Magnesium 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:

Nickel

(Ni)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+, PDB code: 9b1p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+


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 Trpser Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:33.9 occ:1.00 OD1 A:ASP99 2.0 36.8 1.0 O B:HOH310 2.0 40.7 1.0 O A:HOH335 2.1 31.1 1.0 O B:HOH345 2.1 28.9 1.0 OD1 B:ASP99 2.2 49.1 1.0 O A:HOH305 2.2 40.5 1.0 H B:ARG100 3.2 67.1 1.0 CG A:ASP99 3.2 33.1 1.0 CG B:ASP99 3.3 39.2 1.0 O A:HOH380 3.3 34.9 1.0 H A:ARG100 3.6 53.3 1.0 OD2 A:ASP99 3.7 40.4 1.0 OD2 B:ASP99 3.9 49.2 1.0 HA B:ASP99 3.9 32.1 1.0 HA A:ASP99 4.0 38.8 1.0 N B:ARG100 4.0 55.9 1.0 O A:ARG100 4.2 43.9 1.0 O B:HOH350 4.3 32.8 1.0 HB2 B:ARG100 4.3 85.1 1.0 HG11 B:VAL28 4.3 20.5 1.0 N A:ARG100 4.4 44.4 1.0 O A:HOH315 4.4 38.0 1.0 CB A:ASP99 4.4 32.6 1.0 CB B:ASP99 4.5 37.9 1.0 CA B:ASP99 4.5 26.7 1.0 HG11 A:VAL28 4.6 30.5 1.0 O B:ARG100 4.6 71.4 1.0 CA A:ASP99 4.6 32.3 1.0 C B:ASP99 4.8 36.9 1.0 HG2 B:ARG100 4.9 91.6 1.0 CA B:ARG100 5.0 68.0 1.0 CB B:ARG100 5.0 70.9 1.0 HB2 A:ASP99 5.0 39.2 1.0 O B:HOH390 5.0 62.9 1.0 HG13 B:VAL28 5.0 20.5 1.0 C A:ASP99 5.0 37.6 1.0 HG21 A:VAL71 5.0 25.9 1.0

Magnesium binding site 2 out of 4 in the Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+


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 Trpser Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:30.0 occ:1.00 H A:TRP93 2.0 21.7 1.0 OD2 A:ASP34 2.6 17.4 1.0 O A:TRP32 2.7 17.4 1.0 HZ2 F:TRP1 2.9 13.3 1.0 N A:TRP93 2.9 18.1 1.0 HB2 A:TRP93 3.0 19.3 1.0 HE1 F:TRP1 3.0 20.8 1.0 HA A:LEU92 3.0 17.0 1.0 HG A:LEU92 3.2 28.3 1.0 HB3 A:ASP34 3.3 21.6 1.0 HG13 A:VAL31 3.4 17.6 1.0 HB3 A:LEU92 3.5 23.0 1.0 CA A:LEU92 3.6 14.2 1.0 CB A:TRP93 3.6 16.1 1.0 CG A:ASP34 3.7 21.8 1.0 NE1 F:TRP1 3.7 17.4 1.0 CZ2 F:TRP1 3.7 11.1 1.0 HD22 A:ASN37 3.7 20.2 1.0 C A:LEU92 3.7 15.8 1.0 CA A:TRP93 3.8 12.2 1.0 CB A:LEU92 3.8 19.2 1.0 C A:TRP32 3.9 15.9 1.0 CG A:LEU92 4.0 23.5 1.0 CG A:TRP93 4.0 25.3 1.0 CB A:ASP34 4.0 18.0 1.0 H A:TRP32 4.0 18.6 1.0 CE2 F:TRP1 4.0 10.6 1.0 O A:TRP93 4.1 16.5 1.0 CG1 A:VAL31 4.1 14.7 1.0 HG12 A:VAL31 4.2 17.6 1.0 HG11 A:VAL31 4.2 17.6 1.0 HA A:ASP33 4.3 15.8 1.0 C A:TRP93 4.4 13.9 1.0 ND2 A:ASN37 4.4 16.8 1.0 H A:ASP34 4.4 19.6 1.0 N A:ASP34 4.4 16.3 1.0 CD1 A:TRP93 4.4 22.8 1.0 HB3 A:TRP93 4.5 19.3 1.0 HD1 A:TRP93 4.5 27.3 1.0 HD12 A:LEU92 4.6 33.9 1.0 HD21 A:ASN37 4.6 20.2 1.0 C A:ASP33 4.6 18.8 1.0 CD2 A:TRP93 4.6 17.2 1.0 N A:TRP32 4.6 15.5 1.0 HA A:TRP93 4.6 14.6 1.0 HB2 A:ASP34 4.7 21.6 1.0 HB2 A:TRP32 4.7 19.5 1.0 OD1 A:ASP34 4.8 18.3 1.0 HD23 A:LEU92 4.8 18.4 1.0 HB2 A:LEU92 4.8 23.0 1.0 CA A:ASP33 4.8 13.2 1.0 HB2 A:ASN37 4.8 21.9 1.0 N A:ASP33 4.8 15.8 1.0 CA A:ASP34 4.9 13.9 1.0 CA A:TRP32 4.9 13.7 1.0 CD1 A:LEU92 4.9 28.2 1.0 CH2 F:TRP1 4.9 13.3 1.0 N A:LEU92 4.9 14.6 1.0 O A:LEU92 4.9 17.1 1.0 CD1 F:TRP1 4.9 19.4 1.0 O A:GLY91 5.0 19.8 1.0 HE3 A:TRP93 5.0 27.8 1.0 CD2 A:LEU92 5.0 15.3 1.0

Magnesium binding site 3 out of 4 in the Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:21.7 occ:1.00 O B:HOH306 1.9 34.2 1.0 NE2 B:HIS88 1.9 37.3 1.0 O B:HOH340 2.1 39.2 1.0 CE1 B:HIS88 2.6 46.4 1.0 HE1 B:HIS88 2.6 55.7 1.0 CD2 B:HIS88 3.1 43.5 1.0 HD2 B:HIS88 3.5 52.2 1.0 ND1 B:HIS88 3.8 44.4 1.0 CG B:HIS88 4.1 30.2 1.0 HD1 B:HIS88 4.6 53.3 1.0

Magnesium binding site 4 out of 4 in the Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mycolicibacterium Smegmatis Clps with Trpser Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:30.0 occ:1.00 H B:TRP93 1.9 20.3 1.0 OD2 B:ASP34 2.4 26.3 1.0 HA B:LEU92 2.7 18.5 1.0 N B:TRP93 2.7 16.9 1.0 O B:TRP32 2.8 22.4 1.0 HG B:LEU92 2.9 26.6 1.0 HE1 G:TRP1 3.1 32.3 1.0 HZ2 G:TRP1 3.1 26.6 1.0 HB3 B:LEU92 3.2 20.8 1.0 HB2 B:TRP93 3.3 25.9 1.0 CA B:LEU92 3.3 15.4 1.0 HB3 B:ASP34 3.3 43.8 1.0 C B:LEU92 3.5 21.7 1.0 CG B:ASP34 3.5 38.6 1.0 CB B:LEU92 3.5 17.4 1.0 HG13 B:VAL31 3.6 20.6 1.0 HD22 B:ASN37 3.6 22.0 1.0 CG B:LEU92 3.7 22.1 1.0 CA B:TRP93 3.8 19.1 1.0 CB B:TRP93 3.8 21.6 1.0 NE1 G:TRP1 3.8 26.9 1.0 CZ2 G:TRP1 3.9 22.1 1.0 CB B:ASP34 3.9 36.5 1.0 CG B:TRP93 4.0 21.0 1.0 C B:TRP32 4.1 22.4 1.0 O B:TRP93 4.1 17.7 1.0 CE2 G:TRP1 4.2 20.5 1.0 CG1 B:VAL31 4.2 17.2 1.0 H B:TRP32 4.3 26.5 1.0 HG11 B:VAL31 4.3 20.6 1.0 ND2 B:ASN37 4.3 18.3 1.0 HD23 B:LEU92 4.3 20.3 1.0 HG12 B:VAL31 4.4 20.6 1.0 C B:TRP93 4.4 16.3 1.0 H B:ASP34 4.4 28.2 1.0 HD21 B:ASN37 4.4 22.0 1.0 HA B:ASP33 4.5 30.7 1.0 N B:ASP34 4.5 23.5 1.0 CD1 B:TRP93 4.5 30.1 1.0 HB2 B:LEU92 4.5 20.8 1.0 HD12 B:LEU92 4.5 39.4 1.0 HA B:TRP93 4.5 23.0 1.0 CD2 B:TRP93 4.6 23.7 1.0 CD2 B:LEU92 4.6 16.9 1.0 HD1 B:TRP93 4.6 36.2 1.0 OD1 B:ASP34 4.6 29.8 1.0 N B:LEU92 4.6 14.8 1.0 HB2 B:ASP34 4.7 43.8 1.0 C B:ASP33 4.7 32.0 1.0 O B:LEU92 4.7 20.4 1.0 O B:GLY91 4.7 19.1 1.0 CD1 B:LEU92 4.7 32.8 1.0 HB3 B:TRP93 4.7 25.9 1.0 N B:TRP32 4.8 22.0 1.0 HB2 B:ASN37 4.8 26.5 1.0 HB2 B:TRP32 4.9 19.8 1.0 CA B:ASP34 4.9 20.6 1.0 CA B:ASP33 4.9 25.6 1.0 N B:ASP33 5.0 24.9 1.0 HE3 B:TRP93 5.0 24.7 1.0 HD21 B:LEU92 5.0 20.3 1.0 CA B:TRP32 5.0 21.7 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