Fluorine in PDB 8p4n: Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx

Enzymatic activity of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx

All present enzymatic activity of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx:
5.6.1.7;

Other elements in 8p4n:

The structure of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx also contains other interesting chemical elements:

Potassium (K) 7 atoms
Magnesium (Mg) 7 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Fluorine atom in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx (pdb code 8p4n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 21 binding sites of Fluorine where determined in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx, PDB code: 8p4n:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 21 in 8p4n

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Fluorine binding site 1 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1602

b:4.0
occ:1.00
 F1 A:BEF1602 0.0 4.0 1.0
BE A:BEF1602 1.5 4.0 1.0
O3B A:ADP1600 1.9 5.9 1.0
O2B A:ADP1600 2.2 5.9 1.0
PB A:ADP1600 2.5 5.9 1.0
F3 A:BEF1602 2.5 4.0 1.0
F2 A:BEF1602 2.5 4.0 1.0
MG A:MG1601 2.8 22.0 1.0
O A:HOH2001 2.8 6.5 1.0
OD1 A:ASP87 2.8 6.7 1.0
O3A A:ADP1600 3.4 5.9 1.0
O A:HOH2008 3.4 7.9 1.0
O A:HOH2017 3.5 7.3 1.0
O1B A:ADP1600 3.8 5.9 1.0
O2A A:ADP1600 3.8 5.9 1.0
N A:GLY88 3.8 5.0 1.0
CG A:ASP87 4.1 6.7 1.0
PA A:ADP1600 4.1 5.9 1.0
O A:HOH2005 4.2 6.4 1.0
OD1 A:ASP52 4.3 5.8 1.0
K A:K1603 4.5 5.8 1.0
CA A:GLY88 4.6 5.0 1.0
N A:THR89 4.6 4.8 1.0
CA A:ASP87 4.6 6.7 1.0
C A:ASP87 4.7 6.7 1.0
OD2 A:ASP398 4.7 8.5 1.0
OD2 A:ASP87 4.9 6.7 1.0
O1A A:ADP1600 4.9 5.9 1.0
OG1 A:THR89 4.9 4.8 1.0
CB A:ASP87 4.9 6.7 1.0
CG A:ASP398 4.9 8.5 1.0
O A:HOH2003 5.0 10.6 1.0

Fluorine binding site 2 out of 21 in 8p4n

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Fluorine binding site 2 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1602

b:4.0
occ:1.00
 F2 A:BEF1602 0.0 4.0 1.0
BE A:BEF1602 1.5 4.0 1.0
O A:HOH2008 2.2 7.9 1.0
F3 A:BEF1602 2.5 4.0 1.0
F1 A:BEF1602 2.5 4.0 1.0
OD1 A:ASP52 2.5 5.8 1.0
O3B A:ADP1600 2.9 5.9 1.0
OG1 A:THR89 3.0 4.8 1.0
CG A:ASP52 3.8 5.8 1.0
N A:THR89 3.8 4.8 1.0
CG2 A:THR89 3.9 4.8 1.0
CB A:THR89 4.0 4.8 1.0
N A:GLY88 4.0 5.0 1.0
OD1 A:ASP87 4.1 6.7 1.0
PB A:ADP1600 4.2 5.9 1.0
N A:GLY53 4.2 5.2 1.0
CA A:ASP87 4.3 6.7 1.0
O2B A:ADP1600 4.4 5.9 1.0
C A:ASP87 4.5 6.7 1.0
OD2 A:ASP52 4.5 5.8 1.0
CA A:THR89 4.5 4.8 1.0
O A:HOH2017 4.7 7.3 1.0
OD1 A:ASP398 4.8 8.5 1.0
CA A:ASP52 4.8 5.8 1.0
OD2 A:ASP398 4.8 8.5 1.0
N A:THR90 4.8 4.8 1.0
CB A:ASP52 4.8 5.8 1.0
C A:GLY88 4.8 5.0 1.0
CA A:GLY88 4.8 5.0 1.0
MG A:MG1601 4.9 22.0 1.0
C A:ASP52 4.9 5.8 1.0
N A:VAL54 5.0 6.0 1.0
CG A:ASP398 5.0 8.5 1.0
O A:GLY86 5.0 7.0 1.0

Fluorine binding site 3 out of 21 in 8p4n

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Fluorine binding site 3 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1602

b:4.0
occ:1.00
 F3 A:BEF1602 0.0 4.0 1.0
BE A:BEF1602 1.5 4.0 1.0
O3B A:ADP1600 1.9 5.9 1.0
F2 A:BEF1602 2.5 4.0 1.0
F1 A:BEF1602 2.5 4.0 1.0
K A:K1603 2.8 5.8 1.0
OG1 A:THR90 3.0 4.8 1.0
N A:GLY53 3.2 5.2 1.0
PB A:ADP1600 3.2 5.9 1.0
OD1 A:ASP52 3.4 5.8 1.0
O3A A:ADP1600 3.6 5.9 1.0
OG1 A:THR89 3.6 4.8 1.0
O A:HOH2017 3.7 7.3 1.0
O2B A:ADP1600 4.0 5.9 1.0
CB A:THR90 4.0 4.8 1.0
CA A:GLY53 4.0 5.2 1.0
CA A:ASP52 4.0 5.8 1.0
N A:THR90 4.0 4.8 1.0
C A:ASP52 4.1 5.8 1.0
O A:LYS51 4.2 2.5 1.0
O1B A:ADP1600 4.3 5.9 1.0
O A:HOH2008 4.3 7.9 1.0
CG A:ASP52 4.5 5.8 1.0
N A:THR89 4.5 4.8 1.0
PA A:ADP1600 4.6 5.9 1.0
CA A:THR90 4.6 4.8 1.0
O1A A:ADP1600 4.7 5.9 1.0
O A:HOH2001 4.8 6.5 1.0
CB A:ASP52 4.8 5.8 1.0
CB A:THR89 4.8 4.8 1.0
O2A A:ADP1600 5.0 5.9 1.0
C A:THR89 5.0 4.8 1.0

Fluorine binding site 4 out of 21 in 8p4n

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Fluorine binding site 4 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1602

b:10.8
occ:1.00
 F1 B:BEF1602 0.0 10.8 1.0
O3B B:ADP1600 1.5 22.0 1.0
BE B:BEF1602 1.5 10.8 1.0
PB B:ADP1600 2.3 22.0 1.0
O2B B:ADP1600 2.5 22.0 1.0
F3 B:BEF1602 2.5 10.8 1.0
F2 B:BEF1602 2.5 10.8 1.0
O B:HOH1702 2.6 6.2 1.0
MG B:MG1601 3.0 6.4 1.0
O3A B:ADP1600 3.1 22.0 1.0
OD1 B:ASP87 3.3 7.6 1.0
O2A B:ADP1600 3.3 22.0 1.0
O1B B:ADP1600 3.7 22.0 1.0
PA B:ADP1600 3.8 22.0 1.0
N B:GLY88 3.9 7.8 1.0
O B:HOH1703 4.0 8.4 1.0
CG B:ASP87 4.1 7.6 1.0
O B:HOH1717 4.1 8.3 1.0
O B:HOH1701 4.1 5.6 1.0
K B:K1603 4.1 5.2 1.0
OD1 B:ASP398 4.3 9.2 1.0
N B:THR89 4.4 5.7 1.0
OD2 B:ASP87 4.5 7.6 1.0
CA B:GLY88 4.5 7.8 1.0
OG1 B:THR89 4.6 5.7 1.0
OD1 B:ASP52 4.6 6.3 1.0
O1A B:ADP1600 4.6 22.0 1.0
OG1 B:THR90 4.6 4.5 1.0
CA B:ASP87 4.7 7.6 1.0
C B:ASP87 4.7 7.6 1.0
N B:THR90 4.9 4.5 1.0
C B:GLY88 5.0 7.8 1.0
O5' B:ADP1600 5.0 22.0 1.0

Fluorine binding site 5 out of 21 in 8p4n

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Fluorine binding site 5 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1602

b:10.8
occ:1.00
 F2 B:BEF1602 0.0 10.8 1.0
BE B:BEF1602 1.5 10.8 1.0
O B:HOH1701 2.2 5.6 1.0
F1 B:BEF1602 2.5 10.8 1.0
F3 B:BEF1602 2.5 10.8 1.0
OD1 B:ASP52 2.7 6.3 1.0
O3B B:ADP1600 2.9 22.0 1.0
OG1 B:THR89 3.2 5.7 1.0
CG B:ASP52 3.7 6.3 1.0
OD1 B:ASP398 3.8 9.2 1.0
CG2 B:THR89 3.8 5.7 1.0
OD1 B:ASP87 3.9 7.6 1.0
CB B:THR89 4.0 5.7 1.0
N B:THR89 4.1 5.7 1.0
N B:GLY53 4.1 5.7 1.0
OD2 B:ASP52 4.2 6.3 1.0
PB B:ADP1600 4.3 22.0 1.0
N B:GLY88 4.3 7.8 1.0
CA B:ASP87 4.3 7.6 1.0
C B:ASP87 4.6 7.6 1.0
O B:HOH1702 4.6 6.2 1.0
CA B:ASP52 4.6 6.3 1.0
CB B:ASP52 4.7 6.3 1.0
CA B:THR89 4.7 5.7 1.0
O B:HOH1717 4.7 8.3 1.0
O2B B:ADP1600 4.8 22.0 1.0
CG B:ASP398 4.8 9.2 1.0
CG B:ASP87 4.8 7.6 1.0
MG B:MG1601 4.9 6.4 1.0
C B:ASP52 4.9 6.3 1.0
O B:GLY86 5.0 6.7 1.0

Fluorine binding site 6 out of 21 in 8p4n

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Fluorine binding site 6 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1602

b:10.8
occ:1.00
 F3 B:BEF1602 0.0 10.8 1.0
BE B:BEF1602 1.5 10.8 1.0
O3B B:ADP1600 2.1 22.0 1.0
F1 B:BEF1602 2.5 10.8 1.0
F2 B:BEF1602 2.5 10.8 1.0
OG1 B:THR90 2.8 4.5 1.0
K B:K1603 2.8 5.2 1.0
N B:GLY53 3.0 5.7 1.0
OG1 B:THR89 3.2 5.7 1.0
PB B:ADP1600 3.4 22.0 1.0
O3A B:ADP1600 3.5 22.0 1.0
CA B:GLY53 3.8 5.7 1.0
N B:THR90 3.8 4.5 1.0
CB B:THR90 3.9 4.5 1.0
OD1 B:ASP52 3.9 6.3 1.0
C B:ASP52 4.0 6.3 1.0
CA B:ASP52 4.0 6.3 1.0
O B:LYS51 4.2 3.1 1.0
O B:HOH1717 4.3 8.3 1.0
O1B B:ADP1600 4.3 22.0 1.0
O2B B:ADP1600 4.4 22.0 1.0
N B:THR89 4.5 5.7 1.0
CB B:THR89 4.5 5.7 1.0
CG B:ASP52 4.5 6.3 1.0
PA B:ADP1600 4.5 22.0 1.0
CA B:THR90 4.5 4.5 1.0
O B:HOH1701 4.5 5.6 1.0
O1A B:ADP1600 4.7 22.0 1.0
O B:HOH1702 4.7 6.2 1.0
C B:THR89 4.8 5.7 1.0
O2A B:ADP1600 4.8 22.0 1.0
CA B:THR89 4.8 5.7 1.0
CB B:ASP52 4.9 6.3 1.0
C B:GLY53 4.9 5.7 1.0

Fluorine binding site 7 out of 21 in 8p4n

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Fluorine binding site 7 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1602

b:11.0
occ:1.00
 F1 C:BEF1602 0.0 11.0 1.0
BE C:BEF1602 1.5 11.0 1.0
O2B C:ADP1600 2.1 22.0 1.0
O3B C:ADP1600 2.1 22.0 1.0
MG C:MG1601 2.3 8.2 1.0
PB C:ADP1600 2.5 22.0 1.0
O C:HOH2001 2.5 8.3 1.0
F2 C:BEF1602 2.5 11.0 1.0
F3 C:BEF1602 2.5 11.0 1.0
O3A C:ADP1600 3.2 22.0 1.0
O2A C:ADP1600 3.4 22.0 1.0
O C:HOH2017 3.5 9.1 1.0
OD2 C:ASP87 3.6 9.2 1.0
O C:HOH2005 3.7 7.9 1.0
PA C:ADP1600 3.9 22.0 1.0
O1B C:ADP1600 3.9 22.0 1.0
CG C:ASP87 4.0 9.2 1.0
OD1 C:ASP87 4.1 9.2 1.0
N C:GLY88 4.1 7.8 1.0
K C:K1603 4.1 6.2 1.0
OD1 C:ASP52 4.5 7.0 1.0
O C:HOH2003 4.5 9.6 1.0
OD2 C:ASP398 4.7 10.0 1.0
O1A C:ADP1600 4.8 22.0 1.0
O C:HOH2007 4.8 8.9 1.0
CA C:ASP87 4.8 9.2 1.0
CA C:GLY88 4.9 7.8 1.0
N C:THR89 4.9 6.3 1.0
CG C:ASP398 5.0 10.0 1.0

Fluorine binding site 8 out of 21 in 8p4n

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Fluorine binding site 8 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1602

b:11.0
occ:1.00
 F2 C:BEF1602 0.0 11.0 1.0
BE C:BEF1602 1.5 11.0 1.0
O C:HOH2003 2.5 9.6 1.0
F3 C:BEF1602 2.5 11.0 1.0
F1 C:BEF1602 2.5 11.0 1.0
OD1 C:ASP52 2.6 7.0 1.0
O3B C:ADP1600 2.9 22.0 1.0
OG1 C:THR89 3.4 6.3 1.0
CG C:ASP52 3.5 7.0 1.0
N C:GLY53 4.0 6.5 1.0
OD2 C:ASP52 4.1 7.0 1.0
CG2 C:THR89 4.1 6.3 1.0
PB C:ADP1600 4.2 22.0 1.0
MG C:MG1601 4.2 8.2 1.0
N C:THR89 4.3 6.3 1.0
CB C:THR89 4.3 6.3 1.0
O2B C:ADP1600 4.3 22.0 1.0
O C:HOH2017 4.3 9.1 1.0
N C:GLY88 4.3 7.8 1.0
OD2 C:ASP398 4.4 10.0 1.0
CA C:ASP52 4.5 7.0 1.0
OD2 C:ASP87 4.5 9.2 1.0
CB C:ASP52 4.5 7.0 1.0
OD1 C:ASP398 4.6 10.0 1.0
CA C:ASP87 4.6 9.2 1.0
CG C:ASP398 4.7 10.0 1.0
O C:HOH2007 4.7 8.9 1.0
C C:ASP52 4.7 7.0 1.0
O C:HOH2001 4.8 8.3 1.0
K C:K1603 4.9 6.2 1.0
CA C:THR89 4.9 6.3 1.0
C C:ASP87 4.9 9.2 1.0
CA C:GLY53 4.9 6.5 1.0
O3A C:ADP1600 5.0 22.0 1.0
CG C:ASP87 5.0 9.2 1.0

Fluorine binding site 9 out of 21 in 8p4n

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Fluorine binding site 9 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1602

b:11.0
occ:1.00
 F3 C:BEF1602 0.0 11.0 1.0
O3B C:ADP1600 1.5 22.0 1.0
BE C:BEF1602 1.5 11.0 1.0
F2 C:BEF1602 2.5 11.0 1.0
F1 C:BEF1602 2.5 11.0 1.0
PB C:ADP1600 2.7 22.0 1.0
OG1 C:THR90 2.8 5.3 1.0
O3A C:ADP1600 3.0 22.0 1.0
K C:K1603 3.0 6.2 1.0
OG1 C:THR89 3.3 6.3 1.0
N C:THR90 3.5 5.3 1.0
O2B C:ADP1600 3.6 22.0 1.0
N C:GLY53 3.6 6.5 1.0
CB C:THR90 3.7 5.3 1.0
O1B C:ADP1600 3.8 22.0 1.0
N C:THR89 4.0 6.3 1.0
CA C:THR90 4.2 5.3 1.0
CA C:GLY53 4.2 6.5 1.0
PA C:ADP1600 4.3 22.0 1.0
O C:HOH2017 4.3 9.1 1.0
OD1 C:ASP52 4.4 7.0 1.0
CB C:THR89 4.5 6.3 1.0
C C:THR89 4.5 6.3 1.0
CA C:THR89 4.5 6.3 1.0
C C:ASP52 4.6 7.0 1.0
CA C:ASP52 4.7 7.0 1.0
O C:HOH2001 4.7 8.3 1.0
MG C:MG1601 4.7 8.2 1.0
O1A C:ADP1600 4.7 22.0 1.0
O2A C:ADP1600 4.7 22.0 1.0
O C:LYS51 4.7 5.0 1.0
N C:GLY88 4.8 7.8 1.0
C C:GLY88 4.9 7.8 1.0
O C:HOH2003 4.9 9.6 1.0
CG2 C:THR90 5.0 5.3 1.0

Fluorine binding site 10 out of 21 in 8p4n

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Fluorine binding site 10 out of 21 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1602

b:3.6
occ:1.00
 F1 D:BEF1602 0.0 3.6 1.0
BE D:BEF1602 1.5 3.6 1.0
O3B D:ADP1600 1.7 5.3 1.0
MG D:MG1601 2.1 3.9 1.0
O2B D:ADP1600 2.4 5.3 1.0
PB D:ADP1600 2.4 5.3 1.0
F2 D:BEF1602 2.5 3.6 1.0
F3 D:BEF1602 2.5 3.6 1.0
O D:HOH2001 2.9 6.5 1.0
O3A D:ADP1600 3.1 5.3 1.0
O2A D:ADP1600 3.2 5.3 1.0
OD1 D:ASP87 3.4 5.6 1.0
O D:HOH2016 3.6 5.8 1.0
PA D:ADP1600 3.6 5.3 1.0
O D:HOH2007 3.7 22.0 1.0
O1B D:ADP1600 3.8 5.3 1.0
N D:GLY88 3.9 5.3 1.0
K D:K1603 4.0 3.3 1.0
CG D:ASP87 4.1 5.6 1.0
OD2 D:ASP398 4.1 9.7 1.0
O D:HOH2002 4.3 8.8 1.0
O1A D:ADP1600 4.3 5.3 1.0
OD2 D:ASP87 4.4 5.6 1.0
CA D:GLY88 4.6 5.3 1.0
N D:THR89 4.6 5.3 1.0
OD1 D:ASP52 4.7 4.5 1.0
O D:HOH2013 4.9 9.1 1.0
OG1 D:THR90 4.9 5.4 1.0
CA D:ASP87 4.9 5.6 1.0
C D:ASP87 4.9 5.6 1.0
OG1 D:THR89 5.0 5.3 1.0
O5' D:ADP1600 5.0 5.3 1.0

Reference:

J.Wagner, A.I.Caravajal, F.Beck, A.Bracher, W.Wan, S.Bohn, R.Koerner, W.Baumeister, R.Fernandez-Busnadiego, F.U.Hartl. Visualizing Chaperonin Function in Situ By Cryo-Electron Tomography Nature 2024.
ISSN: ESSN 1476-4687
Page generated: Fri Aug 2 21:44:58 2024

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