Magnesium in PDB 9ayo: Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+

The structure of Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+, PDB code: 9ayo 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)	24.05 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.04, 52.51, 54.098, 90, 90, 90
R / Rfree (%)	16.2 / 18.9

The structure of Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+ also contains other interesting chemical elements:

Nickel

(Ni)

5 atoms

The binding sites of Magnesium atom in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+ (pdb code 9ayo). 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 Bound Pheala and NI2+, PDB code: 9ayo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+


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 Bound Pheala and NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:19.2 occ:1.00 H A:TRP93 2.0 14.5 1.0 OD2 A:ASP34 2.7 14.0 1.0 O A:TRP32 2.7 11.4 1.0 N A:TRP93 2.9 12.1 1.0 HE1 A:PHE201 3.0 14.8 1.0 HB2 A:TRP93 3.0 14.5 1.0 HA A:LEU92 3.0 12.5 1.0 HG A:LEU92 3.2 16.3 1.0 HB3 A:ASP34 3.3 12.1 1.0 HD22 A:ASN37 3.5 15.1 1.0 HB3 A:LEU92 3.5 14.9 1.0 HG13 A:VAL31 3.5 16.4 1.0 CB A:TRP93 3.6 12.1 1.0 CA A:LEU92 3.6 10.5 1.0 CG A:ASP34 3.7 13.4 1.0 C A:LEU92 3.7 8.5 1.0 CA A:TRP93 3.7 10.9 1.0 CE1 A:PHE201 3.8 12.3 1.0 CB A:LEU92 3.9 12.5 1.0 HZ A:PHE201 3.9 16.1 1.0 CG A:TRP93 3.9 15.1 1.0 CB A:ASP34 3.9 10.2 1.0 HG12 A:VAL31 4.0 16.4 1.0 C A:TRP32 4.0 13.0 1.0 CG A:LEU92 4.0 13.6 1.0 H A:TRP32 4.1 15.0 1.0 O A:TRP93 4.1 12.9 1.0 CG1 A:VAL31 4.1 13.7 1.0 H A:ASP34 4.2 15.0 1.0 ND2 A:ASN37 4.2 12.7 1.0 CZ A:PHE201 4.3 13.5 1.0 N A:ASP34 4.3 12.5 1.0 CD1 A:TRP93 4.3 19.1 1.0 HG11 A:VAL31 4.3 16.4 1.0 C A:TRP93 4.3 12.6 1.0 HA A:ASP33 4.4 10.8 1.0 HD1 A:TRP93 4.4 22.8 1.0 HD21 A:ASN37 4.4 15.1 1.0 HB3 A:TRP93 4.5 14.5 1.0 CD2 A:TRP93 4.5 9.5 1.0 HD23 A:LEU92 4.5 18.2 1.0 HA A:TRP93 4.6 13.0 1.0 C A:ASP33 4.6 13.7 1.0 N A:TRP32 4.6 12.6 1.0 HB2 A:ASN37 4.6 12.7 1.0 HB2 A:ASP34 4.7 12.1 1.0 CA A:ASP34 4.8 13.4 1.0 OD1 A:ASP34 4.8 12.0 1.0 HB2 A:LEU92 4.8 14.9 1.0 HB2 A:TRP32 4.8 12.7 1.0 HD12 A:LEU92 4.8 23.5 1.0 CA A:ASP33 4.8 9.0 1.0 CD2 A:LEU92 4.9 15.2 1.0 CA A:TRP32 4.9 10.5 1.0 N A:ASP33 4.9 11.6 1.0 O A:LEU92 4.9 12.3 1.0 CD1 A:PHE201 4.9 16.0 1.0 O A:GLY91 5.0 12.9 1.0 HE3 A:TRP93 5.0 17.6 1.0 HG11 A:VAL64 5.0 17.1 1.0 N A:LEU92 5.0 13.3 1.0

Magnesium binding site 2 out of 2 in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+


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 Bound Pheala and NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg207 b:20.7 occ:1.00 H B:TRP93 2.0 14.0 1.0 O B:TRP32 2.8 13.5 1.0 OD2 B:ASP34 2.8 17.8 1.0 N B:TRP93 2.8 11.7 1.0 HA B:LEU92 2.9 8.1 1.0 HG B:LEU92 3.1 17.0 1.0 HE1 B:PHE201 3.1 14.9 1.0 HB3 B:LEU92 3.1 12.8 1.0 HB2 B:TRP93 3.2 14.5 1.0 HB3 B:ASP34 3.3 18.0 1.0 HG13 B:VAL31 3.3 16.5 1.0 CA B:LEU92 3.5 6.8 1.0 CB B:LEU92 3.6 10.7 1.0 C B:LEU92 3.7 15.2 1.0 HD22 B:ASN37 3.7 16.1 1.0 CG B:LEU92 3.8 14.2 1.0 CB B:TRP93 3.8 12.2 1.0 CA B:TRP93 3.8 11.3 1.0 CG B:ASP34 3.8 19.3 1.0 HZ B:PHE201 3.8 15.8 1.0 O B:TRP93 3.9 16.2 1.0 CE1 B:PHE201 3.9 12.5 1.0 HG12 B:VAL31 3.9 16.5 1.0 H B:TRP32 4.0 13.7 1.0 C B:TRP32 4.0 11.2 1.0 CG1 B:VAL31 4.0 13.8 1.0 CB B:ASP34 4.0 15.0 1.0 CG B:TRP93 4.1 13.9 1.0 HG11 B:VAL31 4.2 16.5 1.0 HD23 B:LEU92 4.2 13.1 1.0 H B:ASP34 4.2 17.2 1.0 C B:TRP93 4.3 10.9 1.0 CZ B:PHE201 4.3 13.2 1.0 ND2 B:ASN37 4.4 13.4 1.0 N B:ASP34 4.4 14.4 1.0 HA B:ASP33 4.5 14.3 1.0 HD21 B:ASN37 4.5 16.1 1.0 HB2 B:LEU92 4.5 12.8 1.0 N B:TRP32 4.5 11.4 1.0 CD2 B:LEU92 4.6 10.9 1.0 CD1 B:TRP93 4.6 17.1 1.0 HA B:TRP93 4.6 13.5 1.0 CD2 B:TRP93 4.6 11.3 1.0 HB3 B:TRP93 4.7 14.5 1.0 C B:ASP33 4.7 12.7 1.0 HD1 B:TRP93 4.7 20.4 1.0 HB2 B:ASP34 4.7 18.0 1.0 HD12 B:LEU92 4.8 20.1 1.0 N B:LEU92 4.8 9.3 1.0 O B:LEU92 4.9 14.6 1.0 CA B:TRP32 4.9 11.4 1.0 CA B:ASP34 4.9 13.6 1.0 HB2 B:TRP32 4.9 14.6 1.0 HB2 B:ASN37 4.9 14.0 1.0 CA B:ASP33 4.9 12.0 1.0 HG11 B:VAL64 4.9 13.0 1.0 CD1 B:LEU92 4.9 16.8 1.0 N B:ASP33 4.9 12.6 1.0 HE3 B:TRP93 4.9 23.1 1.0 O B:GLY91 4.9 15.9 1.0 OD1 B:ASP34 4.9 18.4 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