Fluorine in PDB 6x3j: Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)

The structure of Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46), PDB code: 6x3j was solved by H.A.Chaires, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.51 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.800, 109.220, 173.030, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 27.1

The structure of Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	11 atoms

The binding sites of Fluorine atom in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) (pdb code 6x3j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46), PDB code: 6x3j:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)


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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:64.9 occ:1.00 F19 A:O7V401 0.0 64.9 1.0 C54 A:O7V401 1.3 64.9 1.0 H42 A:O7V401 1.9 0.1 1.0 C53 A:O7V401 2.4 65.0 1.0 C55 A:O7V401 2.4 64.6 1.0 H43 A:O7V401 2.5 0.1 1.0 H17 A:O7V401 2.6 0.1 1.0 H12 A:O7V401 2.6 0.1 1.0 H41 A:O7V401 2.7 0.1 1.0 HE1 A:TYR57 2.9 40.9 1.0 C02 A:O7V401 2.9 65.5 1.0 C06 A:O7V401 3.1 64.5 1.0 N07 A:O7V401 3.3 64.7 1.0 H44 A:O7V401 3.3 0.1 1.0 H40 A:O7V401 3.3 0.1 1.0 HH A:TYR59 3.3 49.4 1.0 C14 A:O7V401 3.5 65.6 1.0 C12 A:O7V401 3.6 65.7 1.0 OH A:TYR59 3.6 53.9 1.0 CE1 A:TYR57 3.7 46.0 1.0 HD1 A:TYR57 3.7 40.7 1.0 H16 A:O7V401 3.7 0.1 1.0 H39 A:O7V401 3.8 0.1 1.0 OD2 D:ASP44 3.9 42.9 1.0 C13 A:O7V401 3.9 65.8 1.0 CD1 A:TYR57 4.1 44.4 1.0 H38 A:O7V401 4.1 0.1 1.0 O01 A:O7V401 4.2 65.8 1.0 H15 A:O7V401 4.3 0.1 1.0 O A:HOH508 4.4 33.6 1.0 O10 A:O7V401 4.4 64.4 1.0 H14 A:O7V401 4.4 0.1 1.0 C47 A:O7V401 4.5 65.1 1.0 C08 A:O7V401 4.5 64.6 1.0 HD11 A:LEU98 4.6 45.9 1.0 H11 A:O7V401 4.6 0.1 1.0 CG D:ASP44 4.7 42.3 1.0 CZ A:TYR57 4.8 45.9 1.0 CZ A:TYR59 4.9 53.4 1.0 HD13 A:LEU98 4.9 45.9 1.0

Fluorine binding site 2 out of 7 in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)


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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:57.1 occ:0.79 F19 B:O7V401 0.0 57.1 0.8 C54 B:O7V401 1.3 56.6 0.9 H42 B:O7V401 1.9 0.1 1.0 C55 B:O7V401 2.4 56.5 0.7 C53 B:O7V401 2.4 55.9 1.0 H17 B:O7V401 2.4 0.1 1.0 H43 B:O7V401 2.5 0.1 1.0 H41 B:O7V401 2.6 0.1 1.0 H12 B:O7V401 2.6 0.1 1.0 C02 B:O7V401 2.9 56.2 1.0 C06 B:O7V401 3.0 57.2 1.0 N07 B:O7V401 3.2 58.0 0.8 HE1 D:TYR57 3.2 43.0 1.0 C14 B:O7V401 3.2 58.2 0.7 H44 B:O7V401 3.3 0.1 1.0 H40 B:O7V401 3.3 0.1 1.0 H16 B:O7V401 3.3 0.1 1.0 OD2 B:ASP44 3.4 46.6 1.0 HH D:TYR59 3.5 51.8 1.0 C12 B:O7V401 3.7 57.0 1.0 C13 B:O7V401 3.8 57.8 1.0 OH D:TYR59 3.9 56.3 1.0 H39 B:O7V401 4.0 0.1 1.0 HD1 D:TYR57 4.0 43.1 1.0 O D:HOH407 4.0 36.8 1.0 CE1 D:TYR57 4.1 44.5 1.0 H15 B:O7V401 4.1 0.1 1.0 O01 B:O7V401 4.2 55.7 1.0 H38 B:O7V401 4.3 0.1 1.0 O B:HOH539 4.3 49.0 1.0 CG B:ASP44 4.3 45.4 1.0 O10 B:O7V401 4.3 57.2 1.0 C08 B:O7V401 4.5 58.5 1.0 CD1 D:TYR57 4.5 44.1 1.0 H14 B:O7V401 4.6 0.1 1.0 HD13 D:LEU98 4.6 44.7 1.0 C47 B:O7V401 4.7 59.4 1.0 H11 B:O7V401 4.7 0.1 1.0 HD11 D:LEU98 4.8 44.7 1.0 HH D:TYR57 4.8 42.7 1.0 OD1 B:ASP44 4.8 45.2 1.0 HD12 B:LEU23 4.9 41.3 1.0

Fluorine binding site 3 out of 7 in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)


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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:59.5 occ:1.00 F19 B:O7V402 0.0 59.5 1.0 C54 B:O7V402 1.3 59.8 1.0 H42 B:O7V402 1.9 0.1 1.0 C53 B:O7V402 2.4 60.0 1.0 C55 B:O7V402 2.4 59.8 1.0 H43 B:O7V402 2.6 0.1 1.0 H41 B:O7V402 2.6 0.1 1.0 H17 B:O7V402 2.7 0.1 1.0 H12 B:O7V402 2.8 0.1 1.0 C02 B:O7V402 3.0 60.2 1.0 HE1 B:TYR57 3.0 44.6 1.0 C06 B:O7V402 3.1 59.7 1.0 HH B:TYR59 3.1 44.0 1.0 N07 B:O7V402 3.3 59.6 1.0 H44 B:O7V402 3.3 0.1 1.0 H40 B:O7V402 3.3 0.1 1.0 O B:HOH511 3.3 52.3 1.0 OH B:TYR59 3.3 51.7 1.0 O A:HOH526 3.4 45.6 1.0 C14 B:O7V402 3.6 60.0 1.0 HD1 B:TYR57 3.7 44.5 1.0 C12 B:O7V402 3.7 60.3 1.0 CE1 B:TYR57 3.8 47.9 1.0 H39 B:O7V402 4.0 0.1 1.0 H16 B:O7V402 4.0 0.1 1.0 C13 B:O7V402 4.0 60.3 1.0 OD2 A:ASP44 4.0 48.7 1.0 CD1 B:TYR57 4.1 47.0 1.0 O10 B:O7V402 4.3 59.8 1.0 O01 B:O7V402 4.3 60.4 1.0 H38 B:O7V402 4.3 0.1 1.0 H15 B:O7V402 4.5 0.1 1.0 H14 B:O7V402 4.5 0.1 1.0 C08 B:O7V402 4.5 59.6 1.0 CZ B:TYR59 4.6 51.5 1.0 C47 B:O7V402 4.7 59.5 1.0 CG A:ASP44 4.7 48.2 1.0 HD13 B:LEU98 4.9 36.7 1.0 H11 B:O7V402 4.9 0.1 1.0 O B:HOH542 4.9 86.1 1.0 HD11 B:LEU98 4.9 36.7 1.0

Fluorine binding site 4 out of 7 in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)


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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:67.0 occ:0.65 F19 C:O7V401 0.0 67.0 0.7 F19 C:O7V401 0.1 67.0 0.3 C54 C:O7V401 1.3 66.8 0.3 C54 C:O7V401 1.3 66.8 0.7 H42 C:O7V401 1.9 0.1 0.3 H42 C:O7V401 1.9 0.1 0.7 C53 C:O7V401 2.3 66.8 0.3 C55 C:O7V401 2.3 66.2 0.3 C55 C:O7V401 2.4 66.2 0.7 C53 C:O7V401 2.4 66.8 0.7 H43 C:O7V401 2.4 0.1 0.7 H17 C:O7V401 2.4 0.1 0.7 H12 C:O7V401 2.4 0.1 0.3 H12 C:O7V401 2.5 0.1 0.7 H43 C:O7V401 2.5 0.1 0.3 H17 C:O7V401 2.5 0.1 0.3 H41 C:O7V401 2.5 0.1 0.3 H41 C:O7V401 2.7 0.1 0.7 C02 C:O7V401 2.8 67.3 0.3 C02 C:O7V401 2.9 67.3 0.7 HE1 C:TYR57 3.1 38.5 1.0 H44 C:O7V401 3.2 0.1 0.3 H40 C:O7V401 3.2 0.1 0.3 C06 C:O7V401 3.2 66.3 0.3 H44 C:O7V401 3.2 0.1 0.7 H16 C:O7V401 3.2 0.1 0.7 C06 C:O7V401 3.2 66.3 0.7 C14 C:O7V401 3.2 68.3 0.7 H40 C:O7V401 3.3 0.1 0.7 C14 C:O7V401 3.3 68.3 0.3 H16 C:O7V401 3.4 0.1 0.3 HH C:TYR59 3.4 47.3 1.0 N07 C:O7V401 3.4 66.8 0.7 N07 C:O7V401 3.5 66.8 0.3 OD2 E:ASP44 3.5 53.2 1.0 C12 C:O7V401 3.6 67.7 0.3 C12 C:O7V401 3.7 67.7 0.7 OH C:TYR59 3.7 52.8 1.0 C13 C:O7V401 3.9 68.1 0.3 C13 C:O7V401 3.9 68.1 0.7 HD1 C:TYR57 3.9 38.0 1.0 CE1 C:TYR57 4.0 39.9 1.0 O01 C:O7V401 4.0 67.1 0.3 O01 C:O7V401 4.1 67.1 0.7 H39 C:O7V401 4.1 0.1 0.7 H15 C:O7V401 4.1 0.1 0.7 H15 C:O7V401 4.3 0.1 0.3 H39 C:O7V401 4.3 0.1 0.3 CG E:ASP44 4.4 52.6 1.0 CD1 C:TYR57 4.4 39.4 1.0 O10 C:O7V401 4.4 65.8 0.3 H38 C:O7V401 4.4 0.1 0.7 O10 C:O7V401 4.5 65.8 0.7 H11 C:O7V401 4.5 0.1 0.3 H11 C:O7V401 4.5 0.1 0.7 H14 C:O7V401 4.6 0.1 0.3 HD12 E:LEU23 4.6 39.1 1.0 H14 C:O7V401 4.6 0.1 0.7 H38 C:O7V401 4.7 0.1 0.3 C08 C:O7V401 4.7 66.7 0.7 C08 C:O7V401 4.7 66.7 0.3 C47 C:O7V401 4.8 68.0 0.7 OD1 E:ASP44 4.8 53.1 1.0 HD13 C:LEU98 4.9 39.9 1.0 HD11 C:LEU98 5.0 39.9 1.0 O1 E:SXA407 5.0 66.2 1.0 CZ C:TYR59 5.0 52.9 1.0

Fluorine binding site 5 out of 7 in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)


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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:67.0 occ:0.35 F19 C:O7V401 0.0 67.0 0.3 F19 C:O7V401 0.1 67.0 0.7 C54 C:O7V401 1.3 66.8 0.3 C54 C:O7V401 1.4 66.8 0.7 H42 C:O7V401 1.9 0.1 0.3 H42 C:O7V401 2.0 0.1 0.7 C53 C:O7V401 2.4 66.8 0.3 C55 C:O7V401 2.4 66.2 0.3 C55 C:O7V401 2.4 66.2 0.7 H17 C:O7V401 2.4 0.1 0.7 H43 C:O7V401 2.4 0.1 0.7 C53 C:O7V401 2.5 66.8 0.7 H43 C:O7V401 2.5 0.1 0.3 H12 C:O7V401 2.5 0.1 0.3 H12 C:O7V401 2.5 0.1 0.7 H17 C:O7V401 2.5 0.1 0.3 H41 C:O7V401 2.6 0.1 0.3 H41 C:O7V401 2.8 0.1 0.7 C02 C:O7V401 2.9 67.3 0.3 C02 C:O7V401 2.9 67.3 0.7 HE1 C:TYR57 3.1 38.5 1.0 C06 C:O7V401 3.2 66.3 0.3 H16 C:O7V401 3.2 0.1 0.7 C06 C:O7V401 3.2 66.3 0.7 H44 C:O7V401 3.2 0.1 0.3 C14 C:O7V401 3.3 68.3 0.7 H44 C:O7V401 3.3 0.1 0.7 H40 C:O7V401 3.3 0.1 0.3 HH C:TYR59 3.3 47.3 1.0 C14 C:O7V401 3.4 68.3 0.3 H16 C:O7V401 3.4 0.1 0.3 H40 C:O7V401 3.4 0.1 0.7 N07 C:O7V401 3.4 66.8 0.7 N07 C:O7V401 3.5 66.8 0.3 OD2 E:ASP44 3.5 53.2 1.0 OH C:TYR59 3.6 52.8 1.0 C12 C:O7V401 3.7 67.7 0.3 C12 C:O7V401 3.8 67.7 0.7 HD1 C:TYR57 3.8 38.0 1.0 CE1 C:TYR57 3.9 39.9 1.0 C13 C:O7V401 3.9 68.1 0.3 C13 C:O7V401 3.9 68.1 0.7 H39 C:O7V401 4.0 0.1 0.7 O01 C:O7V401 4.1 67.1 0.3 H15 C:O7V401 4.1 0.1 0.7 O01 C:O7V401 4.2 67.1 0.7 H39 C:O7V401 4.2 0.1 0.3 H15 C:O7V401 4.3 0.1 0.3 CD1 C:TYR57 4.3 39.4 1.0 CG E:ASP44 4.4 52.6 1.0 O10 C:O7V401 4.4 65.8 0.3 H38 C:O7V401 4.4 0.1 0.7 O10 C:O7V401 4.5 65.8 0.7 H11 C:O7V401 4.6 0.1 0.3 H11 C:O7V401 4.6 0.1 0.7 H14 C:O7V401 4.6 0.1 0.3 H38 C:O7V401 4.7 0.1 0.3 HD12 E:LEU23 4.7 39.1 1.0 C08 C:O7V401 4.7 66.7 0.7 C08 C:O7V401 4.7 66.7 0.3 H14 C:O7V401 4.7 0.1 0.7 C47 C:O7V401 4.8 68.0 0.7 OD1 E:ASP44 4.8 53.1 1.0 CZ C:TYR59 4.9 52.9 1.0 HD13 C:LEU98 5.0 39.9 1.0 C47 C:O7V401 5.0 68.0 0.3

Fluorine binding site 6 out of 7 in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)


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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) within 5.0Å range: probe atom residue distance (Å) B Occ E:F401 b:77.3 occ:1.00 F19 E:O7V401 0.0 77.3 1.0 C54 E:O7V401 1.3 77.2 1.0 H42 E:O7V401 1.9 0.1 1.0 C55 E:O7V401 2.4 77.0 1.0 C53 E:O7V401 2.4 77.0 1.0 H43 E:O7V401 2.6 0.1 1.0 H17 E:O7V401 2.6 0.1 1.0 H41 E:O7V401 2.6 0.1 1.0 H12 E:O7V401 2.7 0.1 1.0 HE1 E:TYR57 2.9 47.0 1.0 H16 E:O7V401 2.9 0.1 1.0 C02 E:O7V401 2.9 77.3 1.0 C06 E:O7V401 3.0 77.4 1.0 N07 E:O7V401 3.1 77.7 1.0 O F:HOH534 3.1 70.0 1.0 C14 E:O7V401 3.1 77.9 1.0 HH E:TYR59 3.3 61.7 1.0 H44 E:O7V401 3.3 0.1 1.0 H40 E:O7V401 3.3 0.1 1.0 C12 E:O7V401 3.6 77.6 1.0 OD2 F:ASP44 3.6 49.9 1.0 H39 E:O7V401 3.7 0.1 1.0 C13 E:O7V401 3.7 77.9 1.0 CE1 E:TYR57 3.7 46.7 1.0 OH E:TYR59 3.8 61.8 1.0 HD1 E:TYR57 3.8 46.6 1.0 H38 E:O7V401 4.0 0.1 1.0 H15 E:O7V401 4.1 0.1 1.0 O01 E:O7V401 4.2 77.2 1.0 CD1 E:TYR57 4.2 44.8 1.0 O10 E:O7V401 4.3 77.3 1.0 C08 E:O7V401 4.4 77.9 1.0 C47 E:O7V401 4.4 78.3 1.0 H14 E:O7V401 4.5 0.1 1.0 CG F:ASP44 4.6 47.0 1.0 O F:HOH507 4.6 31.3 1.0 H11 E:O7V401 4.7 0.1 1.0 HD13 E:LEU98 4.8 53.4 1.0 CZ E:TYR57 4.8 45.6 1.0 CL E:CL402 4.9 73.7 1.0 HD11 E:LEU98 4.9 53.4 1.0 C09 E:O7V401 5.0 77.7 1.0

Fluorine binding site 7 out of 7 in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)


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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) within 5.0Å range: probe atom residue distance (Å) B Occ F:F401 b:57.1 occ:1.00 F19 F:O7V401 0.0 57.1 1.0 C54 F:O7V401 1.3 57.4 1.0 H42 F:O7V401 1.9 0.1 1.0 C55 F:O7V401 2.3 56.8 1.0 C53 F:O7V401 2.4 58.0 1.0 H17 F:O7V401 2.4 0.1 1.0 H43 F:O7V401 2.5 0.1 1.0 H12 F:O7V401 2.6 0.1 1.0 H41 F:O7V401 2.6 0.1 1.0 C02 F:O7V401 2.9 58.5 1.0 C06 F:O7V401 3.1 56.4 1.0 HE1 F:TYR57 3.1 41.6 1.0 HH F:TYR59 3.2 42.0 1.0 C14 F:O7V401 3.2 58.1 1.0 H44 F:O7V401 3.3 0.1 1.0 H16 F:O7V401 3.3 0.1 1.0 N07 F:O7V401 3.3 56.5 1.0 H40 F:O7V401 3.3 0.1 1.0 OH F:TYR59 3.4 49.3 1.0 C12 F:O7V401 3.6 58.7 1.0 OD2 C:ASP44 3.6 47.5 1.0 HD1 F:TYR57 3.7 42.5 1.0 C13 F:O7V401 3.7 58.6 1.0 CE1 F:TYR57 3.9 46.0 1.0 O F:HOH504 3.9 55.6 1.0 H15 F:O7V401 4.1 0.1 1.0 H39 F:O7V401 4.1 0.1 1.0 O01 F:O7V401 4.2 59.1 1.0 CD1 F:TYR57 4.2 46.1 1.0 O10 F:O7V401 4.3 56.1 1.0 H38 F:O7V401 4.4 0.1 1.0 H14 F:O7V401 4.5 0.1 1.0 C08 F:O7V401 4.5 56.1 1.0 CL F:CL402 4.7 74.0 1.0 CZ F:TYR59 4.7 49.8 1.0 CG C:ASP44 4.7 46.5 1.0 H11 F:O7V401 4.7 0.1 1.0 HD13 F:LEU98 4.8 37.8 1.0 C47 F:O7V401 4.8 56.8 1.0 HD11 F:LEU98 4.8 37.8 1.0 H2B F:SXA406 5.0 0.1 1.0

Q.Li, J.Pellegrino, D.J.Lee, A.A.Tran, H.A.Chaires, R.Wang, J.E.Park, K.Ji, D.Chow, N.Zhang, A.F.Brilot, J.T.Biel, G.Van Zundert, K.Borrelli, D.Shinabarger, C.Wolfe, B.Murray, M.P.Jacobson, E.Muhle, O.Chesneau, J.S.Fraser, I.B.Seiple. Synthetic Group A Streptogramin Antibiotics That Overcome Vat Resistance. Nature V. 586 145 2020.
ISSN: ESSN 1476-4687
PubMed: 32968273
DOI: 10.1038/S41586-020-2761-3