Nickel in PDB 9b1p: Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+

The structure of Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+, PDB code: 9b1p 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)	14.87 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.313, 52.6, 54.096, 90, 90, 90
R / Rfree (%)	17.1 / 18.9

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

Magnesium

(Mg)

4 atoms

The binding sites of Nickel atom in the Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+ (pdb code 9b1p). 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 Trpser Dipeptide and MG2+, PDB code: 9b1p:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Mycolicibacterium Smegmatis Clps with Trpser 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 Trpser Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:22.1 occ:1.00 OE1 B:GLU78 2.0 19.5 1.0 OE1 B:GLU81 2.1 17.9 1.0 O B:HOH352 2.1 20.4 1.0 O B:HOH302 2.1 19.4 1.0 O B:HOH307 2.2 21.1 1.0 CD B:GLU78 3.0 20.1 1.0 CD B:GLU81 3.0 29.2 1.0 OE2 B:GLU78 3.3 18.8 1.0 OE2 B:GLU81 3.3 28.7 1.0 O B:HOH360 3.9 27.9 1.0 HA B:GLU78 3.9 23.1 1.0 O B:HOH407 4.0 41.2 1.0 O B:HOH382 4.2 42.2 1.0 O B:HOH388 4.3 48.6 1.0 CG B:GLU78 4.3 24.6 1.0 HB2 B:GLU81 4.4 22.8 1.0 CG B:GLU81 4.4 20.8 1.0 HB3 B:GLU81 4.6 22.8 1.0 HB3 B:GLU78 4.6 25.9 1.0 HG2 B:GLU78 4.6 29.5 1.0 CB B:GLU81 4.7 19.0 1.0 CA B:GLU78 4.8 19.2 1.0 CB B:GLU78 4.8 21.6 1.0 HG3 B:GLU81 4.9 24.9 1.0 HG2 B:GLU81 4.9 24.9 1.0 HG3 B:GLU78 5.0 29.5 1.0

Nickel binding site 2 out of 3 in the Mycolicibacterium Smegmatis Clps with Trpser 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 Trpser Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni101 b:25.5 occ:1.00 NE2 A:HIS65 2.0 18.4 1.0 O F:HOH202 2.0 30.2 1.0 N F:TRP1 2.0 19.4 1.0 O F:TRP1 2.0 20.1 1.0 O A:HOH308 2.2 22.2 1.0 H2 F:TRP1 2.5 23.4 1.0 H1 F:TRP1 2.5 23.4 1.0 C F:TRP1 2.8 16.4 1.0 CA F:TRP1 2.9 21.6 1.0 CD2 A:HIS65 2.9 21.7 1.0 CE1 A:HIS65 3.0 20.6 1.0 HD2 A:HIS65 3.1 26.0 1.0 HE1 A:HIS65 3.2 24.7 1.0 HB2 F:TRP1 3.6 19.9 1.0 HA F:TRP1 3.6 25.9 1.0 CB F:TRP1 3.8 16.5 1.0 O A:HOH304 4.0 29.6 1.0 N F:SER2 4.1 17.8 1.0 O F:HOH204 4.1 41.8 1.0 CG A:HIS65 4.1 20.4 1.0 ND1 A:HIS65 4.1 23.1 1.0 OD1 A:ASP33 4.2 18.5 1.0 O F:HOH203 4.2 63.6 1.0 O A:HOH309 4.2 27.0 1.0 OD2 A:ASP33 4.2 19.2 1.0 O A:HOH397 4.3 54.9 1.0 HA F:SER2 4.4 33.9 1.0 HE3 A:MET39 4.5 26.6 0.5 O A:HOH405 4.5 42.1 1.0 HB3 F:TRP1 4.5 19.9 1.0 CG A:ASP33 4.6 24.3 1.0 H F:SER2 4.7 21.4 1.0 O A:ASP34 4.7 20.1 1.0 HA A:PRO35 4.8 36.0 1.0 CG F:TRP1 4.8 15.1 1.0 CA F:SER2 4.8 28.2 1.0 HD1 A:HIS65 4.9 27.7 1.0

Nickel binding site 3 out of 3 in the Mycolicibacterium Smegmatis Clps with Trpser 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 Trpser Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ G:Ni101 b:39.5 occ:1.00 NE2 B:HIS65 1.9 28.7 1.0 N G:TRP1 2.0 33.5 1.0 O G:TRP1 2.1 36.3 1.0 O G:HOH201 2.1 41.2 1.0 O G:HOH202 2.2 41.9 1.0 H1 G:TRP1 2.3 40.3 1.0 O B:HOH334 2.4 37.5 1.0 H2 G:TRP1 2.7 40.3 1.0 CD2 B:HIS65 2.7 31.3 1.0 C G:TRP1 2.8 36.2 1.0 HD2 B:HIS65 2.8 37.5 1.0 CA G:TRP1 2.9 33.8 1.0 CE1 B:HIS65 3.0 30.8 1.0 HE1 B:HIS65 3.4 37.0 1.0 HB2 G:TRP1 3.4 31.8 1.0 HA G:TRP1 3.6 40.5 1.0 CB G:TRP1 3.7 26.5 1.0 CG B:HIS65 3.9 28.9 1.0 ND1 B:HIS65 4.1 32.2 1.0 OD1 B:ASP33 4.1 31.6 1.0 N G:SER2 4.1 44.7 1.0 OD2 B:ASP33 4.3 39.9 1.0 O B:HOH395 4.3 53.1 1.0 O B:HOH305 4.3 27.3 0.4 HA G:SER2 4.4 52.1 1.0 HB3 G:TRP1 4.4 31.8 1.0 CG B:ASP33 4.6 41.7 1.0 O B:ASP34 4.7 26.1 1.0 CG G:TRP1 4.7 21.8 1.0 H G:SER2 4.7 53.6 1.0 HA B:PRO35 4.8 43.7 1.0 CA G:SER2 4.9 43.4 1.0 HD1 B:HIS65 4.9 38.6 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