Magnesium in PDB 5x9v: Crystal Structure of Group III Chaperonin in the Closed State

The structure of Crystal Structure of Group III Chaperonin in the Closed State, PDB code: 5x9v was solved by Y.J.An, S.S.Cha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.15 / 3.00
Space group	P 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	186.166, 186.166, 160.742, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.8

The binding sites of Magnesium atom in the Crystal Structure of Group III Chaperonin in the Closed State (pdb code 5x9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Group III Chaperonin in the Closed State, PDB code: 5x9v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Group III Chaperonin in the Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Group III Chaperonin in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:28.6 occ:1.00 O2G A:ANP601 2.0 32.0 1.0 O1B A:ANP601 2.0 34.6 1.0 OD1 A:ASP87 2.1 28.8 1.0 O1A A:ANP601 2.5 25.1 1.0 CG A:ASP87 2.8 34.3 1.0 OD2 A:ASP87 2.9 34.1 1.0 PB A:ANP601 3.4 29.6 1.0 PG A:ANP601 3.5 35.5 1.0 PA A:ANP601 3.9 23.2 1.0 N3B A:ANP601 4.1 29.9 1.0 NH2 A:ARG155 4.1 33.4 1.0 O A:ALA153 4.2 19.5 1.0 O3A A:ANP601 4.2 24.4 1.0 OD2 A:ASP373 4.2 37.9 1.0 N A:GLY88 4.2 27.8 1.0 CB A:ASP87 4.3 32.9 1.0 C5' A:ANP601 4.3 27.7 1.0 O3G A:ANP601 4.4 48.9 1.0 O1G A:ANP601 4.4 41.9 1.0 CA A:ALA153 4.5 23.7 1.0 O2B A:ANP601 4.5 24.4 1.0 O5' A:ANP601 4.6 24.6 1.0 CB A:ALA153 4.7 21.4 1.0 CZ A:ARG155 4.7 28.6 1.0 C A:ALA153 4.8 20.1 1.0 CA A:ASP87 4.8 27.6 1.0 CG A:ASP373 4.9 38.1 1.0 CB A:ASP373 4.9 36.9 1.0 O2A A:ANP601 5.0 31.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Group III Chaperonin in the Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Group III Chaperonin in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:30.5 occ:1.00 O1A B:ANP601 2.0 36.5 1.0 O1B B:ANP601 2.2 29.6 1.0 OD1 B:ASP87 2.2 33.2 1.0 O2G B:ANP601 2.2 35.3 1.0 OD2 B:ASP87 2.6 32.0 1.0 CG B:ASP87 2.7 32.8 1.0 PA B:ANP601 3.5 35.6 1.0 PB B:ANP601 3.5 33.5 1.0 PG B:ANP601 3.7 29.0 1.0 C5' B:ANP601 3.8 32.5 1.0 O3A B:ANP601 4.0 33.7 1.0 O5' B:ANP601 4.1 24.4 1.0 CB B:ASP87 4.2 26.4 1.0 N3B B:ANP601 4.3 62.4 1.0 N B:GLY88 4.4 30.0 1.0 OD2 B:ASP373 4.4 42.3 1.0 O B:ALA153 4.4 34.2 1.0 CA B:ALA153 4.5 29.9 1.0 O1G B:ANP601 4.5 33.0 1.0 O2A B:ANP601 4.5 35.3 1.0 NH2 B:ARG155 4.5 37.5 1.0 O3G B:ANP601 4.6 31.8 1.0 O2B B:ANP601 4.6 27.2 1.0 CA B:ASP87 4.9 25.8 1.0 CB B:ALA153 4.9 27.0 1.0 C B:ALA153 5.0 32.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Group III Chaperonin in the Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Group III Chaperonin in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:30.8 occ:1.00 O2G C:ANP601 1.8 35.0 1.0 OD1 C:ASP87 2.1 36.6 1.0 O2A C:ANP601 2.2 32.6 1.0 O2B C:ANP601 2.4 28.1 1.0 CG C:ASP87 2.9 34.9 1.0 OD2 C:ASP87 3.1 30.3 1.0 PG C:ANP601 3.3 74.5 1.0 PB C:ANP601 3.7 24.7 1.0 OD2 C:ASP373 3.7 44.2 1.0 PA C:ANP601 3.7 26.3 1.0 NH2 C:ARG155 3.9 37.8 1.0 O1G C:ANP601 4.1 72.3 1.0 O C:ALA153 4.1 28.3 1.0 N3B C:ANP601 4.1 29.1 1.0 O3G C:ANP601 4.2 32.8 1.0 O3A C:ANP601 4.2 34.0 1.0 CB C:ASP87 4.3 31.0 1.0 N C:GLY88 4.3 29.7 1.0 CG C:ASP373 4.5 43.2 1.0 C5' C:ANP601 4.5 25.3 1.0 CZ C:ARG155 4.5 39.4 1.0 O1A C:ANP601 4.5 27.8 1.0 CA C:ALA153 4.6 30.0 1.0 O5' C:ANP601 4.6 26.6 1.0 CB C:ASP373 4.7 31.1 1.0 CA C:ASP87 4.8 37.2 1.0 CB C:ALA153 4.8 28.5 1.0 NE C:ARG155 4.8 32.3 1.0 C C:ALA153 4.8 26.2 1.0 O1B C:ANP601 4.9 21.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Group III Chaperonin in the Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Group III Chaperonin in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:45.9 occ:1.00 O2B D:ANP601 1.9 42.7 1.0 O2G D:ANP601 1.9 54.7 1.0 O2A D:ANP601 1.9 54.7 1.0 OD1 D:ASP87 2.3 37.7 1.0 CG D:ASP87 3.1 42.1 1.0 PB D:ANP601 3.2 34.1 1.0 OD2 D:ASP87 3.2 49.5 1.0 PG D:ANP601 3.3 93.2 1.0 PA D:ANP601 3.3 57.6 1.0 O3A D:ANP601 3.7 46.5 1.0 N3B D:ANP601 3.8 39.4 1.0 C5' D:ANP601 3.9 34.3 1.0 OD2 D:ASP373 4.0 34.9 1.0 O5' D:ANP601 4.1 31.6 1.0 O3G D:ANP601 4.1 36.7 1.0 O1B D:ANP601 4.3 33.2 1.0 O1G D:ANP601 4.4 98.7 1.0 N D:GLY88 4.4 44.8 1.0 O D:ALA153 4.4 31.7 1.0 O1A D:ANP601 4.5 41.9 1.0 CA D:ALA153 4.5 37.7 1.0 CB D:ASP87 4.6 30.9 1.0 NH2 D:ARG155 4.6 56.1 1.0 CB D:ALA153 4.8 35.5 1.0 CG D:ASP373 4.8 34.3 1.0 C D:ALA153 5.0 34.0 1.0

Y.J.An, S.E.Rowland, J.H.Na, D.Spigolon, S.K.Hong, Y.J.Yoon, J.H.Lee, F.T.Robb, S.S.Cha. Structural and Mechanistic Characterization of An Archaeal-Like Chaperonin From A Thermophilic Bacterium Nat Commun V. 8 827 2017.
ISSN: ESSN 2041-1723
PubMed: 29018216
DOI: 10.1038/S41467-017-00980-Z