Magnesium in PDB 9b06: Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+

The structure of Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+, PDB code: 9b06 was solved by C.J.Presloid, J.Jiang, P.C.Beardslee, H.R.Anderson, T.M.Swayne, K.R.Schmitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.62 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.244, 52.707, 54.044, 90, 90, 90
R / Rfree (%)	14.1 / 18.9

The structure of Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+ also contains other interesting chemical elements:

Nickel

(Ni)

3 atoms

The binding sites of Magnesium atom in the Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+ (pdb code 9b06). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+, PDB code: 9b06:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:26.2 occ:1.00 OD1 B:ASP99 1.9 31.4 1.0 O B:HOH323 2.0 24.1 1.0 O A:HOH309 2.0 28.8 1.0 OD1 A:ASP99 2.1 29.1 1.0 O A:HOH301 2.1 35.6 1.0 O B:HOH318 2.4 32.1 1.0 CG B:ASP99 3.1 26.4 1.0 H B:ARG100 3.2 55.5 1.0 CG A:ASP99 3.3 28.3 1.0 H A:ARG100 3.5 30.4 1.0 OD2 B:ASP99 3.6 33.1 1.0 O A:HOH402 3.6 34.8 1.0 HA A:ASP99 3.8 24.3 1.0 HA B:ASP99 3.9 36.0 1.0 OD2 A:ASP99 3.9 32.7 1.0 O A:ARG100 3.9 32.0 1.0 N B:ARG100 4.1 46.3 1.0 N A:ARG100 4.2 25.4 1.0 O B:HOH394 4.2 44.9 1.0 O A:HOH328 4.3 37.2 1.0 CB B:ASP99 4.3 28.8 1.0 O B:HOH370 4.3 42.6 1.0 CA A:ASP99 4.4 20.2 1.0 CB A:ASP99 4.4 22.7 1.0 HG11 A:VAL28 4.5 17.9 1.0 CA B:ASP99 4.5 30.0 1.0 HB2 B:ARG100 4.6 60.8 1.0 HG11 B:VAL28 4.7 19.4 1.0 C A:ASP99 4.7 28.6 1.0 HB2 B:ASP99 4.8 34.5 1.0 C B:ASP99 4.8 37.9 1.0 O A:HOH374 4.9 65.7 1.0 C A:ARG100 4.9 33.3 1.0 HG21 A:VAL28 4.9 18.9 1.0 HB2 A:ASP99 4.9 27.3 1.0 HB3 B:ASP99 4.9 34.5 1.0 OXT B:ARG100 5.0 74.1 1.0 CA B:ARG100 5.0 55.9 1.0 C B:ARG100 5.0 68.3 1.0

Magnesium binding site 2 out of 2 in the Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg205 b:23.3 occ:1.00 O B:HOH301 1.9 22.4 1.0 NE2 B:HIS88 2.1 25.8 1.0 HE1 B:HIS88 2.3 34.7 1.0 CE1 B:HIS88 2.5 29.0 1.0 CD2 B:HIS88 3.5 31.2 1.0 ND1 B:HIS88 3.8 31.0 1.0 HD2 B:HIS88 4.0 37.4 1.0 CG B:HIS88 4.3 21.0 1.0 HD1 B:HIS88 4.4 37.2 1.0 O B:HOH357 4.6 48.1 1.0

C.J.Presloid, J.Jiang, P.Kandel, H.R.Anderson, P.C.Beardslee, T.M.Swayne, K.R.Schmitz. Clps Directs Degradation of N-Degron Substrates with Primary Destabilizing Residues in Mycolicibacterium Smegmatis. Mol.Microbiol. 2024.
ISSN: ESSN 1365-2958
PubMed: 39626090
DOI: 10.1111/MMI.15334