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Fluorine in PDB 7v5c: Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound)

Enzymatic activity of Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound)

All present enzymatic activity of Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound):
7.4.2.6;

Other elements in 7v5c:

The structure of Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound) (pdb code 7v5c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound), PDB code: 7v5c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7v5c

Go back to Fluorine Binding Sites List in 7v5c
Fluorine binding site 1 out of 6 in the Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:87.2
occ:1.00
 F1 A:BEF802 0.0 87.2 1.0
BE A:BEF802 1.8 87.2 1.0
NZ A:LYS541 2.4 85.1 1.0
CE A:LYS541 2.8 85.1 1.0
F2 A:BEF802 3.0 87.2 1.0
F3 A:BEF802 3.1 87.2 1.0
NE2 A:HIS695 3.2 111.4 1.0
CE1 A:HIS695 3.3 111.4 1.0
O3B A:ADP801 3.4 79.9 1.0
CA A:SER537 3.9 95.8 1.0
OE2 A:GLU664 4.0 102.4 1.0
PB A:ADP801 4.2 79.9 1.0
CD A:LYS541 4.3 85.1 1.0
CD2 A:HIS695 4.3 111.4 1.0
O1B A:ADP801 4.4 79.9 1.0
O A:SER537 4.4 95.8 1.0
C A:SER537 4.4 95.8 1.0
ND1 A:HIS695 4.4 111.4 1.0
MG A:MG803 4.5 83.1 1.0
N A:SER537 4.5 95.8 1.0
NE2 A:GLN583 4.6 92.1 1.0
O2B A:ADP801 4.7 79.9 1.0
CB A:SER537 4.8 95.8 1.0
CB A:LYS541 4.9 85.1 1.0
CG A:HIS695 5.0 111.4 1.0

Fluorine binding site 2 out of 6 in 7v5c

Go back to Fluorine Binding Sites List in 7v5c
Fluorine binding site 2 out of 6 in the Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:87.2
occ:1.00
 F2 A:BEF802 0.0 87.2 1.0
BE A:BEF802 1.8 87.2 1.0
O3B A:ADP801 2.5 79.9 1.0
O A:SER537 2.6 95.8 1.0
O1B A:ADP801 2.7 79.9 1.0
PB A:ADP801 3.0 79.9 1.0
F1 A:BEF802 3.0 87.2 1.0
F3 A:BEF802 3.1 87.2 1.0
N B:GLY642 3.4 83.2 1.0
C A:SER537 3.4 95.8 1.0
CB B:SER640 3.5 79.0 1.0
OG B:SER640 3.7 79.0 1.0
O3A A:ADP801 3.9 79.9 1.0
N B:GLY641 3.9 80.3 1.0
CA A:SER537 3.9 95.8 1.0
CA B:GLY642 4.0 83.2 1.0
O2B A:ADP801 4.3 79.9 1.0
N A:GLY538 4.3 90.6 1.0
C B:GLY641 4.4 80.3 1.0
C B:SER640 4.5 79.0 1.0
CA B:SER640 4.5 79.0 1.0
CA B:GLY641 4.5 80.3 1.0
CA A:GLY538 4.6 90.6 1.0
CB A:SER537 4.6 95.8 1.0
MG A:MG803 4.7 83.1 1.0
NE2 A:GLN583 4.7 92.1 1.0
N B:GLN643 4.9 81.0 1.0
C B:GLY642 4.9 83.2 1.0

Fluorine binding site 3 out of 6 in 7v5c

Go back to Fluorine Binding Sites List in 7v5c
Fluorine binding site 3 out of 6 in the Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:87.2
occ:1.00
 F3 A:BEF802 0.0 87.2 1.0
BE A:BEF802 1.8 87.2 1.0
MG A:MG803 1.8 83.1 1.0
O1B A:ADP801 2.6 79.9 1.0
NE2 A:GLN583 2.7 92.1 1.0
OE1 A:GLN583 2.9 92.1 1.0
CD A:GLN583 3.0 92.1 1.0
F1 A:BEF802 3.1 87.2 1.0
F2 A:BEF802 3.1 87.2 1.0
PB A:ADP801 3.3 79.9 1.0
OG A:SER542 3.5 83.2 1.0
O2B A:ADP801 3.7 79.9 1.0
O3B A:ADP801 3.7 79.9 1.0
N B:GLY641 4.1 80.3 1.0
CA B:GLY641 4.4 80.3 1.0
CG A:GLN583 4.4 92.1 1.0
OE2 A:GLU664 4.6 102.4 1.0
CB A:SER542 4.6 83.2 1.0
OD1 A:ASP663 4.7 93.8 1.0
N B:GLY642 4.8 83.2 1.0
O3A A:ADP801 4.8 79.9 1.0
CE A:LYS541 4.8 85.1 1.0
C B:GLY641 5.0 80.3 1.0
NZ A:LYS541 5.0 85.1 1.0
N A:SER542 5.0 83.2 1.0

Fluorine binding site 4 out of 6 in 7v5c

Go back to Fluorine Binding Sites List in 7v5c
Fluorine binding site 4 out of 6 in the Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:88.4
occ:1.00
 F1 B:BEF802 0.0 88.4 1.0
BE B:BEF802 1.8 88.4 1.0
NZ B:LYS541 2.4 85.0 1.0
CE B:LYS541 2.8 85.0 1.0
OE1 B:GLU664 3.0 101.0 1.0
F2 B:BEF802 3.0 88.4 1.0
F3 B:BEF802 3.1 88.4 1.0
NE2 B:HIS695 3.3 109.3 1.0
CE1 B:HIS695 3.4 109.3 1.0
O3B B:ADP801 3.5 81.0 1.0
CA B:SER537 4.0 98.8 1.0
CD B:GLU664 4.0 101.0 1.0
PB B:ADP801 4.2 81.0 1.0
CD B:LYS541 4.3 85.0 1.0
OE2 B:GLU664 4.3 101.0 1.0
O1B B:ADP801 4.4 81.0 1.0
CD2 B:HIS695 4.4 109.3 1.0
MG B:MG803 4.5 87.7 1.0
O B:SER537 4.5 98.8 1.0
ND1 B:HIS695 4.5 109.3 1.0
C B:SER537 4.5 98.8 1.0
NE2 B:GLN583 4.6 91.8 1.0
N B:SER537 4.6 98.8 1.0
O2B B:ADP801 4.6 81.0 1.0
O A:LEU669 4.8 105.0 1.0
CB B:LYS541 4.8 85.0 1.0
CB B:SER537 4.9 98.8 1.0

Fluorine binding site 5 out of 6 in 7v5c

Go back to Fluorine Binding Sites List in 7v5c
Fluorine binding site 5 out of 6 in the Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:88.4
occ:1.00
 F2 B:BEF802 0.0 88.4 1.0
BE B:BEF802 1.8 88.4 1.0
O3B B:ADP801 2.5 81.0 1.0
O B:SER537 2.6 98.8 1.0
O1B B:ADP801 2.7 81.0 1.0
PB B:ADP801 3.0 81.0 1.0
F1 B:BEF802 3.0 88.4 1.0
F3 B:BEF802 3.1 88.4 1.0
C B:SER537 3.4 98.8 1.0
N A:GLY642 3.4 83.8 1.0
CB A:SER640 3.5 78.9 1.0
OG A:SER640 3.7 78.9 1.0
CA B:SER537 3.9 98.8 1.0
N A:GLY641 3.9 81.6 1.0
O3A B:ADP801 4.0 81.0 1.0
CA A:GLY642 4.0 83.8 1.0
O2B B:ADP801 4.3 81.0 1.0
N B:GLY538 4.3 91.4 1.0
C A:GLY641 4.3 81.6 1.0
C A:SER640 4.5 78.9 1.0
CA A:GLY641 4.5 81.6 1.0
CA A:SER640 4.5 78.9 1.0
CA B:GLY538 4.6 91.4 1.0
CB B:SER537 4.6 98.8 1.0
NE2 B:GLN583 4.7 91.8 1.0
MG B:MG803 4.8 87.7 1.0
C A:GLY642 4.9 83.8 1.0
N A:GLN643 4.9 80.8 1.0

Fluorine binding site 6 out of 6 in 7v5c

Go back to Fluorine Binding Sites List in 7v5c
Fluorine binding site 6 out of 6 in the Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cryo-Em Structure of the Mouse ABCB9 (Adp.BEF3-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:88.4
occ:1.00
 F3 B:BEF802 0.0 88.4 1.0
BE B:BEF802 1.8 88.4 1.0
MG B:MG803 1.8 87.7 1.0
O1B B:ADP801 2.6 81.0 1.0
NE2 B:GLN583 2.7 91.8 1.0
OE1 B:GLN583 3.0 91.8 1.0
F1 B:BEF802 3.1 88.4 1.0
F2 B:BEF802 3.1 88.4 1.0
CD B:GLN583 3.1 91.8 1.0
PB B:ADP801 3.3 81.0 1.0
OG B:SER542 3.3 84.8 1.0
O2B B:ADP801 3.6 81.0 1.0
OE1 B:GLU664 3.6 101.0 1.0
O3B B:ADP801 3.7 81.0 1.0
N A:GLY641 4.1 81.6 1.0
CA A:GLY641 4.4 81.6 1.0
CG B:GLN583 4.5 91.8 1.0
CB B:SER542 4.5 84.8 1.0
O3A B:ADP801 4.7 81.0 1.0
CE B:LYS541 4.8 85.0 1.0
N A:GLY642 4.9 83.8 1.0
CD B:GLU664 4.9 101.0 1.0
N B:SER542 4.9 84.8 1.0
O1A B:ADP801 4.9 81.0 1.0
NZ B:LYS541 5.0 85.0 1.0

Reference:

J.G.Park, S.Kim, E.Jang, S.H.Choi, H.Han, S.Ju, J.W.Kim, D.S.Min, M.S.Jin. The Lysosomal Transporter Tapl Has A Dual Role As Peptide Translocator and Phosphatidylserine Floppase. Nat Commun V. 13 5851 2022.
ISSN: ESSN 2041-1723
PubMed: 36195619
DOI: 10.1038/S41467-022-33593-2
Page generated: Fri Aug 2 14:24:03 2024

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