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Fluorine in PDB 4j0b: Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3

Protein crystallography data

The structure of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3, PDB code: 4j0b was solved by J.R.Partridge, L.A.Lavery, D.A.Agard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 2.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.779, 96.566, 124.977, 90.00, 134.29, 90.00
R / Rfree (%) 20.5 / 24.8

Other elements in 4j0b:

The structure of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 also contains other interesting chemical elements:

Cobalt (Co) 4 atoms
Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 (pdb code 4j0b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3, PDB code: 4j0b:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4j0b

Go back to Fluorine Binding Sites List in 4j0b
Fluorine binding site 1 out of 6 in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F804

b:41.2
occ:1.00
 F1 A:BEF804 0.0 41.2 1.0
BE A:BEF804 1.6 34.2 1.0
MG A:MG805 1.8 51.5 1.0
O1B A:ADP803 2.6 43.4 1.0
F3 A:BEF804 2.6 41.4 1.0
F2 A:BEF804 2.6 44.3 1.0
O A:HOH960 2.7 41.1 1.0
O A:HOH917 2.8 40.7 1.0
O2B A:ADP803 2.9 51.5 1.0
O A:HOH970 2.9 35.2 1.0
O A:HOH918 3.0 40.2 1.0
O1A A:ADP803 3.0 47.5 1.0
PB A:ADP803 3.2 48.9 1.0
OE1 A:GLU130 3.3 46.6 1.0
O3A A:ADP803 3.7 47.5 1.0
N A:GLY219 4.0 44.7 1.0
CA A:GLY214 4.0 50.8 1.0
CA A:GLY219 4.0 43.9 1.0
PA A:ADP803 4.0 44.4 1.0
OD1 A:ASN134 4.0 45.0 1.0
NH2 A:ARG417 4.1 53.3 1.0
NE A:ARG417 4.3 55.1 1.0
CD A:GLU130 4.5 47.1 1.0
CZ A:ARG417 4.5 52.7 1.0
O3B A:ADP803 4.6 46.5 1.0
N A:GLN215 4.7 66.5 1.0
C A:GLY214 4.7 50.7 1.0
N A:GLY214 4.9 51.1 1.0
O2A A:ADP803 4.9 39.3 1.0
CG A:ASN134 5.0 45.9 1.0
C A:GLY219 5.0 45.0 1.0

Fluorine binding site 2 out of 6 in 4j0b

Go back to Fluorine Binding Sites List in 4j0b
Fluorine binding site 2 out of 6 in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F804

b:44.3
occ:1.00
 F2 A:BEF804 0.0 44.3 1.0
BE A:BEF804 1.6 34.2 1.0
F3 A:BEF804 2.5 41.4 1.0
O1B A:ADP803 2.5 43.4 1.0
F1 A:BEF804 2.6 41.2 1.0
O A:HOH918 2.7 40.2 1.0
N A:VAL218 2.8 50.4 1.0
N A:GLY219 2.8 44.7 1.0
N A:GLY217 3.1 53.2 1.0
CB A:PHE216 3.3 48.2 1.0
O3A A:ADP803 3.5 47.5 1.0
PB A:ADP803 3.6 48.9 1.0
CA A:VAL218 3.6 50.8 1.0
C A:VAL218 3.6 49.7 1.0
CA A:GLY219 3.7 43.9 1.0
C A:GLY217 3.7 56.1 1.0
C A:PHE216 3.7 50.0 1.0
CG2 A:VAL218 3.8 48.4 1.0
CA A:GLY217 3.8 55.2 1.0
CA A:PHE216 3.8 48.7 1.0
N A:PHE216 3.8 48.0 1.0
O1A A:ADP803 4.0 47.5 1.0
MG A:MG805 4.0 51.5 1.0
PA A:ADP803 4.1 44.4 1.0
CB A:VAL218 4.3 50.7 1.0
O2B A:ADP803 4.3 51.5 1.0
O2A A:ADP803 4.3 39.3 1.0
CG A:PHE216 4.4 48.0 1.0
CD2 A:PHE216 4.4 47.9 1.0
O A:PHE216 4.7 51.2 1.0
OE1 A:GLU130 4.7 46.6 1.0
O3B A:ADP803 4.8 46.5 1.0
O A:GLY217 4.8 58.4 1.0
O A:VAL218 4.8 50.4 1.0
O A:HOH961 4.9 58.7 1.0
O A:HOH917 4.9 40.7 1.0
NE A:ARG417 4.9 55.1 1.0
NH2 A:ARG417 4.9 53.3 1.0
CG1 A:VAL218 4.9 51.9 1.0
N A:GLN215 4.9 66.5 1.0
C A:GLY219 5.0 45.0 1.0

Fluorine binding site 3 out of 6 in 4j0b

Go back to Fluorine Binding Sites List in 4j0b
Fluorine binding site 3 out of 6 in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F804

b:41.4
occ:1.00
 F3 A:BEF804 0.0 41.4 1.0
BE A:BEF804 1.6 34.2 1.0
O1B A:ADP803 2.4 43.4 1.0
F2 A:BEF804 2.5 44.3 1.0
F1 A:BEF804 2.6 41.2 1.0
NH2 A:ARG417 2.6 53.3 1.0
O A:HOH918 3.0 40.2 1.0
N A:PHE216 3.0 48.0 1.0
N A:GLN215 3.1 66.5 1.0
CD2 A:PHE216 3.4 47.9 1.0
CB A:PHE216 3.4 48.2 1.0
CZ A:ARG417 3.5 52.7 1.0
NE A:ARG417 3.5 55.1 1.0
CA A:GLY214 3.7 50.8 1.0
CA A:PHE216 3.8 48.7 1.0
CG A:PHE216 3.8 48.0 1.0
C A:GLY214 3.9 50.7 1.0
PB A:ADP803 3.9 48.9 1.0
O A:HOH970 4.0 35.2 1.0
C A:GLN215 4.0 67.5 1.0
CA A:GLN215 4.1 67.0 1.0
N A:GLY217 4.2 53.2 1.0
MG A:MG805 4.2 51.5 1.0
O2B A:ADP803 4.4 51.5 1.0
CE2 A:PHE216 4.4 48.3 1.0
C A:PHE216 4.5 50.0 1.0
O A:HOH960 4.5 41.1 1.0
O3A A:ADP803 4.7 47.5 1.0
CG A:GLN215 4.7 66.9 1.0
NH1 A:ARG417 4.8 49.3 1.0
O A:ILE213 4.8 43.4 1.0
N A:GLY214 4.8 51.1 1.0
CD A:ARG417 4.9 54.5 1.0
O3B A:ADP803 4.9 46.5 1.0
OE1 A:GLU130 4.9 46.6 1.0
CD1 A:PHE216 5.0 48.1 1.0
O A:GLY214 5.0 50.8 1.0

Fluorine binding site 4 out of 6 in 4j0b

Go back to Fluorine Binding Sites List in 4j0b
Fluorine binding site 4 out of 6 in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F804

b:57.4
occ:1.00
 F1 B:BEF804 0.0 57.4 1.0
BE B:BEF804 1.5 77.1 1.0
F3 B:BEF804 2.5 52.6 1.0
O1B B:ADP803 2.5 69.6 1.0
O B:HOH948 2.6 51.3 1.0
F2 B:BEF804 2.6 58.1 1.0
N B:GLY219 2.7 51.2 1.0
N B:VAL218 3.0 57.2 1.0
O3A B:ADP803 3.3 57.4 1.0
N B:GLY217 3.4 59.4 1.0
CA B:GLY219 3.4 50.7 1.0
PB B:ADP803 3.5 60.3 1.0
CB B:PHE216 3.6 53.4 1.0
C B:VAL218 3.6 57.2 1.0
CA B:VAL218 3.7 57.5 1.0
CG2 B:VAL218 3.8 55.2 1.0
O1A B:ADP803 3.9 51.6 1.0
C B:PHE216 3.9 55.3 1.0
N B:PHE216 3.9 54.0 1.0
C B:GLY217 4.0 61.4 1.0
MG B:MG805 4.0 49.7 1.0
CA B:PHE216 4.0 54.2 1.0
PA B:ADP803 4.1 55.8 1.0
O2B B:ADP803 4.1 52.4 1.0
CA B:GLY217 4.1 61.2 1.0
OE1 B:GLU130 4.3 53.7 1.0
CB B:VAL218 4.3 56.9 1.0
O2A B:ADP803 4.4 55.2 1.0
CD2 B:PHE216 4.5 53.0 1.0
O B:HOH919 4.5 52.9 1.0
CG B:PHE216 4.5 53.1 1.0
O3B B:ADP803 4.7 54.4 1.0
O B:VAL218 4.8 57.8 1.0
C B:GLY219 4.8 52.1 1.0
NH2 B:ARG417 4.8 84.6 1.0
NE B:ARG417 4.8 79.3 1.0
O B:PHE216 4.9 56.1 1.0
O B:HOH933 4.9 44.1 1.0
CG1 B:VAL218 4.9 57.3 1.0

Fluorine binding site 5 out of 6 in 4j0b

Go back to Fluorine Binding Sites List in 4j0b
Fluorine binding site 5 out of 6 in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F804

b:58.1
occ:1.00
 F2 B:BEF804 0.0 58.1 1.0
BE B:BEF804 1.6 77.1 1.0
O1B B:ADP803 2.5 69.6 1.0
NH2 B:ARG417 2.5 84.6 1.0
F3 B:BEF804 2.6 52.6 1.0
F1 B:BEF804 2.6 57.4 1.0
N B:GLN215 3.0 67.7 1.0
N B:PHE216 3.1 54.0 1.0
O B:HOH948 3.3 51.3 1.0
CA B:GLY214 3.4 56.3 1.0
CZ B:ARG417 3.4 79.9 1.0
NE B:ARG417 3.5 79.3 1.0
CD2 B:PHE216 3.6 53.0 1.0
C B:GLY214 3.6 56.8 1.0
O B:HOH933 3.7 44.1 1.0
CB B:PHE216 3.8 53.4 1.0
PB B:ADP803 3.9 60.3 1.0
CA B:GLN215 4.0 68.6 1.0
CA B:PHE216 4.0 54.2 1.0
C B:GLN215 4.0 68.8 1.0
CG B:GLN215 4.0 68.6 1.0
CG B:PHE216 4.0 53.1 1.0
O B:HOH906 4.2 53.5 1.0
MG B:MG805 4.3 49.7 1.0
O2B B:ADP803 4.3 52.4 1.0
N B:GLY217 4.4 59.4 1.0
O B:ILE213 4.5 56.5 1.0
N B:GLY214 4.5 56.4 1.0
CE2 B:PHE216 4.5 53.6 1.0
CB B:GLN215 4.6 68.7 1.0
NH1 B:ARG417 4.7 75.3 1.0
C B:PHE216 4.7 55.3 1.0
OE1 B:GLU130 4.7 53.7 1.0
O3A B:ADP803 4.7 57.4 1.0
O B:GLY214 4.8 57.2 1.0
C B:ILE213 4.9 56.3 1.0
CD B:ARG417 4.9 74.3 1.0
O3B B:ADP803 4.9 54.4 1.0

Fluorine binding site 6 out of 6 in 4j0b

Go back to Fluorine Binding Sites List in 4j0b
Fluorine binding site 6 out of 6 in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F804

b:52.6
occ:1.00
 F3 B:BEF804 0.0 52.6 1.0
BE B:BEF804 1.5 77.1 1.0
MG B:MG805 1.8 49.7 1.0
O1B B:ADP803 2.4 69.6 1.0
F1 B:BEF804 2.5 57.4 1.0
F2 B:BEF804 2.6 58.1 1.0
O2B B:ADP803 2.6 52.4 1.0
O B:HOH906 2.7 53.5 1.0
O B:HOH919 2.8 52.9 1.0
O1A B:ADP803 2.9 51.6 1.0
PB B:ADP803 2.9 60.3 1.0
O B:HOH933 3.0 44.1 1.0
O B:HOH948 3.4 51.3 1.0
OE1 B:GLU130 3.5 53.7 1.0
O3A B:ADP803 3.5 57.4 1.0
CA B:GLY214 3.8 56.3 1.0
PA B:ADP803 3.9 55.8 1.0
CA B:GLY219 3.9 50.7 1.0
N B:GLY219 3.9 51.2 1.0
OD1 B:ASN134 4.0 60.5 1.0
NH2 B:ARG417 4.1 84.6 1.0
O3B B:ADP803 4.4 54.4 1.0
NE B:ARG417 4.5 79.3 1.0
C B:GLY214 4.6 56.8 1.0
N B:GLN215 4.7 67.7 1.0
CD B:GLU130 4.7 54.0 1.0
CZ B:ARG417 4.7 79.9 1.0
N B:GLY214 4.8 56.4 1.0
O2A B:ADP803 4.8 55.2 1.0
CG B:ASN134 4.9 61.1 1.0
N B:GLY217 5.0 59.4 1.0
C B:GLY219 5.0 52.1 1.0

Reference:

L.A.Lavery, J.R.Partridge, T.A.Ramelot, D.Elnatan, M.A.Kennedy, D.A.Agard. Structural Asymmetry in the Closed State of Mitochondrial HSP90 (TRAP1) Supports A Two-Step Atp Hydrolysis Mechanism. Mol.Cell V. 53 330 2014.
ISSN: ISSN 1097-2765
PubMed: 24462206
DOI: 10.1016/J.MOLCEL.2013.12.023
Page generated: Thu Aug 1 02:42:15 2024

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