ASP306 5.0 31.3 1.0

F.J.Medrano, S.Hernando-Amado, J.L.Martinez, A.Romero. A New Type of Class C Beta-Lactamases Defined By Pib-1. A Metal-Dependent Carbapenem-Hydrolyzing Beta-Lactamase, From Pseudomonas Aeruginosa: Structural and Functional Analysis. Int.J.Biol.Macromol. 34298 2024.
ISSN: ISSN 0141-8130
PubMed: 39097051
DOI: 10.1016/J.IJBIOMAC.2024.134298