Fluorine 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:

Magnesium	(Mg)	14 atoms
Potassium	(K)	14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 42 binding sites of Fluorine where determined in the Crystal Structure of the Groel Mutant A109C in Complex with Groes and Adp BEF2, PDB code: 5opx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 42 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 Fluorine with other atoms in the F 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:F602 b:81.4 occ:1.00 F1 A:BEF602 0.0 81.4 1.0 BE A:BEF602 1.6 79.2 1.0 MG A:MG601 2.3 59.0 1.0 OD1 A:ASP87 2.5 87.2 1.0 F2 A:BEF602 2.5 79.6 1.0 F3 A:BEF602 2.5 78.5 1.0 O1A A:ADP600 2.6 75.9 1.0 O3B A:ADP600 2.7 69.8 1.0 O1B A:ADP600 2.8 74.3 1.0 OD2 A:ASP398 3.1 0.6 1.0 PB A:ADP600 3.1 71.4 1.0 O3A A:ADP600 3.4 71.2 1.0 PA A:ADP600 3.6 73.0 1.0 CG A:ASP87 3.7 86.3 1.0 K A:K603 3.7 94.7 1.0 CG A:ASP398 4.1 0.2 1.0 OD2 A:ASP87 4.2 85.8 1.0 N A:GLY88 4.5 84.3 1.0 O5' A:ADP600 4.5 74.8 1.0 O2B A:ADP600 4.6 70.1 1.0 OD1 A:ASP52 4.6 93.1 1.0 OG1 A:THR89 4.7 84.4 1.0 CB A:ASP398 4.7 0.8 1.0 O2A A:ADP600 4.7 70.9 1.0 CB A:ASP87 4.9 86.0 1.0 CA A:ASP87 4.9 83.8 1.0

Fluorine binding site 2 out of 42 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 Fluorine with other atoms in the F 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 A:F602 b:79.6 occ:1.00 F2 A:BEF602 0.0 79.6 1.0 BE A:BEF602 1.5 79.2 1.0 F3 A:BEF602 2.5 78.5 1.0 OD2 A:ASP398 2.5 0.6 1.0 F1 A:BEF602 2.5 81.4 1.0 OD1 A:ASP52 2.8 93.1 1.0 OG1 A:THR89 2.9 84.4 1.0 O3B A:ADP600 3.1 69.8 1.0 OD1 A:ASP87 3.3 87.2 1.0 CG A:ASP398 3.4 0.2 1.0 OD1 A:ASP398 3.7 0.5 1.0 CA A:ASP87 4.0 83.8 1.0 CB A:THR89 4.0 82.2 1.0 CG A:ASP52 4.1 95.0 1.0 N A:GLY88 4.1 84.3 1.0 CG2 A:THR89 4.1 85.0 1.0 N A:THR89 4.1 80.5 1.0 CG A:ASP87 4.2 86.3 1.0 PB A:ADP600 4.3 71.4 1.0 C A:ASP87 4.4 83.1 1.0 O A:GLY86 4.4 80.9 1.0 O1B A:ADP600 4.4 74.3 1.0 N A:GLY53 4.4 75.5 1.0 MG A:MG601 4.5 59.0 1.0 CB A:ASP398 4.6 0.8 1.0 CA A:THR89 4.7 79.7 1.0 CA A:ASP52 4.7 85.4 1.0 CB A:ASP87 4.7 86.0 1.0 CB A:ASP52 4.9 92.4 1.0 N A:ASP87 4.9 80.7 1.0 OD2 A:ASP52 4.9 97.5 1.0 K A:K603 4.9 94.7 1.0 N A:THR90 5.0 72.9 1.0 C A:ASP52 5.0 80.5 1.0

Fluorine binding site 3 out of 42 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 Fluorine with other atoms in the F 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 A:F602 b:78.5 occ:1.00 F3 A:BEF602 0.0 78.5 1.0 BE A:BEF602 1.5 79.2 1.0 O3B A:ADP600 2.1 69.8 1.0 F2 A:BEF602 2.5 79.6 1.0 F1 A:BEF602 2.5 81.4 1.0 K A:K603 2.8 94.7 1.0 OG1 A:THR89 2.8 84.4 1.0 OG1 A:THR90 3.0 70.7 1.0 N A:GLY53 3.1 75.5 1.0 PB A:ADP600 3.3 71.4 1.0 O3A A:ADP600 3.5 71.2 1.0 N A:THR90 3.6 72.9 1.0 CB A:THR90 3.8 71.5 1.0 CA A:GLY53 3.8 71.5 1.0 OD1 A:ASP52 3.9 93.1 1.0 C A:ASP52 4.1 80.5 1.0 O1B A:ADP600 4.1 74.3 1.0 CA A:ASP52 4.1 85.4 1.0 O1A A:ADP600 4.1 75.9 1.0 O A:LYS51 4.2 76.3 1.0 CB A:THR89 4.2 82.2 1.0 N A:THR89 4.2 80.5 1.0 CA A:THR90 4.3 70.8 1.0 OD2 A:ASP398 4.3 0.6 1.0 OD1 A:ASP87 4.4 87.2 1.0 PA A:ADP600 4.4 73.0 1.0 O2B A:ADP600 4.4 70.1 1.0 C A:THR89 4.5 74.5 1.0 CA A:THR89 4.6 79.7 1.0 MG A:MG601 4.7 59.0 1.0 CG A:ASP52 4.8 95.0 1.0 N A:VAL54 4.9 67.6 1.0 C A:GLY53 4.9 69.3 1.0 N A:GLY88 5.0 84.3 1.0 C A:LYS51 5.0 79.0 1.0

Fluorine binding site 4 out of 42 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 Fluorine with other atoms in the F 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 B:F602 b:90.7 occ:1.00 F1 B:BEF602 0.0 90.7 1.0 BE B:BEF602 1.6 89.1 1.0 MG B:MG601 2.4 48.6 1.0 OD1 B:ASP87 2.5 77.2 1.0 F3 B:BEF602 2.5 85.3 1.0 F2 B:BEF602 2.5 91.3 1.0 O1A B:ADP600 2.6 69.6 1.0 O1B B:ADP600 2.7 63.8 1.0 O3B B:ADP600 2.9 65.7 1.0 PB B:ADP600 3.1 65.4 1.0 OD2 B:ASP398 3.2 0.0 1.0 O3A B:ADP600 3.4 65.7 1.0 PA B:ADP600 3.5 66.8 1.0 K B:K603 3.6 84.2 1.0 CG B:ASP87 3.7 74.9 1.0 OD2 B:ASP87 4.2 72.6 1.0 CG B:ASP398 4.2 0.4 1.0 N B:GLY88 4.5 75.5 1.0 O5' B:ADP600 4.5 69.8 1.0 OD1 B:ASP52 4.6 96.7 1.0 O2B B:ADP600 4.6 64.5 1.0 O2A B:ADP600 4.7 65.2 1.0 OG1 B:THR89 4.7 68.1 1.0 CB B:ASP398 4.8 0.6 1.0 CB B:ASP87 4.9 75.2 1.0 CA B:ASP87 4.9 73.6 1.0

Fluorine binding site 5 out of 42 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 Fluorine with other atoms in the F 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 B:F602 b:91.3 occ:1.00 F2 B:BEF602 0.0 91.3 1.0 BE B:BEF602 1.6 89.1 1.0 F3 B:BEF602 2.5 85.3 1.0 F1 B:BEF602 2.5 90.7 1.0 OD2 B:ASP398 2.6 0.0 1.0 OD1 B:ASP52 2.8 96.7 1.0 OG1 B:THR89 2.9 68.1 1.0 O1B B:ADP600 3.1 63.8 1.0 OD1 B:ASP87 3.2 77.2 1.0 CG B:ASP398 3.4 0.4 1.0 OD1 B:ASP398 3.7 0.3 1.0 CA B:ASP87 4.0 73.6 1.0 CB B:THR89 4.1 69.4 1.0 CG B:ASP52 4.1 94.4 1.0 N B:GLY88 4.1 75.5 1.0 CG2 B:THR89 4.1 72.5 1.0 N B:THR89 4.1 68.2 1.0 CG B:ASP87 4.2 74.9 1.0 PB B:ADP600 4.3 65.4 1.0 N B:GLY53 4.4 79.0 1.0 C B:ASP87 4.4 73.7 1.0 O B:GLY86 4.4 77.5 1.0 O3B B:ADP600 4.5 65.7 1.0 MG B:MG601 4.5 48.6 1.0 CA B:ASP52 4.7 86.2 1.0 CB B:ASP398 4.7 0.6 1.0 CA B:THR89 4.7 68.0 1.0 CB B:ASP87 4.7 75.2 1.0 CB B:ASP52 4.9 91.6 1.0 K B:K603 4.9 84.2 1.0 OD2 B:ASP52 4.9 93.3 1.0 C B:ASP52 5.0 82.5 1.0 N B:ASP87 5.0 73.1 1.0 N B:THR90 5.0 67.1 1.0

Fluorine binding site 6 out of 42 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 Fluorine with other atoms in the F 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 B:F602 b:85.3 occ:1.00 F3 B:BEF602 0.0 85.3 1.0 BE B:BEF602 1.5 89.1 1.0 O1B B:ADP600 2.1 63.8 1.0 F2 B:BEF602 2.5 91.3 1.0 F1 B:BEF602 2.5 90.7 1.0 K B:K603 2.7 84.2 1.0 OG1 B:THR89 2.9 68.1 1.0 OG1 B:THR90 2.9 63.8 1.0 N B:GLY53 3.2 79.0 1.0 PB B:ADP600 3.3 65.4 1.0 O3A B:ADP600 3.5 65.7 1.0 N B:THR90 3.6 67.1 1.0 CB B:THR90 3.8 65.4 1.0 CA B:GLY53 3.9 73.6 1.0 OD1 B:ASP52 4.0 96.7 1.0 O3B B:ADP600 4.1 65.7 1.0 C B:ASP52 4.1 82.5 1.0 O1A B:ADP600 4.2 69.6 1.0 O B:LYS51 4.2 80.4 1.0 CA B:ASP52 4.2 86.2 1.0 CB B:THR89 4.2 69.4 1.0 N B:THR89 4.3 68.2 1.0 CA B:THR90 4.3 67.4 1.0 PA B:ADP600 4.4 66.8 1.0 OD1 B:ASP87 4.4 77.2 1.0 OD2 B:ASP398 4.4 0.0 1.0 O2B B:ADP600 4.5 64.5 1.0 C B:THR89 4.5 66.2 1.0 CA B:THR89 4.6 68.0 1.0 MG B:MG601 4.7 48.6 1.0 CG B:ASP52 4.9 94.4 1.0 N B:GLY88 4.9 75.5 1.0 N B:VAL54 5.0 70.2 1.0 OG1 B:THR30 5.0 65.6 1.0 C B:GLY53 5.0 71.9 1.0

Fluorine binding site 7 out of 42 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 Fluorine with other atoms in the F 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 C:F602 b:0.2 occ:1.00 F1 C:BEF602 0.0 0.2 1.0 BE C:BEF602 1.6 0.6 1.0 MG C:MG601 2.5 57.4 1.0 F3 C:BEF602 2.5 0.4 1.0 OD1 C:ASP87 2.5 99.8 1.0 O1A C:ADP600 2.5 87.4 1.0 F2 C:BEF602 2.5 0.9 1.0 O1B C:ADP600 2.7 88.8 1.0 O3B C:ADP600 2.9 92.7 1.0 PB C:ADP600 3.1 91.5 1.0 OD2 C:ASP398 3.2 0.6 1.0 O3A C:ADP600 3.4 86.7 1.0 PA C:ADP600 3.5 85.2 1.0 K C:K603 3.6 81.9 1.0 CG C:ASP87 3.7 0.2 1.0 OD2 C:ASP87 4.2 0.0 1.0 CG C:ASP398 4.3 0.4 1.0 N C:GLY88 4.5 0.6 1.0 O5' C:ADP600 4.5 84.7 1.0 O2B C:ADP600 4.6 95.0 1.0 O2A C:ADP600 4.7 82.8 1.0 OD1 C:ASP52 4.7 0.1 1.0 OG1 C:THR89 4.7 96.0 1.0 CB C:ASP398 4.8 0.1 1.0 CB C:ASP87 4.9 0.2 1.0 CA C:ASP87 5.0 98.4 1.0

Fluorine binding site 8 out of 42 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 Fluorine with other atoms in the F 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 C:F602 b:0.9 occ:1.00 F2 C:BEF602 0.0 0.9 1.0 BE C:BEF602 1.5 0.6 1.0 F3 C:BEF602 2.5 0.4 1.0 F1 C:BEF602 2.5 0.2 1.0 OD2 C:ASP398 2.6 0.6 1.0 OD1 C:ASP52 2.9 0.1 1.0 OG1 C:THR89 2.9 96.0 1.0 O1B C:ADP600 3.1 88.8 1.0 OD1 C:ASP87 3.2 99.8 1.0 CG C:ASP398 3.5 0.4 1.0 OD1 C:ASP398 3.8 0.7 1.0 CA C:ASP87 4.0 98.4 1.0 N C:GLY88 4.1 0.6 1.0 CB C:THR89 4.1 95.4 1.0 CG C:ASP52 4.1 0.6 1.0 N C:THR89 4.1 98.7 1.0 CG2 C:THR89 4.2 97.5 1.0 CG C:ASP87 4.2 0.2 1.0 PB C:ADP600 4.3 91.5 1.0 N C:GLY53 4.4 94.6 1.0 C C:ASP87 4.4 98.5 1.0 O3B C:ADP600 4.4 92.7 1.0 O C:GLY86 4.5 0.7 1.0 MG C:MG601 4.6 57.4 1.0 CA C:ASP52 4.6 98.4 1.0 CB C:ASP398 4.7 0.1 1.0 CA C:THR89 4.7 94.8 1.0 CB C:ASP87 4.7 0.2 1.0 CB C:ASP52 4.9 0.7 1.0 C C:ASP52 4.9 96.8 1.0 K C:K603 4.9 81.9 1.0 N C:THR90 4.9 89.9 1.0 N C:ASP87 5.0 0.0 1.0 OD2 C:ASP52 5.0 0.4 1.0

Fluorine binding site 9 out of 42 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 Fluorine with other atoms in the F 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 C:F602 b:0.4 occ:1.00 F3 C:BEF602 0.0 0.4 1.0 BE C:BEF602 1.5 0.6 1.0 O1B C:ADP600 2.0 88.8 1.0 F2 C:BEF602 2.5 0.9 1.0 F1 C:BEF602 2.5 0.2 1.0 K C:K603 2.8 81.9 1.0 OG1 C:THR89 2.9 96.0 1.0 OG1 C:THR90 2.9 89.3 1.0 N C:GLY53 3.2 94.6 1.0 PB C:ADP600 3.3 91.5 1.0 O3A C:ADP600 3.5 86.7 1.0 N C:THR90 3.6 89.9 1.0 CB C:THR90 3.8 91.5 1.0 CA C:GLY53 3.9 90.9 1.0 OD1 C:ASP52 4.0 0.1 1.0 O C:LYS51 4.1 86.1 1.0 CA C:ASP52 4.1 98.4 1.0 O3B C:ADP600 4.1 92.7 1.0 C C:ASP52 4.1 96.8 1.0 O1A C:ADP600 4.2 87.4 1.0 CB C:THR89 4.3 95.4 1.0 CA C:THR90 4.3 90.0 1.0 N C:THR89 4.3 98.7 1.0 OD2 C:ASP398 4.4 0.6 1.0 OD1 C:ASP87 4.4 99.8 1.0 O2B C:ADP600 4.4 95.0 1.0 PA C:ADP600 4.4 85.2 1.0 C C:THR89 4.6 91.7 1.0 CA C:THR89 4.6 94.8 1.0 MG C:MG601 4.8 57.4 1.0 CG C:ASP52 4.9 0.6 1.0 C C:LYS51 4.9 89.0 1.0 OG1 C:THR30 4.9 72.9 1.0 N C:GLY88 5.0 0.6 1.0

Fluorine binding site 10 out of 42 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 Fluorine with other atoms in the F 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 D:F602 b:0.8 occ:1.00 F1 D:BEF602 0.0 0.8 1.0 BE D:BEF602 1.6 0.2 1.0 MG D:MG601 2.2 78.4 1.0 OD1 D:ASP87 2.5 96.2 1.0 F3 D:BEF602 2.5 0.6 1.0 O1A D:ADP600 2.6 91.1 1.0 F2 D:BEF602 2.6 0.8 1.0 O3B D:ADP600 2.7 88.7 1.0 O1B D:ADP600 2.8 96.1 1.0 OD2 D:ASP398 3.1 0.7 1.0 PB D:ADP600 3.1 90.0 1.0 O3A D:ADP600 3.4 88.4 1.0 PA D:ADP600 3.5 90.1 1.0 K D:K603 3.6 89.1 1.0 CG D:ASP87 3.7 99.7 1.0 OD2 D:ASP87 4.2 0.5 1.0 CG D:ASP398 4.2 0.6 1.0 N D:GLY88 4.5 0.5 1.0 O5' D:ADP600 4.6 91.6 1.0 O2B D:ADP600 4.6 90.0 1.0 OD1 D:ASP52 4.7 0.8 1.0 OG1 D:THR89 4.7 0.3 1.0 O2A D:ADP600 4.7 89.6 1.0 CB D:ASP398 4.7 0.4 1.0 CB D:ASP87 4.9 0.0 1.0 CA D:ASP87 4.9 0.4 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