Magnesium in PDB 5opx: Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2

The structure of Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2, PDB code: 5opx was solved by X.Yan, Q.Shi, A.Bracher, G.Milicic, A.K.Singh, F.U.Hartl, M.Hayer-Hartl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 3.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	217.567, 230.504, 235.391, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 25.6

The structure of Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2 also contains other interesting chemical elements:

Fluorine	(F)	42 atoms
Potassium	(K)	14 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2 (pdb code 5opx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2, PDB code: 5opx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


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 the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:59.0 occ:1.00 O1A A:ADP600 2.1 75.9 1.0 O1B A:ADP600 2.2 74.3 1.0 OD1 A:ASP87 2.3 87.2 1.0 F1 A:BEF602 2.3 81.4 1.0 OD2 A:ASP87 2.8 85.8 1.0 CG A:ASP87 2.9 86.3 1.0 PA A:ADP600 3.1 73.0 1.0 O5' A:ADP600 3.3 74.8 1.0 PB A:ADP600 3.4 71.4 1.0 BE A:BEF602 3.6 79.2 1.0 O3A A:ADP600 3.7 71.2 1.0 O A:SER151 3.8 90.8 1.0 O3B A:ADP600 4.0 69.8 1.0 OG A:SER151 4.3 92.2 1.0 CB A:ASP87 4.5 86.0 1.0 CA A:SER151 4.5 90.7 1.0 OD2 A:ASP398 4.5 0.6 1.0 F2 A:BEF602 4.5 79.6 1.0 O2A A:ADP600 4.5 70.9 1.0 C A:SER151 4.6 88.9 1.0 C5' A:ADP600 4.6 78.6 1.0 F3 A:BEF602 4.7 78.5 1.0 N A:GLY88 4.7 84.3 1.0 O2B A:ADP600 4.7 70.1 1.0

Magnesium binding site 2 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


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 the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:48.6 occ:1.00 O1A B:ADP600 2.1 69.6 1.0 OD1 B:ASP87 2.3 77.2 1.0 O3B B:ADP600 2.3 65.7 1.0 F1 B:BEF602 2.4 90.7 1.0 OD2 B:ASP87 2.8 72.6 1.0 CG B:ASP87 2.9 74.9 1.0 PA B:ADP600 3.2 66.8 1.0 O5' B:ADP600 3.3 69.8 1.0 PB B:ADP600 3.5 65.4 1.0 BE B:BEF602 3.6 89.1 1.0 O3A B:ADP600 3.7 65.7 1.0 O B:SER151 3.8 81.4 1.0 O1B B:ADP600 4.0 63.8 1.0 OG B:SER151 4.2 88.6 1.0 CA B:SER151 4.4 85.7 1.0 CB B:ASP87 4.4 75.2 1.0 F2 B:BEF602 4.5 91.3 1.0 OD2 B:ASP398 4.6 0.0 1.0 C B:SER151 4.6 81.9 1.0 O2A B:ADP600 4.6 65.2 1.0 C5' B:ADP600 4.6 71.5 1.0 F3 B:BEF602 4.7 85.3 1.0 N B:GLY88 4.7 75.5 1.0 O2B B:ADP600 4.7 64.5 1.0 CB B:SER151 5.0 86.3 1.0

Magnesium binding site 3 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


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 the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:57.4 occ:1.00 O1A C:ADP600 2.1 87.4 1.0 O3B C:ADP600 2.2 92.7 1.0 OD1 C:ASP87 2.4 99.8 1.0 F1 C:BEF602 2.5 0.2 1.0 OD2 C:ASP87 2.8 0.0 1.0 CG C:ASP87 3.0 0.2 1.0 PA C:ADP600 3.2 85.2 1.0 O5' C:ADP600 3.2 84.7 1.0 PB C:ADP600 3.4 91.5 1.0 O3A C:ADP600 3.7 86.7 1.0 BE C:BEF602 3.7 0.6 1.0 O C:SER151 3.9 0.2 1.0 O1B C:ADP600 4.0 88.8 1.0 OG C:SER151 4.3 0.4 1.0 CA C:SER151 4.4 0.5 1.0 CB C:ASP87 4.5 0.2 1.0 C5' C:ADP600 4.5 83.8 1.0 O2A C:ADP600 4.6 82.8 1.0 O2B C:ADP600 4.6 95.0 1.0 F2 C:BEF602 4.6 0.9 1.0 C C:SER151 4.6 0.4 1.0 N C:GLY88 4.7 0.6 1.0 F3 C:BEF602 4.8 0.4 1.0 OD2 C:ASP398 4.8 0.6 1.0 CB C:SER151 5.0 0.5 1.0

Magnesium binding site 4 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


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 the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:78.4 occ:1.00 O1A D:ADP600 2.0 91.1 1.0 F1 D:BEF602 2.2 0.8 1.0 O1B D:ADP600 2.4 96.1 1.0 OD1 D:ASP87 2.4 96.2 1.0 OD2 D:ASP87 2.9 0.5 1.0 CG D:ASP87 3.1 99.7 1.0 PA D:ADP600 3.1 90.1 1.0 O5' D:ADP600 3.4 91.6 1.0 PB D:ADP600 3.5 90.0 1.0 BE D:BEF602 3.6 0.2 1.0 O D:SER151 3.7 0.7 1.0 O3A D:ADP600 3.7 88.4 1.0 O3B D:ADP600 4.0 88.7 1.0 OG D:SER151 4.3 0.7 1.0 CA D:SER151 4.4 0.2 1.0 OD2 D:ASP398 4.4 0.7 1.0 O2A D:ADP600 4.5 89.6 1.0 C D:SER151 4.5 0.8 1.0 F2 D:BEF602 4.5 0.8 1.0 F3 D:BEF602 4.6 0.6 1.0 CB D:ASP87 4.6 0.0 1.0 C5' D:ADP600 4.7 92.2 1.0 O2B D:ADP600 4.8 90.0 1.0 N D:GLY88 4.9 0.5 1.0 K D:K603 5.0 89.1 1.0 CB D:SER151 5.0 0.8 1.0

Magnesium binding site 5 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:62.2 occ:1.00 O1A E:ADP600 2.1 89.3 1.0 F1 E:BEF602 2.2 96.3 1.0 OD1 E:ASP87 2.3 82.1 1.0 O1B E:ADP600 2.3 96.5 1.0 OD2 E:ASP87 2.8 84.9 1.0 CG E:ASP87 3.0 84.2 1.0 PA E:ADP600 3.2 87.6 1.0 O5' E:ADP600 3.4 87.8 1.0 PB E:ADP600 3.5 94.9 1.0 BE E:BEF602 3.5 97.3 1.0 O3A E:ADP600 3.7 90.5 1.0 O E:SER151 3.8 96.8 1.0 O3B E:ADP600 4.0 94.5 1.0 OG E:SER151 4.3 97.3 1.0 OD2 E:ASP398 4.4 0.3 1.0 F2 E:BEF602 4.4 98.9 1.0 CA E:SER151 4.5 96.4 1.0 CB E:ASP87 4.5 85.8 1.0 F3 E:BEF602 4.6 96.2 1.0 O2A E:ADP600 4.6 87.5 1.0 C E:SER151 4.6 94.6 1.0 N E:GLY88 4.7 87.7 1.0 C5' E:ADP600 4.8 87.7 1.0 O2B E:ADP600 4.8 93.2 1.0

Magnesium binding site 6 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:59.1 occ:1.00 O1A F:ADP600 2.0 77.8 1.0 F1 F:BEF602 2.3 90.7 1.0 O1B F:ADP600 2.3 84.2 1.0 OD1 F:ASP87 2.3 86.5 1.0 OD2 F:ASP87 2.9 80.4 1.0 CG F:ASP87 3.0 83.1 1.0 PA F:ADP600 3.2 75.6 1.0 O5' F:ADP600 3.4 75.1 1.0 PB F:ADP600 3.4 84.7 1.0 BE F:BEF602 3.5 88.7 1.0 O3A F:ADP600 3.6 79.3 1.0 O F:SER151 3.7 88.3 1.0 O3B F:ADP600 4.0 81.8 1.0 OG F:SER151 4.3 87.0 1.0 OD2 F:ASP398 4.4 0.8 1.0 F2 F:BEF602 4.4 91.9 1.0 CA F:SER151 4.5 87.1 1.0 CB F:ASP87 4.5 82.1 1.0 C F:SER151 4.6 86.0 1.0 O2A F:ADP600 4.6 73.3 1.0 F3 F:BEF602 4.6 84.3 1.0 C5' F:ADP600 4.7 75.4 1.0 N F:GLY88 4.8 79.8 1.0 O2B F:ADP600 4.8 84.4 1.0

Magnesium binding site 7 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg601 b:57.5 occ:1.00 O1A G:ADP600 2.0 78.5 1.0 O1B G:ADP600 2.3 70.5 1.0 F1 G:BEF602 2.3 68.4 1.0 OD1 G:ASP87 2.4 80.1 1.0 OD2 G:ASP87 2.9 76.7 1.0 CG G:ASP87 3.0 78.9 1.0 PA G:ADP600 3.2 72.6 1.0 O5' G:ADP600 3.4 69.6 1.0 PB G:ADP600 3.5 68.6 1.0 BE G:BEF602 3.6 70.5 1.0 O G:SER151 3.7 86.2 1.0 O3A G:ADP600 3.7 69.0 1.0 O3B G:ADP600 4.1 69.3 1.0 OG G:SER151 4.2 93.3 1.0 CA G:SER151 4.3 88.5 1.0 C G:SER151 4.5 86.0 1.0 OD2 G:ASP398 4.5 0.2 1.0 F2 G:BEF602 4.5 69.7 1.0 CB G:ASP87 4.6 79.5 1.0 O2A G:ADP600 4.6 68.1 1.0 F3 G:BEF602 4.7 73.2 1.0 C5' G:ADP600 4.7 67.8 1.0 O2B G:ADP600 4.8 69.2 1.0 N G:GLY88 4.9 78.2 1.0 CB G:SER151 4.9 90.5 1.0

Magnesium binding site 8 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg601 b:48.0 occ:1.00 O2A H:ADP600 1.9 68.8 1.0 F1 H:BEF602 2.3 87.3 1.0 O2B H:ADP600 2.3 67.1 1.0 OD1 H:ASP87 2.4 87.8 1.0 OD2 H:ASP87 2.9 88.3 1.0 CG H:ASP87 3.1 86.4 1.0 PA H:ADP600 3.1 67.0 1.0 O5' H:ADP600 3.4 67.1 1.0 PB H:ADP600 3.5 66.2 1.0 BE H:BEF602 3.6 85.6 1.0 O3A H:ADP600 3.6 65.8 1.0 O H:SER151 3.7 87.0 1.0 O3B H:ADP600 4.0 64.8 1.0 OG H:SER151 4.3 90.7 1.0 CA H:SER151 4.5 87.8 1.0 OD2 H:ASP398 4.5 0.8 1.0 O1A H:ADP600 4.5 64.6 1.0 C H:SER151 4.5 86.4 1.0 F2 H:BEF602 4.6 82.2 1.0 CB H:ASP87 4.6 82.6 1.0 F3 H:BEF602 4.6 86.0 1.0 C5' H:ADP600 4.7 67.7 1.0 O1B H:ADP600 4.8 66.7 1.0 N H:GLY88 4.9 78.7 1.0 K H:K603 5.0 69.2 1.0

Magnesium binding site 9 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg601 b:52.7 occ:1.00 O2A I:ADP600 2.1 76.7 1.0 O2B I:ADP600 2.2 72.6 1.0 OD1 I:ASP87 2.3 74.3 1.0 F1 I:BEF602 2.3 80.5 1.0 OD2 I:ASP87 2.8 74.1 1.0 CG I:ASP87 2.9 75.2 1.0 PA I:ADP600 3.2 75.0 1.0 O5' I:ADP600 3.4 73.9 1.0 PB I:ADP600 3.4 72.4 1.0 BE I:BEF602 3.6 80.2 1.0 O3A I:ADP600 3.7 72.1 1.0 O I:SER151 3.9 81.6 1.0 O3B I:ADP600 4.0 70.4 1.0 OG I:SER151 4.3 97.2 1.0 CB I:ASP87 4.4 75.4 1.0 F2 I:BEF602 4.5 83.6 1.0 CA I:SER151 4.5 88.0 1.0 OD2 I:ASP398 4.6 90.1 1.0 O1A I:ADP600 4.6 74.2 1.0 C5' I:ADP600 4.6 73.7 1.0 N I:GLY88 4.6 72.6 1.0 C I:SER151 4.6 83.2 1.0 F3 I:BEF602 4.7 76.3 1.0 O1B I:ADP600 4.7 71.6 1.0

Magnesium binding site 10 out of 14 in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg601 b:53.0 occ:1.00 O2A J:ADP600 2.1 91.5 1.0 OD1 J:ASP87 2.2 89.7 1.0 O2B J:ADP600 2.2 90.8 1.0 F1 J:BEF602 2.3 84.5 1.0 OD2 J:ASP87 2.8 92.8 1.0 CG J:ASP87 2.9 89.9 1.0 PA J:ADP600 3.2 87.5 1.0 O5' J:ADP600 3.4 88.0 1.0 PB J:ADP600 3.4 92.1 1.0 BE J:BEF602 3.5 83.4 1.0 O3A J:ADP600 3.7 89.3 1.0 O J:SER151 3.8 98.1 1.0 O3B J:ADP600 4.0 88.8 1.0 OG J:SER151 4.2 97.7 1.0 OD2 J:ASP398 4.4 0.0 1.0 CB J:ASP87 4.4 88.2 1.0 F2 J:BEF602 4.5 82.7 1.0 CA J:SER151 4.5 0.2 1.0 F3 J:BEF602 4.6 81.7 1.0 O1A J:ADP600 4.6 83.5 1.0 C J:SER151 4.6 98.0 1.0 N J:GLY88 4.7 86.5 1.0 C5' J:ADP600 4.7 86.7 1.0 O1B J:ADP600 4.7 93.4 1.0

X.Yan, Q.Shi, A.Bracher, G.Milicic, A.K.Singh, F.U.Hartl, M.Hayer-Hartl. Groel Ring Separation and Exchange in the Chaperonin Reaction. Cell V. 172 605 2018.
ISSN: ISSN 1097-4172
PubMed: 29336887
DOI: 10.1016/J.CELL.2017.12.010