Nickel 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:

Magnesium

(Mg)

2 atoms

The binding sites of Nickel atom in the Mycolicibacterium Smegmatis Clps with Bound NI2+ (pdb code 9ayn). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Mycolicibacterium Smegmatis Clps with Bound NI2+, PDB code: 9ayn:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound NI2+


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 Bound NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:15.3 occ:0.64 OD1 A:ASP99 2.0 20.3 1.0 O B:HOH322 2.0 25.7 1.0 OD1 B:ASP99 2.0 19.5 1.0 O A:HOH311 2.0 25.5 1.0 O B:HOH360 2.1 27.3 1.0 O A:HOH322 2.1 23.4 1.0 CG B:ASP99 3.0 18.8 1.0 CG A:ASP99 3.0 20.2 1.0 H B:ARG100 3.2 36.5 1.0 OD2 B:ASP99 3.3 19.9 1.0 OD2 A:ASP99 3.4 21.3 1.0 H A:ARG100 3.8 31.1 1.0 O B:HOH451 3.8 37.7 1.0 HB2 B:ARG100 3.9 47.5 1.0 O A:HOH423 3.9 35.5 1.0 N B:ARG100 4.0 30.4 1.0 HA A:ASP99 4.1 21.5 1.0 HA B:ASP99 4.2 21.6 1.0 O A:ARG100 4.3 31.5 1.0 O A:HOH422 4.3 39.2 1.0 HG2 B:ARG100 4.3 50.1 1.0 CB B:ASP99 4.4 18.0 1.0 CB A:ASP99 4.4 19.0 1.0 HG11 A:VAL28 4.4 14.5 1.0 N A:ARG100 4.5 25.9 1.0 CB B:ARG100 4.6 39.6 1.0 OXT B:ARG100 4.6 40.1 1.0 O A:HOH331 4.7 46.6 1.0 CA A:ASP99 4.7 17.9 1.0 CA B:ASP99 4.7 18.0 1.0 HG11 B:VAL28 4.7 14.5 1.0 HB2 A:ASP99 4.8 22.8 1.0 O B:HOH348 4.8 41.9 1.0 CA B:ARG100 4.8 36.8 1.0 HB3 B:ASP99 4.9 21.6 1.0 CG B:ARG100 4.9 41.8 1.0 C B:ASP99 4.9 24.1 1.0 HB2 B:ASP99 4.9 21.6 1.0 HG21 A:VAL71 5.0 12.9 1.0 HB3 A:ASP99 5.0 22.8 1.0 C A:ASP99 5.0 23.0 1.0

Nickel binding site 2 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound NI2+


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 Bound NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:20.5 occ:0.49 NI A:NI202 0.0 20.5 0.5 NI A:NI202 1.9 11.9 0.5 O A:HOH366 2.0 37.7 0.9 O A:HOH439 2.1 46.9 1.0 O A:HOH350 2.1 29.1 0.5 NE2 A:HIS65 2.3 23.3 0.6 CD2 A:HIS65 3.0 22.6 0.6 HD2 A:HIS65 3.1 27.1 0.6 O A:HOH467 3.2 49.5 1.0 O A:HOH316 3.2 19.8 1.0 CE1 A:HIS65 3.4 23.5 0.6 HE1 A:HIS65 3.7 28.2 0.6 ND1 A:HIS65 4.0 10.9 0.4 O A:HOH453 4.2 62.1 1.0 O A:HOH415 4.2 45.0 1.0 CG A:HIS65 4.2 20.5 0.6 O A:HOH418 4.2 45.2 1.0 HA A:PRO35 4.3 20.4 1.0 OD2 A:ASP33 4.3 14.4 1.0 ND1 A:HIS65 4.3 22.6 0.6 O A:HOH374 4.4 34.5 1.0 OD1 A:ASP33 4.4 13.5 1.0 HE1 A:HIS65 4.5 13.6 0.4 O A:HOH308 4.6 67.8 1.0 CE1 A:HIS65 4.6 11.4 0.4 O A:ASP34 4.7 13.0 1.0 HB2 A:HIS65 4.7 11.4 0.4 CG A:ASP33 4.8 12.4 1.0

Nickel binding site 3 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound NI2+


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 Bound NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:11.9 occ:0.51 NI A:NI202 0.0 11.9 0.5 NE2 A:HIS65 1.1 23.3 0.6 CD2 A:HIS65 1.7 22.6 0.6 NI A:NI202 1.9 20.5 0.5 CE1 A:HIS65 1.9 23.5 0.6 ND1 A:HIS65 2.1 10.9 0.4 O A:HOH316 2.2 19.8 1.0 HD2 A:HIS65 2.2 27.1 0.6 HE1 A:HIS65 2.5 28.2 0.6 CG A:HIS65 2.5 20.5 0.6 O A:HOH350 2.6 29.1 0.5 ND1 A:HIS65 2.6 22.6 0.6 O A:HOH366 2.9 37.7 0.9 CE1 A:HIS65 3.0 11.4 0.4 HE1 A:HIS65 3.0 13.6 0.4 CG A:HIS65 3.3 9.9 0.4 HB2 A:HIS65 3.3 11.4 0.4 HD1 A:HIS65 3.3 27.2 0.6 CB A:HIS65 3.7 9.5 0.4 HA A:HIS65 3.8 11.8 1.0 CB A:HIS65 3.9 16.2 0.6 O A:HOH439 3.9 46.9 1.0 OD2 A:ASP33 4.1 14.4 1.0 OD1 A:ASP33 4.1 13.5 1.0 O A:HIS65 4.1 12.8 1.0 NE2 A:HIS65 4.2 11.5 0.4 O A:HOH418 4.2 45.2 1.0 CA A:HIS65 4.3 9.9 0.4 CA A:HIS65 4.3 12.2 0.6 CD2 A:HIS65 4.3 10.5 0.4 HB2 A:HIS65 4.3 19.4 0.6 HB3 A:HIS65 4.4 19.4 0.6 O A:HOH467 4.5 49.5 1.0 CG A:ASP33 4.5 12.4 1.0 HB3 A:HIS65 4.6 11.4 0.4 C A:HIS65 4.6 11.4 1.0 HG2 A:MET39 4.9 15.8 1.0 HE2 A:HIS65 4.9 13.8 0.4

Nickel binding site 4 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Mycolicibacterium Smegmatis Clps with Bound NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:9.3 occ:1.00 OE1 B:GLU78 2.0 10.5 1.0 OE1 B:GLU81 2.1 9.4 1.0 O B:HOH314 2.1 10.3 1.0 O B:HOH371 2.1 10.5 1.0 O B:HOH313 2.1 12.7 1.0 CD B:GLU78 3.0 11.1 1.0 CD B:GLU81 3.0 9.6 1.0 OE2 B:GLU81 3.3 11.2 1.0 OE2 B:GLU78 3.3 11.3 1.0 O B:HOH377 3.8 21.9 1.0 HA B:GLU78 3.9 13.4 1.0 O B:HOH435 4.2 21.8 1.0 O B:HOH445 4.2 36.8 1.0 O B:HOH478 4.2 28.3 1.0 CG B:GLU78 4.4 12.7 1.0 CG B:GLU81 4.4 9.4 1.0 HB2 B:GLU81 4.4 10.8 1.0 HB3 B:GLU78 4.6 14.7 1.0 HB3 B:GLU81 4.7 10.8 1.0 HG2 B:GLU78 4.7 15.2 1.0 CB B:GLU81 4.7 9.0 1.0 CA B:GLU78 4.7 11.2 1.0 CB B:GLU78 4.8 12.2 1.0 HG3 B:GLU81 4.9 11.3 1.0 HG2 B:GLU81 4.9 11.3 1.0

Nickel binding site 5 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Mycolicibacterium Smegmatis Clps with Bound NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:52.8 occ:1.00 NE2 B:HIS65 2.1 25.9 1.0 O B:HOH398 2.2 50.4 1.0 O B:HOH424 2.6 49.4 1.0 O B:HOH490 2.7 51.2 1.0 O B:HOH440 3.0 55.0 1.0 CE1 B:HIS65 3.1 26.0 1.0 CD2 B:HIS65 3.1 24.8 1.0 HE1 B:HIS65 3.3 31.2 1.0 HD2 B:HIS65 3.3 29.7 1.0 ND1 B:HIS65 4.2 25.0 1.0 CG B:HIS65 4.2 22.8 1.0 OD1 B:ASN66 4.6 22.2 1.0 O B:HOH466 4.7 72.6 1.0 O B:HOH504 4.7 67.0 1.0 O B:HOH403 4.8 63.6 1.0 O B:HOH413 4.9 51.0 1.0 O B:HOH431 4.9 49.1 1.0 HD1 B:HIS65 5.0 30.1 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