Nickel 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:

Magnesium

(Mg)

2 atoms

The binding sites of Nickel 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 Nickel atom.
In total 3 binding sites of Nickel where determined in the Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+, PDB code: 9b06:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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:Ni203 b:20.9 occ:1.00 O A:LCZ201 2.0 14.8 1.0 NE2 A:HIS65 2.0 12.9 1.0 O A:HOH357 2.1 19.7 1.0 O A:HOH330 2.1 18.9 1.0 N A:LCZ201 2.1 8.7 1.0 O A:HOH358 2.2 20.0 1.0 HN1 A:LCZ201 2.3 10.4 1.0 C A:LCZ201 2.8 13.2 1.0 CD2 A:HIS65 2.9 16.0 1.0 HN2 A:LCZ201 2.9 10.4 1.0 CA A:LCZ201 2.9 10.6 1.0 HD2 A:HIS65 2.9 19.1 1.0 CE1 A:HIS65 3.1 18.6 1.0 HE1 A:HIS65 3.4 22.3 1.0 HB1 A:LCZ201 3.6 15.1 1.0 HA A:LCZ201 3.7 12.7 1.0 CB A:LCZ201 3.9 12.6 1.0 O A:HOH386 4.0 28.6 1.0 N A:THR202 4.0 11.7 1.0 CG A:HIS65 4.1 16.3 1.0 ND1 A:HIS65 4.1 16.8 1.0 O A:HOH440 4.2 57.3 1.0 O A:HOH434 4.2 52.3 1.0 HA A:THR202 4.3 15.4 1.0 HA A:PRO35 4.3 19.8 1.0 OD2 A:ASP33 4.3 14.4 1.0 OD1 A:ASP33 4.3 13.2 1.0 HG A:LCZ201 4.3 17.1 1.0 O A:HOH310 4.5 17.5 0.4 O A:HOH428 4.5 34.4 0.6 O A:HOH413 4.5 47.4 1.0 O A:ASP34 4.6 10.7 1.0 HB2 A:LCZ201 4.6 15.1 1.0 H A:THR202 4.7 14.0 1.0 O A:HOH379 4.7 27.3 1.0 O A:HOH428 4.7 28.4 0.5 CG A:LCZ201 4.7 14.2 1.0 CA A:THR202 4.8 12.8 1.0 CG A:ASP33 4.8 17.0 1.0 O A:HOH438 4.9 51.1 1.0 HG23 A:THR202 4.9 25.2 1.0 HD1 A:HIS65 4.9 20.1 1.0 HG22 A:THR202 5.0 25.2 1.0

Nickel binding site 2 out of 3 in the Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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:Ni203 b:15.1 occ:1.00 OE1 B:GLU78 2.0 10.5 1.0 O B:HOH349 2.0 14.5 1.0 OE1 B:GLU81 2.1 13.0 1.0 O B:HOH304 2.1 13.2 1.0 O B:HOH311 2.1 11.2 1.0 CD B:GLU78 3.0 10.1 1.0 CD B:GLU81 3.0 19.9 1.0 OE2 B:GLU81 3.3 18.2 1.0 OE2 B:GLU78 3.3 15.3 1.0 HA B:GLU78 3.9 18.2 1.0 O B:HOH384 3.9 27.3 1.0 O B:HOH398 4.2 30.4 1.0 O B:HOH428 4.3 37.4 1.0 CG B:GLU78 4.3 13.4 1.0 HB2 B:GLU81 4.4 16.2 1.0 CG B:GLU81 4.4 18.1 1.0 HB3 B:GLU81 4.5 16.2 1.0 HB3 B:GLU78 4.6 16.9 1.0 HG2 B:GLU78 4.6 16.1 1.0 CB B:GLU81 4.7 13.5 1.0 CA B:GLU78 4.7 15.2 1.0 CB B:GLU78 4.8 14.1 1.0 HG3 B:GLU81 4.9 21.7 1.0 HG2 B:GLU81 4.9 21.7 1.0 HG3 B:GLU78 5.0 16.1 1.0

Nickel binding site 3 out of 3 in the Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Mycolicibacterium Smegmatis Clps with Leuthr Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni204 b:21.3 occ:1.00 HN2 B:LCZ201 1.8 18.2 1.0 H3 B:LCZ201 1.9 18.2 1.0 O B:LCZ201 2.0 20.9 1.0 NE2 B:HIS65 2.1 12.9 1.0 O B:HOH327 2.2 17.3 1.0 O B:HOH355 2.2 22.7 1.0 N B:LCZ201 2.2 15.2 1.0 O B:HOH345 2.2 20.2 1.0 C B:LCZ201 2.8 17.2 1.0 CD2 B:HIS65 2.9 20.2 1.0 CA B:LCZ201 3.0 14.4 1.0 HD2 B:HIS65 3.0 24.3 1.0 HN1 B:LCZ201 3.0 18.2 1.0 CE1 B:HIS65 3.2 21.4 1.0 HB1 B:LCZ201 3.4 20.9 1.0 HE1 B:HIS65 3.5 25.6 1.0 HA B:LCZ201 3.7 17.2 1.0 CB B:LCZ201 3.8 17.5 1.0 N B:THR202 4.1 17.9 1.0 CG B:HIS65 4.1 14.6 1.0 O B:HOH426 4.1 69.1 1.0 ND1 B:HIS65 4.2 16.9 1.0 OD1 B:ASP33 4.2 13.9 1.0 OD2 B:ASP33 4.3 14.1 1.0 HA B:PRO35 4.3 25.0 1.0 HA B:THR202 4.3 18.5 1.0 HG B:LCZ201 4.5 22.6 1.0 HB2 B:LCZ201 4.5 20.9 1.0 O B:HOH338 4.5 38.5 1.0 O B:ASP34 4.5 16.2 1.0 CG B:ASP33 4.7 17.6 1.0 H B:THR202 4.7 21.4 1.0 HG22 B:THR202 4.7 31.6 1.0 CG B:LCZ201 4.8 18.8 1.0 CA B:THR202 4.8 15.4 1.0 HG23 B:THR202 4.9 31.6 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