Magnesium 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:

Nickel

(Ni)

1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Mycolicibacterium Smegmatis Clps with Tyrarg Dipeptide and MG2+, PDB code: 9b10:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Mycolicibacterium Smegmatis Clps with Tyrarg 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 Tyrarg Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:12.2 occ:0.83 H A:TRP93 2.1 8.9 1.0 OD2 A:ASP34 2.7 9.9 1.0 O A:TRP32 2.7 8.7 1.0 HH A:TYR201 2.7 9.4 1.0 HE1 A:TYR201 2.9 9.9 1.0 OH A:TYR201 3.0 7.8 1.0 N A:TRP93 3.0 7.4 1.0 HB2 A:TRP93 3.1 9.8 1.0 HB3 A:LEU92 3.1 9.0 0.5 HG A:LEU92 3.1 9.7 0.5 HA A:LEU92 3.1 9.1 0.5 HA A:LEU92 3.1 8.8 0.5 HG13 A:VAL31 3.3 8.7 1.0 HD22 A:LEU92 3.3 8.8 0.5 HB3 A:LEU92 3.4 9.7 0.5 HB3 A:ASP34 3.4 11.5 1.0 CE1 A:TYR201 3.6 8.3 1.0 CA A:LEU92 3.7 7.4 0.5 CA A:LEU92 3.7 7.6 0.5 CZ A:TYR201 3.7 8.0 1.0 HG12 A:VAL31 3.7 8.7 1.0 CB A:TRP93 3.7 8.1 1.0 CG A:ASP34 3.7 9.6 1.0 CB A:LEU92 3.8 7.5 0.5 CB A:LEU92 3.8 8.1 0.5 C A:LEU92 3.8 7.8 1.0 CG1 A:VAL31 3.8 7.2 1.0 CA A:TRP93 3.9 7.4 1.0 CG A:LEU92 3.9 8.1 0.5 C A:TRP32 3.9 8.5 1.0 H A:TRP32 4.0 8.6 1.0 HG11 A:VAL31 4.0 8.7 1.0 CB A:ASP34 4.0 9.6 1.0 CG A:TRP93 4.0 9.9 1.0 O A:TRP93 4.1 11.8 1.0 CD2 A:LEU92 4.1 7.3 0.5 H A:ASP34 4.1 10.8 1.0 HD23 A:LEU92 4.2 8.8 0.5 HA A:ASP33 4.3 11.5 1.0 N A:ASP34 4.3 9.0 1.0 HD23 A:LEU92 4.3 9.9 0.5 HD13 A:LEU92 4.3 9.6 0.5 C A:TRP93 4.4 7.8 1.0 CD1 A:TRP93 4.5 11.6 1.0 CG A:LEU92 4.5 7.3 0.5 OD1 A:ASN37 4.5 11.3 1.0 N A:TRP32 4.5 7.2 1.0 HD1 A:TRP93 4.5 13.9 1.0 HB2 A:LEU92 4.6 9.0 0.5 C A:ASP33 4.6 9.1 1.0 HB3 A:TRP93 4.6 9.8 1.0 HG11 A:VAL64 4.6 11.0 1.0 CD2 A:LEU92 4.7 8.2 0.5 HA A:TRP93 4.7 8.9 1.0 CD2 A:TRP93 4.7 10.3 1.0 HB2 A:ASN37 4.7 11.0 1.0 HB2 A:LEU92 4.7 9.7 0.5 CA A:ASP33 4.7 9.6 1.0 N A:ASP33 4.8 8.8 1.0 HB2 A:ASP34 4.8 11.5 1.0 CA A:ASP34 4.8 10.0 1.0 CA A:TRP32 4.8 8.1 1.0 HB2 A:TRP32 4.8 9.8 1.0 CD1 A:TYR201 4.9 8.8 1.0 OD1 A:ASP34 4.9 11.1 1.0 HD21 A:LEU92 4.9 8.8 0.5 HD12 A:LEU92 4.9 10.8 0.5 CD1 A:LEU92 4.9 8.0 0.5 HG22 A:VAL42 5.0 8.9 1.0

Magnesium binding site 2 out of 5 in the Mycolicibacterium Smegmatis Clps with Tyrarg 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 Tyrarg Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:6.3 occ:1.00 O A:HOH329 2.0 16.2 1.0 O A:HOH350 2.1 16.4 0.8 O A:HOH396 2.2 25.0 1.0 NE2 A:HIS65 2.2 18.7 1.0 N A:TYR201 2.3 14.9 1.0 O A:TYR201 2.3 16.8 1.0 H A:TYR201 2.4 17.9 1.0 H2 A:TYR201 3.0 17.9 1.0 C A:TYR201 3.0 14.2 1.0 O A:HOH350 3.0 15.1 0.2 CD2 A:HIS65 3.0 16.6 1.0 HD2 A:HIS65 3.1 19.9 1.0 CA A:TYR201 3.1 10.7 1.0 CE1 A:HIS65 3.3 18.7 1.0 HE1 A:HIS65 3.6 22.4 1.0 HB2 A:TYR201 3.6 14.7 1.0 HA A:TYR201 3.9 12.8 1.0 CB A:TYR201 4.0 12.3 1.0 O A:HOH357 4.0 27.3 1.0 O A:HOH450 4.2 48.4 1.0 OD2 A:ASP33 4.2 14.2 1.0 HA A:PRO35 4.2 18.6 1.0 N A:ARG202 4.2 12.5 1.0 OD1 A:ASP33 4.2 12.3 1.0 O A:HOH402 4.2 64.1 1.0 CG A:HIS65 4.2 16.2 1.0 O A:HOH443 4.3 41.2 1.0 ND1 A:HIS65 4.3 18.2 1.0 O A:HOH342 4.4 22.0 1.0 HA A:ARG202 4.4 14.1 1.0 O A:HOH305 4.5 40.9 1.0 O A:ASP34 4.5 10.8 1.0 CG A:ASP33 4.6 12.3 1.0 HB3 A:TYR201 4.6 14.7 1.0 H A:ARG202 4.9 15.0 1.0 CA A:ARG202 4.9 11.8 1.0 CG A:TYR201 4.9 8.4 1.0

Magnesium binding site 3 out of 5 in the Mycolicibacterium Smegmatis Clps with Tyrarg 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 Tyrarg Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:19.6 occ:0.83 OD1 B:ASP99 2.0 24.0 1.0 OD1 A:ASP99 2.0 23.4 1.0 O A:HOH303 2.0 33.7 1.0 O A:HOH364 2.0 19.8 1.0 O B:HOH369 2.3 32.0 1.0 O B:HOH302 2.3 31.4 1.0 H B:ARG100 3.0 31.3 1.0 CG B:ASP99 3.0 21.0 1.0 CG A:ASP99 3.1 23.1 1.0 OD2 B:ASP99 3.5 23.3 1.0 O A:HOH406 3.6 29.1 1.0 OD2 A:ASP99 3.6 25.3 1.0 H A:ARG100 3.6 28.1 0.4 H A:ARG100 3.6 28.1 0.6 N B:ARG100 3.8 26.1 1.0 O A:HOH385 3.9 21.6 0.5 HA B:ASP99 3.9 20.3 1.0 HA A:ASP99 3.9 22.2 1.0 HB2 B:ARG100 4.0 49.5 1.0 O A:ARG100 4.0 24.9 1.0 O B:HOH392 4.2 59.3 1.0 O B:HOH349 4.2 28.7 1.0 OXT B:ARG100 4.3 48.9 1.0 CB B:ASP99 4.3 18.1 1.0 N A:ARG100 4.3 23.4 1.0 CB A:ASP99 4.4 20.6 1.0 CA B:ASP99 4.4 16.9 1.0 CA A:ASP99 4.5 18.5 1.0 HG2 B:ARG100 4.6 61.5 1.0 C B:ASP99 4.6 22.4 1.0 HG11 A:VAL28 4.7 13.2 1.0 CB B:ARG100 4.7 41.2 1.0 CA B:ARG100 4.7 60.1 1.0 O A:HOH385 4.7 24.2 0.5 HG11 B:VAL28 4.8 13.1 1.0 HB3 B:ASP99 4.8 21.7 1.0 HB2 B:ASP99 4.9 21.7 1.0 C A:ASP99 4.9 21.8 1.0 C B:ARG100 4.9 64.2 1.0 HB2 A:ASP99 4.9 24.7 1.0

Magnesium binding site 4 out of 5 in the Mycolicibacterium Smegmatis Clps with Tyrarg 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 Tyrarg Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg207 b:12.3 occ:0.81 H B:TRP93 2.1 9.0 1.0 O B:TRP32 2.7 8.7 1.0 OD2 B:ASP34 2.7 9.9 1.0 HE1 B:TYR204 2.9 9.4 1.0 OH B:TYR204 2.9 9.2 1.0 HB3 B:LEU92 2.9 8.8 0.3 N B:TRP93 3.0 7.5 1.0 HA B:LEU92 3.1 7.8 0.7 HA B:LEU92 3.1 8.2 0.3 HG B:LEU92 3.1 9.2 0.7 HG13 B:VAL31 3.1 8.7 1.0 HB2 B:TRP93 3.2 9.5 1.0 HB3 B:LEU92 3.2 8.8 0.7 HD22 B:LEU92 3.3 9.1 0.3 HB3 B:ASP34 3.5 12.3 1.0 CE1 B:TYR204 3.6 7.8 1.0 HH B:TYR204 3.6 11.0 1.0 CA B:LEU92 3.6 6.9 0.3 CA B:LEU92 3.6 6.5 0.7 CB B:LEU92 3.6 7.3 0.3 CB B:LEU92 3.7 7.3 0.7 CZ B:TYR204 3.7 8.7 1.0 HG12 B:VAL31 3.7 8.7 1.0 CG B:ASP34 3.7 10.0 1.0 CG1 B:VAL31 3.7 7.2 1.0 C B:LEU92 3.8 8.4 1.0 CG B:LEU92 3.8 7.7 0.7 CB B:TRP93 3.8 8.0 1.0 CA B:TRP93 3.9 7.1 1.0 C B:TRP32 3.9 7.8 1.0 HG11 B:VAL31 3.9 8.7 1.0 H B:TRP32 4.0 8.8 1.0 O B:TRP93 4.0 8.9 1.0 CD2 B:LEU92 4.0 7.6 0.3 CB B:ASP34 4.1 10.3 1.0 HD23 B:LEU92 4.1 10.3 0.7 H B:ASP34 4.2 10.4 1.0 HD23 B:LEU92 4.2 9.1 0.3 CG B:TRP93 4.2 9.1 1.0 HD13 B:LEU92 4.2 7.1 0.3 HA B:ASP33 4.2 9.8 1.0 N B:ASP34 4.3 8.7 1.0 CG B:LEU92 4.3 5.8 0.3 C B:TRP93 4.4 7.3 1.0 HB2 B:LEU92 4.4 8.8 0.3 N B:TRP32 4.5 7.4 1.0 CD2 B:LEU92 4.5 8.6 0.7 C B:ASP33 4.5 8.2 1.0 HB2 B:LEU92 4.6 8.8 0.7 HG11 B:VAL64 4.6 9.9 1.0 OD1 B:ASN37 4.6 13.5 1.0 HB3 B:TRP93 4.7 9.5 1.0 CD1 B:TRP93 4.7 11.2 1.0 CA B:ASP33 4.7 8.1 1.0 CD2 B:TRP93 4.7 8.3 1.0 HA B:TRP93 4.7 8.5 1.0 N B:ASP33 4.8 7.9 1.0 CD1 B:LEU92 4.8 5.9 0.3 CA B:TRP32 4.8 7.7 1.0 HB2 B:ASP34 4.8 12.3 1.0 HD1 B:TRP93 4.8 13.4 1.0 CA B:ASP34 4.8 8.9 1.0 CD1 B:TYR204 4.8 8.4 1.0 HD21 B:LEU92 4.9 9.1 0.3 OD1 B:ASP34 4.9 12.7 1.0 HB2 B:TRP32 4.9 11.6 1.0 HD21 B:LEU92 4.9 10.3 0.7 HB2 B:ASN37 5.0 11.8 1.0 HD12 B:LEU92 5.0 9.8 0.7 HE3 B:TRP93 5.0 12.3 1.0 N B:LEU92 5.0 8.0 1.0 O B:LEU92 5.0 10.4 1.0

Magnesium binding site 5 out of 5 in the Mycolicibacterium Smegmatis Clps with Tyrarg Dipeptide and 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 Tyrarg Dipeptide and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg208 b:7.8 occ:1.00 O B:HOH396 2.0 23.2 1.0 O B:HOH406 2.0 21.7 1.0 O B:HOH318 2.1 19.9 1.0 N B:TYR204 2.2 21.1 1.0 O B:TYR204 2.3 21.3 1.0 HE2 B:HIS65 2.4 30.1 1.0 H B:TYR204 2.5 25.3 1.0 HD2 B:HIS65 2.8 42.9 1.0 H2 B:TYR204 2.9 25.3 1.0 C B:TYR204 2.9 13.5 1.0 NE2 B:HIS65 3.0 25.1 1.0 CA B:TYR204 3.0 12.1 1.0 CD2 B:HIS65 3.1 35.8 1.0 HA B:TYR204 3.7 14.5 1.0 HB2 B:TYR204 3.8 13.3 1.0 CB B:TYR204 4.0 11.1 1.0 O B:HOH455 4.0 55.4 1.0 N B:ARG205 4.1 12.5 1.0 O B:HOH360 4.1 49.0 1.0 CE1 B:HIS65 4.2 44.3 1.0 OD2 B:ASP33 4.2 13.3 1.0 OD1 B:ASP33 4.3 11.1 1.0 HA B:ARG205 4.3 15.9 1.0 O B:HOH398 4.4 36.0 1.0 HA B:PRO35 4.4 15.5 1.0 O B:HOH372 4.4 60.2 1.0 CG B:HIS65 4.4 18.1 1.0 O B:HOH412 4.5 56.5 1.0 O B:HOH454 4.5 50.5 1.0 O B:ASP34 4.5 10.5 1.0 CG B:ASP33 4.7 11.2 1.0 HE1 B:HIS65 4.7 53.1 1.0 HB3 B:TYR204 4.7 13.3 1.0 H B:ARG205 4.8 15.0 1.0 CA B:ARG205 4.8 13.3 1.0 ND1 B:HIS65 4.9 45.2 1.0 HG2 B:ARG205 5.0 30.3 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