Magnesium in PDB 9az5: Mycolicibacterium Smegmatis Clps with Bound MG2+

The structure of Mycolicibacterium Smegmatis Clps with Bound MG2+, PDB code: 9az5 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)	27.30 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.367, 52.289, 54.605, 90, 90, 90
R / Rfree (%)	14.9 / 18.5

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

Nickel

(Ni)

1 atom

The binding sites of Magnesium atom in the Mycolicibacterium Smegmatis Clps with Bound MG2+ (pdb code 9az5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Mycolicibacterium Smegmatis Clps with Bound MG2+, PDB code: 9az5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound 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 Bound MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:19.6 occ:1.00 OD1 A:ASP99 2.0 25.8 1.0 O A:HOH311 2.0 29.6 1.0 O B:HOH339 2.0 27.7 1.0 O A:HOH351 2.0 30.5 1.0 OD1 B:ASP99 2.1 26.4 1.0 O B:HOH319 2.1 44.1 1.0 CG A:ASP99 3.1 25.5 1.0 CG B:ASP99 3.1 25.8 1.0 H B:ARG100 3.3 44.1 1.0 O A:HOH395 3.4 46.4 1.0 OD2 A:ASP99 3.5 27.1 1.0 OD2 B:ASP99 3.6 26.6 1.0 H A:ARG100 3.8 37.4 1.0 HA A:ASP99 4.0 26.6 1.0 HA B:ASP99 4.0 28.7 1.0 N B:ARG100 4.2 36.8 1.0 O A:ARG100 4.3 38.4 1.0 CB A:ASP99 4.3 24.1 1.0 O B:HOH396 4.4 38.6 1.0 CB B:ASP99 4.4 25.5 1.0 N A:ARG100 4.4 31.2 1.0 OXT B:ARG100 4.4 46.2 1.0 O B:HOH394 4.5 46.4 1.0 HG11 A:VAL28 4.5 15.5 1.0 CA A:ASP99 4.6 22.1 1.0 CA B:ASP99 4.6 23.9 1.0 HB2 B:ARG100 4.7 54.0 1.0 HB2 A:ASP99 4.8 29.0 1.0 HG11 B:VAL28 4.8 14.8 1.0 C A:ASP99 4.9 28.6 1.0 HB3 B:ASP99 4.9 30.6 1.0 C B:ASP99 5.0 28.9 1.0 HB3 A:ASP99 5.0 29.0 1.0

Magnesium binding site 2 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound 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 Bound MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:26.4 occ:1.00 ND1 A:HIS65 2.0 27.7 1.0 HB2 A:HIS65 2.6 19.1 1.0 CG A:HIS65 2.9 24.4 1.0 CE1 A:HIS65 3.0 30.6 1.0 CB A:HIS65 3.1 15.9 1.0 HE1 A:HIS65 3.2 36.7 1.0 HA A:HIS65 3.3 15.7 1.0 CA A:HIS65 3.7 13.1 1.0 OD1 A:ASP33 3.9 14.9 1.0 O A:HIS65 3.9 15.3 1.0 HB3 A:HIS65 4.0 19.1 1.0 CD2 A:HIS65 4.0 28.4 1.0 NE2 A:HIS65 4.1 30.8 1.0 OD2 A:ASP33 4.1 16.6 1.0 C A:HIS65 4.2 14.1 1.0 O A:HOH394 4.3 37.9 1.0 CG A:ASP33 4.3 14.3 1.0 HG2 A:MET39 4.4 18.1 1.0 O A:HOH407 4.5 33.2 1.0 HG3 A:MET39 4.6 18.1 1.0 HE3 A:MET39 4.7 21.6 1.0 SD A:MET39 4.7 18.1 1.0 CG A:MET39 4.8 15.1 1.0 HD2 A:HIS65 4.8 34.1 1.0 HE2 A:HIS65 4.8 37.0 1.0

Magnesium binding site 3 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound 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 Bound MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:19.9 occ:1.00 H A:TRP93 2.1 11.6 1.0 OD2 A:ASP34 2.7 17.7 1.0 O A:TRP32 2.8 11.1 1.0 N A:TRP93 2.9 9.7 1.0 HB2 A:TRP93 3.0 11.7 1.0 HA A:LEU92 3.0 10.1 0.4 HA A:LEU92 3.0 9.7 0.6 HB3 A:ASP34 3.1 13.9 1.0 HG A:LEU92 3.2 11.0 0.6 HB3 A:LEU92 3.2 11.2 0.4 HG13 A:VAL31 3.3 11.5 1.0 HD22 A:LEU92 3.4 9.7 0.4 HD22 A:ASN37 3.5 17.4 1.0 HB3 A:LEU92 3.6 11.3 0.6 CB A:TRP93 3.6 9.8 1.0 CG A:ASP34 3.6 15.4 1.0 CA A:LEU92 3.6 8.4 0.4 CA A:LEU92 3.7 8.1 0.6 O A:HOH372 3.7 38.5 0.5 C A:LEU92 3.8 9.2 1.0 CB A:ASP34 3.8 11.6 1.0 CA A:TRP93 3.8 9.3 1.0 HG12 A:VAL31 3.8 11.5 1.0 CB A:LEU92 3.9 9.3 0.4 CB A:LEU92 3.9 9.4 0.6 CG A:TRP93 3.9 11.5 1.0 CG1 A:VAL31 3.9 9.6 1.0 CG A:LEU92 4.0 9.2 0.6 C A:TRP32 4.0 9.6 1.0 H A:ASP34 4.1 14.8 1.0 HG11 A:VAL31 4.1 11.5 1.0 CD2 A:LEU92 4.2 8.1 0.4 H A:TRP32 4.2 10.5 1.0 O A:TRP93 4.2 15.1 1.0 HD23 A:LEU92 4.2 9.7 0.4 N A:ASP34 4.2 12.3 1.0 ND2 A:ASN37 4.3 14.6 1.0 CD1 A:TRP93 4.3 12.7 1.0 HA A:ASP33 4.4 14.1 1.0 HD1 A:TRP93 4.4 15.3 1.0 C A:TRP93 4.4 9.9 1.0 HB2 A:ASP34 4.5 13.9 1.0 HD23 A:LEU92 4.5 12.5 0.6 HB3 A:TRP93 4.5 11.7 1.0 CG A:LEU92 4.5 8.8 0.4 CD2 A:TRP93 4.5 10.7 1.0 HD13 A:LEU92 4.5 10.8 0.4 HD21 A:ASN37 4.5 17.4 1.0 N A:TRP32 4.6 8.8 1.0 HA A:TRP93 4.6 11.2 1.0 C A:ASP33 4.6 11.2 1.0 HB2 A:LEU92 4.6 11.2 0.4 CA A:ASP34 4.7 11.9 1.0 HG11 A:VAL64 4.7 14.8 1.0 HB2 A:ASN37 4.7 17.7 1.0 OD1 A:ASP34 4.8 17.8 1.0 CD2 A:LEU92 4.8 10.4 0.6 HB2 A:LEU92 4.8 11.3 0.6 CA A:ASP33 4.9 11.7 1.0 CA A:TRP32 4.9 9.3 1.0 HB2 A:TRP32 4.9 10.7 1.0 N A:ASP33 4.9 10.2 1.0 HD12 A:LEU92 4.9 11.4 0.6 O A:GLY91 4.9 11.6 1.0 HE3 A:TRP93 5.0 14.1 1.0 O A:LEU92 5.0 11.3 1.0 HD21 A:LEU92 5.0 9.7 0.4 N A:LEU92 5.0 9.8 1.0 HG22 A:VAL42 5.0 11.9 1.0

Magnesium binding site 4 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound 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 Bound MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:31.1 occ:1.00 O B:HOH351 2.0 44.1 1.0 NE2 B:HIS88 2.2 18.8 1.0 O B:HOH443 2.4 68.7 1.0 CE1 B:HIS88 3.2 19.4 1.0 CD2 B:HIS88 3.2 18.2 1.0 HE1 B:HIS88 3.3 23.3 1.0 HD2 B:HIS88 3.4 21.8 1.0 ND1 B:HIS88 4.3 18.8 1.0 CG B:HIS88 4.3 14.6 1.0 O B:HOH333 4.5 52.1 1.0 O B:HOH449 4.8 34.2 1.0

Magnesium binding site 5 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mycolicibacterium Smegmatis Clps with Bound MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:21.3 occ:1.00 HD21 B:ASN37 2.0 24.4 1.0 HA B:LEU92 2.7 9.4 1.0 OD2 B:ASP34 2.8 17.4 1.0 O B:GLY91 2.8 13.0 1.0 HB3 B:ASP34 2.8 14.3 1.0 ND2 B:ASN37 2.8 20.4 1.0 HB2 B:ASP34 2.9 14.3 1.0 O B:HOH346 2.9 9.9 1.0 HD22 B:ASN37 3.1 24.4 1.0 CB B:ASP34 3.2 11.9 1.0 NE1 B:TRP93 3.4 11.1 1.0 CG B:ASP34 3.4 15.8 1.0 CD1 B:TRP93 3.4 10.2 1.0 H B:TRP93 3.5 10.7 1.0 HE1 B:TRP93 3.6 13.3 1.0 HD23 B:LEU92 3.6 15.2 1.0 CA B:LEU92 3.6 7.9 1.0 HD1 B:TRP93 3.7 12.3 1.0 CE2 B:TRP93 3.7 10.5 1.0 O B:HOH331 3.8 36.0 1.0 CG B:TRP93 3.8 9.7 1.0 HD22 B:LEU92 3.8 15.2 1.0 C B:GLY91 3.8 10.6 1.0 CG B:ASN37 3.8 21.2 1.0 O B:HOH355 3.9 41.9 1.0 N B:TRP93 3.9 8.9 1.0 CD2 B:TRP93 4.0 9.8 1.0 C B:LEU92 4.0 8.2 1.0 OD1 B:ASN37 4.1 23.6 1.0 CD2 B:LEU92 4.1 12.7 1.0 N B:LEU92 4.2 9.0 1.0 O B:HOH385 4.4 15.2 1.0 CZ2 B:TRP93 4.4 12.1 1.0 O B:HOH367 4.5 30.8 1.0 HB2 B:TRP93 4.6 10.4 1.0 CB B:LEU92 4.6 8.0 1.0 OD1 B:ASP34 4.6 18.4 1.0 CA B:ASP34 4.6 11.4 1.0 HB3 B:LEU92 4.6 9.6 1.0 CB B:TRP93 4.6 8.7 1.0 HZ2 B:TRP93 4.7 14.5 1.0 O B:HOH317 4.7 36.1 1.0 CA B:TRP93 4.8 8.5 1.0 H B:ASP34 4.8 13.5 1.0 CE3 B:TRP93 4.9 10.3 1.0 HD21 B:LEU92 4.9 15.2 1.0 O B:LEU92 5.0 11.9 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