Magnesium in PDB 9ayn: Mycolicibacterium Smegmatis Clps with Bound NI2+

The structure of Mycolicibacterium Smegmatis Clps with Bound NI2+, PDB code: 9ayn 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)	27.32 / 0.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.493, 52.262, 54.641, 90, 90, 90
R / Rfree (%)	11.9 / 13.9

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

Nickel

(Ni)

5 atoms

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

Magnesium binding site 1 out of 2 in the Mycolicibacterium Smegmatis Clps with Bound 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 NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:15.2 occ:1.00 H A:TRP93 2.0 10.4 1.0 OD2 A:ASP34 2.7 13.7 1.0 O A:TRP32 2.8 10.3 1.0 N A:TRP93 2.8 8.7 1.0 HB2 A:TRP93 2.9 11.2 1.0 HA A:LEU92 3.0 10.1 1.0 HB3 A:LEU92 3.1 10.0 0.5 HG A:LEU92 3.2 11.1 0.5 HB3 A:ASP34 3.2 14.4 1.0 HG13 A:VAL31 3.2 10.1 1.0 HD22 A:LEU92 3.3 11.8 0.5 HB3 A:LEU92 3.4 10.6 0.5 HD22 A:ASN37 3.6 16.4 1.0 CA A:LEU92 3.6 8.4 0.5 CB A:TRP93 3.6 9.3 1.0 CA A:LEU92 3.6 8.5 0.5 O A:HOH304 3.7 59.4 1.0 CG A:ASP34 3.7 13.1 1.0 C A:LEU92 3.7 8.8 1.0 CA A:TRP93 3.7 8.6 1.0 CB A:LEU92 3.8 8.4 0.5 CB A:LEU92 3.8 8.8 0.5 CG1 A:VAL31 3.8 8.4 1.0 CB A:ASP34 3.9 12.0 1.0 HG12 A:VAL31 3.9 10.1 1.0 HG11 A:VAL31 3.9 10.1 1.0 CG A:LEU92 3.9 9.2 0.5 CG A:TRP93 3.9 9.6 1.0 O A:HOH407 4.0 42.5 1.0 C A:TRP32 4.0 9.0 1.0 H A:ASP34 4.0 13.1 1.0 O A:TRP93 4.1 14.4 1.0 CD2 A:LEU92 4.1 9.8 0.5 H A:TRP32 4.1 10.2 1.0 N A:ASP34 4.3 10.9 1.0 ND2 A:ASN37 4.3 13.7 1.0 C A:TRP93 4.3 9.0 1.0 CD1 A:TRP93 4.4 11.4 1.0 HD23 A:LEU92 4.4 11.8 0.5 HD23 A:LEU92 4.4 11.8 0.5 HD13 A:LEU92 4.4 10.8 0.5 HA A:ASP33 4.4 11.8 1.0 HD1 A:TRP93 4.4 13.7 1.0 CG A:LEU92 4.4 8.8 0.5 HD21 A:ASN37 4.5 16.4 1.0 HB3 A:TRP93 4.5 11.2 1.0 HA A:TRP93 4.5 10.3 1.0 HB2 A:LEU92 4.5 10.0 0.5 CD2 A:TRP93 4.6 10.1 1.0 HB2 A:ASP34 4.6 14.4 1.0 N A:TRP32 4.6 8.5 1.0 C A:ASP33 4.7 10.1 1.0 HG11 A:VAL64 4.7 12.9 1.0 CD2 A:LEU92 4.7 9.9 0.5 CA A:ASP34 4.7 11.4 1.0 HB2 A:LEU92 4.7 10.6 0.5 HB2 A:ASN37 4.8 15.5 1.0 OD1 A:ASP34 4.8 14.5 1.0 HD21 A:LEU92 4.8 11.8 0.5 HB2 A:TRP32 4.8 11.4 1.0 HD12 A:LEU92 4.9 11.2 0.5 O A:LEU92 4.9 10.3 1.0 CA A:ASP33 4.9 9.8 1.0 CA A:TRP32 4.9 9.0 1.0 O A:GLY91 4.9 10.9 1.0 N A:ASP33 4.9 9.8 1.0 N A:LEU92 4.9 8.5 1.0 CD1 A:LEU92 5.0 9.0 0.5

Magnesium binding site 2 out of 2 in the Mycolicibacterium Smegmatis Clps with Bound 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 NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:17.4 occ:1.00 HD22 B:ASN37 2.0 19.2 1.0 HA B:LEU92 2.7 9.6 1.0 HB3 B:ASP34 2.7 12.0 1.0 O B:GLY91 2.8 11.5 1.0 OD2 B:ASP34 2.8 12.5 1.0 ND2 B:ASN37 2.8 16.0 1.0 O B:HOH359 2.9 9.7 1.0 HB2 B:ASP34 3.0 12.0 1.0 CB B:ASP34 3.2 10.0 1.0 HD21 B:ASN37 3.2 19.2 1.0 CG B:ASP34 3.4 11.0 1.0 NE1 B:TRP93 3.4 10.0 1.0 CD1 B:TRP93 3.5 9.8 1.0 H B:TRP93 3.5 9.2 1.0 HD22 B:LEU92 3.6 12.4 1.0 HD23 B:LEU92 3.6 12.4 1.0 CA B:LEU92 3.6 8.0 1.0 HE1 B:TRP93 3.6 12.0 1.0 HD1 B:TRP93 3.7 11.8 1.0 CE2 B:TRP93 3.7 8.9 1.0 O B:HOH327 3.8 49.8 1.0 CG B:TRP93 3.8 8.8 1.0 C B:GLY91 3.8 9.3 1.0 CG B:ASN37 3.8 17.1 1.0 N B:TRP93 3.9 7.6 1.0 O B:HOH332 3.9 38.8 1.0 CD2 B:TRP93 4.0 8.3 1.0 OD1 B:ASN37 4.0 18.8 1.0 CD2 B:LEU92 4.0 10.3 1.0 C B:LEU92 4.1 8.4 1.0 N B:LEU92 4.2 8.1 1.0 O B:HOH394 4.2 12.9 1.0 CZ2 B:TRP93 4.4 9.9 1.0 HB2 B:TRP93 4.5 10.3 1.0 O B:HOH363 4.5 68.7 1.0 O B:HOH367 4.6 33.3 1.0 CB B:LEU92 4.6 7.6 1.0 CB B:TRP93 4.6 8.5 1.0 HB3 B:LEU92 4.6 9.1 1.0 CA B:ASP34 4.6 9.7 1.0 OD1 B:ASP34 4.6 12.2 1.0 HZ2 B:TRP93 4.7 11.9 1.0 HD21 B:LEU92 4.8 12.4 1.0 CA B:TRP93 4.8 7.7 1.0 H B:ASP34 4.8 11.2 1.0 CE3 B:TRP93 4.9 9.3 1.0 CG B:LEU92 4.9 9.5 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