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Fluorine in PDB 7yy3: Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7

Enzymatic activity of Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7

All present enzymatic activity of Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7:
2.7.7.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7, PDB code: 7yy3 was solved by S.E.Thomas, A.G.Coyne, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.05 / 1.54
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.931, 125.405, 119.364, 90, 90, 90
R / Rfree (%) 21 / 23.6

Other elements in 7yy3:

The structure of Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 (pdb code 7yy3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7, PDB code: 7yy3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7yy3

Go back to Fluorine Binding Sites List in 7yy3
Fluorine binding site 1 out of 3 in the Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7


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 Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:26.2
occ:1.00
F14 A:FIC201 0.0 26.2 1.0
C5 A:FIC201 1.4 26.0 1.0
C4 A:FIC201 2.4 25.7 1.0
C6 A:FIC201 2.4 24.4 1.0
N A:GLY69 3.2 18.0 1.0
CB A:ALA34 3.3 17.8 1.0
CA A:GLY69 3.3 16.9 1.0
CD2 A:PHE76 3.4 21.0 1.0
CE2 A:PHE76 3.5 21.2 1.0
O A:VAL35 3.6 18.7 1.0
C9 A:FIC201 3.7 25.4 1.0
C7 A:FIC201 3.7 23.4 1.0
C A:GLY69 3.7 18.1 1.0
C A:ALA34 3.7 16.7 1.0
C A:SER68 3.8 16.2 1.0
CA A:ALA34 3.8 18.4 1.0
N A:VAL35 3.9 17.0 1.0
C A:VAL35 3.9 17.9 1.0
O A:GLY69 3.9 20.6 1.0
CG A:PHE76 4.0 16.6 1.0
CZ A:PHE76 4.1 21.9 1.0
C8 A:FIC201 4.1 27.3 1.0
O A:ALA34 4.2 17.7 1.0
N A:LEU36 4.2 19.4 1.0
CA A:LEU36 4.4 22.0 1.0
O A:SER68 4.4 18.1 1.0
O A:GLU67 4.4 22.6 1.0
N A:GLN70 4.5 18.5 1.0
CA A:SER68 4.5 17.5 1.0
CD1 A:PHE76 4.5 16.8 1.0
CA A:VAL35 4.5 17.2 1.0
CE1 A:PHE76 4.6 19.0 1.0
CB A:PHE76 4.7 18.7 1.0
C3 A:FIC201 4.9 22.3 1.0

Fluorine binding site 2 out of 3 in 7yy3

Go back to Fluorine Binding Sites List in 7yy3
Fluorine binding site 2 out of 3 in the Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7


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 Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:28.1
occ:1.00
F14 B:FIC201 0.0 28.1 1.0
C5 B:FIC201 1.4 24.3 1.0
C4 B:FIC201 2.4 22.6 1.0
C6 B:FIC201 2.4 28.2 1.0
N B:GLY69 3.1 23.1 1.0
CA B:GLY69 3.2 26.4 1.0
CB B:ALA34 3.3 21.9 1.0
CE2 B:PHE76 3.5 24.4 1.0
CD2 B:PHE76 3.5 23.5 1.0
O B:VAL35 3.6 24.1 1.0
C B:GLY69 3.6 25.2 1.0
C9 B:FIC201 3.6 25.1 1.0
C7 B:FIC201 3.6 24.2 1.0
C B:ALA34 3.7 20.2 1.0
C B:SER68 3.7 22.9 1.0
CA B:ALA34 3.8 20.6 1.0
O B:GLY69 3.8 26.1 1.0
N B:VAL35 3.8 21.5 1.0
C B:VAL35 3.9 22.6 1.0
C8 B:FIC201 4.1 24.4 1.0
O B:ALA34 4.1 21.0 1.0
CZ B:PHE76 4.1 23.4 1.0
CG B:PHE76 4.1 23.6 1.0
O B:SER68 4.3 26.3 1.0
N B:LEU36 4.3 21.8 1.0
N B:GLN70 4.4 28.7 1.0
CA B:SER68 4.4 24.0 1.0
CA B:LEU36 4.5 24.9 1.0
CA B:VAL35 4.5 19.9 1.0
CD1 B:PHE76 4.6 22.7 1.0
CE1 B:PHE76 4.6 24.4 1.0
O B:GLU67 4.7 23.9 1.0
CB B:PHE76 4.9 24.8 1.0
C3 B:FIC201 4.9 29.1 1.0

Fluorine binding site 3 out of 3 in 7yy3

Go back to Fluorine Binding Sites List in 7yy3
Fluorine binding site 3 out of 3 in the Crystal Structure of Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7


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 Mycobacterium Abscessus Phosphopantetheine Adenylyltransferase in Complex with Fragment 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:37.1
occ:1.00
F14 C:FIC201 0.0 37.1 1.0
C5 C:FIC201 1.4 32.0 1.0
C6 C:FIC201 2.4 35.9 1.0
C4 C:FIC201 2.4 28.4 1.0
N C:GLY69 3.1 32.3 1.0
CA C:GLY69 3.2 33.5 1.0
CB C:ALA34 3.4 27.9 1.0
CD2 C:PHE76 3.5 30.2 1.0
CE2 C:PHE76 3.5 28.9 1.0
O C:VAL35 3.6 31.8 1.0
C C:GLY69 3.6 30.1 1.0
C7 C:FIC201 3.6 35.8 1.0
C9 C:FIC201 3.7 31.2 1.0
C C:ALA34 3.7 28.2 1.0
N C:VAL35 3.7 26.1 1.0
C C:SER68 3.8 33.6 1.0
O C:GLY69 3.8 33.5 1.0
CA C:ALA34 3.8 22.6 1.0
C C:VAL35 3.9 32.9 1.0
CG C:PHE76 4.1 26.8 1.0
CZ C:PHE76 4.1 25.2 1.0
C8 C:FIC201 4.1 37.1 1.0
O C:ALA34 4.1 25.8 1.0
N C:LEU36 4.3 28.0 1.0
O C:SER68 4.3 33.2 1.0
CA C:LEU36 4.4 27.7 1.0
N C:GLN70 4.4 28.4 1.0
CA C:SER68 4.5 28.2 1.0
CA C:VAL35 4.5 25.7 1.0
O C:GLU67 4.5 35.0 1.0
CD1 C:PHE76 4.6 22.8 1.0
CE1 C:PHE76 4.7 23.9 1.0
CB C:PHE76 4.8 25.1 1.0
C3 C:FIC201 5.0 34.3 1.0

Reference:

S.E.Thomas, W.J.Mccarthy, J.El Bakali, K.P.Brown, S.Y.Kim, M.Blaszczyk, V.Mendes, C.Abell, R.A.Floto, A.G.Coyne, T.L.Blundell. Structural Characterization of Mycobacterium Abscessus Phosphopantetheine Adenylyl Transferase Ligand Interactions: Implications For Fragment-Based Drug Design. Front Mol Biosci V. 9 80432 2022.
ISSN: ESSN 2296-889X
PubMed: 35712348
DOI: 10.3389/FMOLB.2022.880432
Page generated: Wed Jul 16 02:19:40 2025

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