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Fluorine in PDB 4pkn: Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco

Protein crystallography data

The structure of Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco, PDB code: 4pkn was solved by X.Fei, X.Ye, N.Laronde-Leblanc, G.H.Lorimer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 122.19 / 3.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 171.952, 173.653, 411.270, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.1

Other elements in 4pkn:

The structure of Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco also contains other interesting chemical elements:

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

Fluorine Binding Sites:

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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco (pdb code 4pkn). 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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco, PDB code: 4pkn:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 42 in 4pkn

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Fluorine binding site 1 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F602

b:0.8
occ:1.00
 F1 G:BEF602 0.0 0.8 1.0
BE G:BEF602 1.8 19.7 1.0
OD1 G:ASP87 2.2 59.2 1.0
OD2 G:ASP398 2.7 86.4 1.0
F3 G:BEF602 3.0 29.4 1.0
F2 G:BEF602 3.1 42.6 1.0
CG G:ASP87 3.2 58.0 1.0
CA G:ASP87 3.3 52.4 1.0
CG G:ASP398 3.4 85.8 1.0
O3B G:ADP601 3.5 20.5 1.0
OD1 G:ASP52 3.5 73.3 1.0
O G:GLY86 3.5 43.6 1.0
CB G:ASP87 3.7 56.6 1.0
MG G:MG603 3.8 41.0 1.0
CB G:ASP398 4.0 76.2 1.0
N G:GLY88 4.0 73.9 1.0
OD1 G:ASP398 4.1 91.1 1.0
C G:ASP87 4.1 54.6 1.0
C G:GLY86 4.3 43.7 1.0
OG1 G:THR89 4.3 38.7 1.0
N G:ASP87 4.3 48.2 1.0
OD2 G:ASP87 4.3 56.8 1.0
CG G:ASP52 4.5 75.8 1.0
PB G:ADP601 4.5 25.6 1.0
O1B G:ADP601 4.6 24.9 1.0
N G:THR89 4.9 50.9 1.0
OD2 G:ASP52 4.9 78.6 1.0
O3A G:ADP601 4.9 50.1 1.0

Fluorine binding site 2 out of 42 in 4pkn

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Fluorine binding site 2 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F602

b:42.6
occ:1.00
 F2 G:BEF602 0.0 42.6 1.0
BE G:BEF602 1.8 19.7 1.0
MG G:MG603 2.0 41.0 1.0
O1A G:ADP601 2.3 37.2 1.0
OD1 G:ASP87 2.7 59.2 1.0
O3A G:ADP601 2.7 50.1 1.0
O1B G:ADP601 2.9 24.9 1.0
F1 G:BEF602 3.1 0.8 1.0
F3 G:BEF602 3.1 29.4 1.0
PA G:ADP601 3.1 33.2 1.0
O3B G:ADP601 3.1 20.5 1.0
PB G:ADP601 3.1 25.6 1.0
CG G:ASP87 3.8 58.0 1.0
K G:K604 3.8 51.2 1.0
O5' G:ADP601 4.0 35.0 1.0
OD2 G:ASP87 4.1 56.8 1.0
O2A G:ADP601 4.3 29.4 1.0
O G:SER151 4.4 68.6 1.0
O2B G:ADP601 4.6 20.6 1.0
OD2 G:ASP398 4.7 86.4 1.0
N G:GLY88 4.8 73.9 1.0
C5' G:ADP601 5.0 37.8 1.0

Fluorine binding site 3 out of 42 in 4pkn

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Fluorine binding site 3 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F602

b:29.4
occ:1.00
 F3 G:BEF602 0.0 29.4 1.0
BE G:BEF602 1.8 19.7 1.0
O3B G:ADP601 2.0 20.5 1.0
OG1 G:THR89 2.7 38.7 1.0
K G:K604 3.0 51.2 1.0
O3A G:ADP601 3.0 50.1 1.0
F1 G:BEF602 3.0 0.8 1.0
F2 G:BEF602 3.1 42.6 1.0
PB G:ADP601 3.1 25.6 1.0
OG1 G:THR90 3.2 51.5 1.0
N G:GLY53 3.4 39.0 1.0
OD1 G:ASP52 3.6 73.3 1.0
N G:THR90 3.8 49.5 1.0
N G:THR89 4.0 50.9 1.0
CB G:THR89 4.0 40.8 1.0
O2B G:ADP601 4.1 20.6 1.0
O1B G:ADP601 4.1 24.9 1.0
OD1 G:ASP87 4.1 59.2 1.0
CA G:GLY53 4.1 38.3 1.0
CB G:THR90 4.1 48.4 1.0
CA G:ASP52 4.3 51.1 1.0
C G:ASP52 4.4 46.8 1.0
CA G:THR89 4.4 45.5 1.0
PA G:ADP601 4.4 33.2 1.0
N G:GLY88 4.5 73.9 1.0
O G:LYS51 4.5 48.6 1.0
MG G:MG603 4.5 41.0 1.0
CA G:THR90 4.6 50.8 1.0
O1A G:ADP601 4.6 37.2 1.0
C G:THR89 4.6 47.5 1.0
CG G:ASP52 4.7 75.8 1.0
CG2 G:THR89 4.7 45.4 1.0
C G:GLY88 4.8 71.8 1.0
OD2 G:ASP398 4.9 86.4 1.0

Fluorine binding site 4 out of 42 in 4pkn

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Fluorine binding site 4 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:46.1
occ:1.00
 F1 A:BEF602 0.0 46.1 1.0
BE A:BEF602 1.8 62.8 1.0
OG1 A:THR90 2.1 48.3 1.0
O3B A:ADP601 2.3 31.7 1.0
K A:K604 2.6 76.3 1.0
O3A A:ADP601 2.8 75.9 1.0
F2 A:BEF602 3.0 41.9 1.0
F3 A:BEF602 3.1 52.2 1.0
PB A:ADP601 3.2 33.0 1.0
OG1 A:THR89 3.2 67.6 1.0
CB A:THR90 3.3 48.4 1.0
N A:GLY53 3.3 62.7 1.0
N A:THR90 3.4 48.8 1.0
CA A:GLY53 3.8 53.9 1.0
CA A:THR90 3.9 48.5 1.0
O2B A:ADP601 3.9 31.1 1.0
O A:LYS51 4.1 59.6 1.0
PA A:ADP601 4.2 65.8 1.0
N A:THR89 4.3 51.4 1.0
OD1 A:ASP52 4.3 83.4 1.0
C A:ASP52 4.3 66.8 1.0
O1B A:ADP601 4.4 32.6 1.0
MG A:MG603 4.4 27.0 1.0
O2A A:ADP601 4.4 60.9 1.0
CG2 A:THR90 4.5 48.2 1.0
C A:THR89 4.5 49.0 1.0
CB A:THR89 4.5 60.7 1.0
CA A:ASP52 4.5 76.5 1.0
OG1 A:THR30 4.6 48.1 1.0
CA A:THR89 4.7 50.9 1.0
OD1 A:ASP87 4.9 51.6 1.0
O1A A:ADP601 4.9 70.6 1.0
N A:GLY88 4.9 65.8 1.0
C A:GLY88 5.0 61.6 1.0

Fluorine binding site 5 out of 42 in 4pkn

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Fluorine binding site 5 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:41.9
occ:1.00
 F2 A:BEF602 0.0 41.9 1.0
BE A:BEF602 1.8 62.8 1.0
OD1 A:ASP87 2.7 51.6 1.0
O3B A:ADP601 2.7 31.7 1.0
F1 A:BEF602 3.0 46.1 1.0
F3 A:BEF602 3.1 52.2 1.0
N A:GLY88 3.2 65.8 1.0
OG1 A:THR89 3.2 67.6 1.0
OD1 A:ASP52 3.4 83.4 1.0
CA A:ASP87 3.4 52.2 1.0
C A:ASP87 3.6 53.3 1.0
N A:THR89 3.6 51.4 1.0
OD2 A:ASP398 3.6 62.3 1.0
CG A:ASP87 3.7 52.3 1.0
PB A:ADP601 3.8 33.0 1.0
MG A:MG603 3.9 27.0 1.0
O3A A:ADP601 4.0 75.9 1.0
O1B A:ADP601 4.1 32.6 1.0
CB A:ASP87 4.1 52.9 1.0
CA A:GLY88 4.2 63.7 1.0
CB A:THR89 4.2 60.7 1.0
CG A:ASP398 4.3 65.1 1.0
CG2 A:THR89 4.3 64.3 1.0
O A:GLY86 4.3 61.1 1.0
C A:GLY88 4.4 61.6 1.0
CA A:THR89 4.5 50.9 1.0
N A:ASP87 4.5 52.8 1.0
CG A:ASP52 4.6 84.4 1.0
OD1 A:ASP398 4.6 65.6 1.0
O A:ASP87 4.7 53.7 1.0
OD2 A:ASP87 4.7 52.9 1.0
N A:GLY53 4.7 62.7 1.0
C A:GLY86 4.8 61.9 1.0
N A:THR90 4.8 48.8 1.0

Fluorine binding site 6 out of 42 in 4pkn

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Fluorine binding site 6 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:52.2
occ:1.00
 F3 A:BEF602 0.0 52.2 1.0
BE A:BEF602 1.8 62.8 1.0
MG A:MG603 2.8 27.0 1.0
O3A A:ADP601 2.8 75.9 1.0
F1 A:BEF602 3.1 46.1 1.0
F2 A:BEF602 3.1 41.9 1.0
O1A A:ADP601 3.3 70.6 1.0
OD1 A:ASP87 3.3 51.6 1.0
OD2 A:ASP398 3.4 62.3 1.0
K A:K604 3.6 76.3 1.0
PA A:ADP601 3.7 65.8 1.0
O3B A:ADP601 3.7 31.7 1.0
PB A:ADP601 3.8 33.0 1.0
O1B A:ADP601 4.2 32.6 1.0
O A:LYS51 4.4 59.6 1.0
OD1 A:ASP52 4.4 83.4 1.0
O A:SER151 4.5 71.9 1.0
CG A:ASP398 4.5 65.1 1.0
CG A:ASP87 4.5 52.3 1.0
O2A A:ADP601 4.6 60.9 1.0
CA A:ASP52 4.7 76.5 1.0
O5' A:ADP601 4.9 63.6 1.0
NZ A:LYS51 4.9 50.4 1.0

Fluorine binding site 7 out of 42 in 4pkn

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Fluorine binding site 7 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:7.1
occ:1.00
 F1 B:BEF602 0.0 7.1 1.0
BE B:BEF602 1.8 66.0 1.0
O3A B:ADP601 2.3 36.6 1.0
OG1 B:THR90 2.3 78.0 1.0
K B:K604 2.9 0.9 1.0
F2 B:BEF602 3.1 26.0 1.0
F3 B:BEF602 3.1 12.8 1.0
O3B B:ADP601 3.1 33.8 1.0
PB B:ADP601 3.3 36.4 1.0
OG1 B:THR30 3.3 54.1 1.0
PA B:ADP601 3.3 32.2 1.0
CB B:THR90 3.4 77.9 1.0
O B:LYS51 3.4 75.7 1.0
O2A B:ADP601 3.5 26.4 1.0
O1A B:ADP601 3.8 33.8 1.0
N B:GLY53 3.9 55.4 1.0
O B:THR30 3.9 59.6 1.0
O2B B:ADP601 4.0 42.0 1.0
CG2 B:THR90 4.2 76.0 1.0
MG B:MG603 4.4 32.1 1.0
CA B:GLY53 4.5 55.0 1.0
O1B B:ADP601 4.5 39.7 1.0
CB B:THR30 4.5 53.8 1.0
N B:THR90 4.5 70.5 1.0
C B:LYS51 4.5 72.8 1.0
CA B:THR90 4.6 76.0 1.0
CA B:ASP52 4.6 65.6 1.0
C B:THR30 4.6 55.8 1.0
C B:ASP52 4.7 59.8 1.0
O5' B:ADP601 4.7 66.3 1.0
OG1 B:THR89 4.8 58.1 1.0
OD1 B:ASP52 5.0 94.5 1.0
NZ B:LYS51 5.0 73.0 1.0

Fluorine binding site 8 out of 42 in 4pkn

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Fluorine binding site 8 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:26.0
occ:1.00
 F2 B:BEF602 0.0 26.0 1.0
BE B:BEF602 1.8 66.0 1.0
OG1 B:THR89 2.1 58.1 1.0
O3B B:ADP601 2.5 33.8 1.0
F3 B:BEF602 3.0 12.8 1.0
F1 B:BEF602 3.1 7.1 1.0
OD1 B:ASP52 3.2 94.5 1.0
OG1 B:THR90 3.3 78.0 1.0
N B:GLY53 3.3 55.4 1.0
CB B:THR89 3.4 59.5 1.0
N B:THR89 3.5 58.2 1.0
N B:THR90 3.6 70.5 1.0
PB B:ADP601 3.8 36.4 1.0
O3A B:ADP601 3.9 36.6 1.0
CA B:GLY53 3.9 55.0 1.0
CA B:THR89 3.9 59.5 1.0
OD1 B:ASP87 4.1 83.9 1.0
CG2 B:THR89 4.1 62.5 1.0
N B:GLY88 4.2 70.0 1.0
C B:THR89 4.2 61.6 1.0
OD2 B:ASP398 4.3 0.6 1.0
CB B:THR90 4.3 77.9 1.0
C B:ASP52 4.4 59.8 1.0
CG B:ASP52 4.4 92.8 1.0
N B:VAL54 4.5 55.8 1.0
C B:GLY88 4.5 57.7 1.0
CA B:ASP52 4.5 65.6 1.0
CA B:THR90 4.5 76.0 1.0
O1B B:ADP601 4.6 39.7 1.0
C B:GLY53 4.7 55.2 1.0
CA B:GLY88 4.8 62.5 1.0
C B:ASP87 4.8 77.3 1.0
K B:K604 4.8 0.9 1.0
O2B B:ADP601 4.8 42.0 1.0
CA B:ASP87 4.9 79.0 1.0

Fluorine binding site 9 out of 42 in 4pkn

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Fluorine binding site 9 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:12.8
occ:1.00
 F3 B:BEF602 0.0 12.8 1.0
BE B:BEF602 1.8 66.0 1.0
OD1 B:ASP87 2.1 83.9 1.0
MG B:MG603 2.2 32.1 1.0
O3A B:ADP601 2.5 36.6 1.0
O3B B:ADP601 3.0 33.8 1.0
F2 B:BEF602 3.0 26.0 1.0
PB B:ADP601 3.1 36.4 1.0
F1 B:BEF602 3.1 7.1 1.0
O1B B:ADP601 3.1 39.7 1.0
K B:K604 3.2 0.9 1.0
CG B:ASP87 3.3 83.4 1.0
O1A B:ADP601 3.3 33.8 1.0
OD2 B:ASP398 3.4 0.6 1.0
PA B:ADP601 3.5 32.2 1.0
OD2 B:ASP87 3.8 85.3 1.0
N B:GLY88 4.1 70.0 1.0
CG B:ASP398 4.2 0.2 1.0
O5' B:ADP601 4.4 66.3 1.0
CB B:ASP87 4.5 81.2 1.0
O2B B:ADP601 4.5 42.0 1.0
CA B:ASP87 4.6 79.0 1.0
OD1 B:ASP52 4.7 94.5 1.0
O B:SER151 4.7 65.6 1.0
CB B:ASP398 4.7 98.6 1.0
O2A B:ADP601 4.8 26.4 1.0
OG1 B:THR90 4.8 78.0 1.0
C B:ASP87 4.9 77.3 1.0
OG B:SER151 4.9 74.4 1.0
CA B:GLY88 5.0 62.5 1.0

Fluorine binding site 10 out of 42 in 4pkn

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Fluorine binding site 10 out of 42 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F602

b:65.6
occ:1.00
 F1 F:BEF602 0.0 65.6 1.0
BE F:BEF602 1.8 58.2 1.0
OD1 F:ASP87 2.6 80.1 1.0
F2 F:BEF602 3.0 60.3 1.0
F3 F:BEF602 3.1 44.2 1.0
CA F:ASP87 3.2 67.0 1.0
O3B F:ADP601 3.3 34.5 1.0
OD1 F:ASP52 3.4 87.8 1.0
N F:GLY88 3.4 56.0 1.0
OG1 F:THR89 3.4 50.2 1.0
OD2 F:ASP398 3.4 73.8 1.0
CG F:ASP87 3.6 79.8 1.0
C F:ASP87 3.7 62.5 1.0
O F:GLY86 3.7 60.5 1.0
CG F:ASP398 3.8 72.6 1.0
CB F:ASP87 3.9 70.3 1.0
OD1 F:ASP398 3.9 71.5 1.0
N F:THR89 4.0 57.2 1.0
N F:ASP87 4.2 68.1 1.0
CG2 F:THR89 4.2 56.5 1.0
C F:GLY86 4.3 59.7 1.0
CB F:THR89 4.3 51.6 1.0
MG F:MG603 4.4 33.2 1.0
CG F:ASP52 4.4 92.0 1.0
PB F:ADP601 4.5 35.9 1.0
O1B F:ADP601 4.5 37.6 1.0
CA F:GLY88 4.6 57.5 1.0
O F:ASP87 4.7 60.3 1.0
OD2 F:ASP87 4.7 77.6 1.0
CA F:THR89 4.8 52.1 1.0
C F:GLY88 4.8 56.4 1.0
CB F:ASP398 4.9 71.0 1.0
OD2 F:ASP52 4.9 95.9 1.0

Reference:

X.Fei, X.Ye, N.A.Laronde, G.H.Lorimer. Formation and Structures of Groel:GROES2 Chaperonin Footballs, the Protein-Folding Functional Form. Proc.Natl.Acad.Sci.Usa V. 111 12775 2014.
ISSN: ESSN 1091-6490
PubMed: 25136110
DOI: 10.1073/PNAS.1412922111
Page generated: Thu Aug 1 04:53:56 2024

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