Nickel in PDB 9b10: Mycolicibacterium Smegmatis Clps with Tyrarg Dipeptide and MG2+

The structure of Mycolicibacterium Smegmatis Clps with Tyrarg Dipeptide and MG2+, PDB code: 9b10 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)	37.74 / 1.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.438, 52.765, 54.004, 90, 90, 90
R / Rfree (%)	14.1 / 15.5

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

Magnesium

(Mg)

5 atoms

The binding sites of Nickel atom in the Mycolicibacterium Smegmatis Clps with Tyrarg Dipeptide and MG2+ (pdb code 9b10). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Mycolicibacterium Smegmatis Clps with Tyrarg Dipeptide and MG2+, PDB code: 9b10:

Nickel binding site 1 out of 1 in the Mycolicibacterium Smegmatis Clps with Tyrarg 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 Tyrarg Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni206 b:9.6 occ:0.86 O B:HOH312 2.0 11.2 1.0 OE1 B:GLU78 2.0 13.0 1.0 O B:HOH309 2.0 14.2 1.0 OE1 B:GLU81 2.0 10.8 1.0 O B:HOH373 2.1 13.3 1.0 CD B:GLU78 3.0 14.6 1.0 CD B:GLU81 3.0 13.3 1.0 OE2 B:GLU78 3.3 14.5 1.0 OE2 B:GLU81 3.3 14.4 1.0 O B:HOH380 3.8 25.9 1.0 HA B:GLU78 3.9 11.7 1.0 O B:HOH415 4.1 29.0 1.0 O B:HOH421 4.2 43.7 1.0 CG B:GLU78 4.3 14.3 1.0 CG B:GLU81 4.4 11.1 1.0 HB2 B:GLU81 4.4 12.2 1.0 HB3 B:GLU81 4.6 12.2 1.0 HB3 B:GLU78 4.6 14.4 1.0 HG2 B:GLU78 4.7 17.1 1.0 CB B:GLU81 4.7 10.2 1.0 CA B:GLU78 4.7 9.8 1.0 CB B:GLU78 4.8 12.0 1.0 HG3 B:GLU81 4.9 13.3 1.0 HG2 B:GLU81 4.9 13.3 1.0 HE B:ARG77 5.0 50.4 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