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Fluorine in PDB 4p75: Phers in Complex with Compound 4A

Enzymatic activity of Phers in Complex with Compound 4A

All present enzymatic activity of Phers in Complex with Compound 4A:
6.1.1.20;

Protein crystallography data

The structure of Phers in Complex with Compound 4A, PDB code: 4p75 was solved by A.D.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.20 / 2.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.000, 219.560, 107.520, 90.00, 102.02, 90.00
R / Rfree (%) 18.4 / 21.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Phers in Complex with Compound 4A (pdb code 4p75). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Phers in Complex with Compound 4A, PDB code: 4p75:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4p75

Go back to Fluorine Binding Sites List in 4p75
Fluorine binding site 1 out of 6 in the Phers in Complex with Compound 4A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Phers in Complex with Compound 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:61.4
occ:1.00
 F2 C:2NM301 0.0 61.4 1.0
C10 C:2NM301 1.3 56.1 1.0
F C:2NM301 2.1 59.2 1.0
F1 C:2NM301 2.1 55.7 1.0
C9 C:2NM301 2.3 48.7 1.0
N C:2NM301 3.1 47.9 1.0
C8 C:2NM301 3.3 44.4 1.0
CD1 C:LEU133 3.3 49.3 1.0
CB C:ALA226 4.0 41.3 1.0
CD2 C:LEU133 4.0 51.3 1.0
CG C:LEU133 4.1 49.5 1.0
CB C:GLN95 4.1 45.4 1.0
CG2 C:VAL207 4.2 45.7 1.0
N1 C:2NM301 4.2 47.9 1.0
C7 C:2NM301 4.3 45.7 1.0
CG1 C:VAL207 4.5 45.5 1.0
CB C:LEU133 4.5 44.9 1.0
CD C:GLN95 4.6 79.2 1.0
CE C:MET99 4.7 53.2 1.0
CG C:GLN95 4.7 59.0 1.0
NE2 C:GLN95 4.8 57.6 1.0
CG1 C:VAL211 4.8 47.3 1.0
SD C:MET99 4.9 56.8 1.0
OE1 C:GLN95 5.0 88.5 1.0
CB C:VAL207 5.0 46.0 1.0

Fluorine binding site 2 out of 6 in 4p75

Go back to Fluorine Binding Sites List in 4p75
Fluorine binding site 2 out of 6 in the Phers in Complex with Compound 4A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Phers in Complex with Compound 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:59.2
occ:1.00
 F C:2NM301 0.0 59.2 1.0
C10 C:2NM301 1.3 56.1 1.0
F2 C:2NM301 2.1 61.4 1.0
F1 C:2NM301 2.2 55.7 1.0
C9 C:2NM301 2.3 48.7 1.0
C8 C:2NM301 2.9 44.4 1.0
CG1 C:VAL211 3.4 47.3 1.0
N C:2NM301 3.5 47.9 1.0
CD2 C:LEU64 3.7 63.3 1.0
CG1 C:VAL207 3.9 45.5 1.0
CB C:PHE171 4.1 52.0 1.0
C7 C:2NM301 4.2 45.7 1.0
O C:PHE171 4.3 55.3 1.0
N1 C:2NM301 4.4 47.9 1.0
CB C:VAL211 4.4 49.2 1.0
CG2 C:VAL207 4.5 45.7 1.0
CG2 C:VAL211 4.6 49.1 1.0
CB C:VAL207 4.8 46.0 1.0
CB C:ALA226 4.9 41.3 1.0
CE C:MET99 4.9 53.2 1.0
CG C:PHE171 4.9 53.4 1.0
C C:PHE171 5.0 55.0 1.0

Fluorine binding site 3 out of 6 in 4p75

Go back to Fluorine Binding Sites List in 4p75
Fluorine binding site 3 out of 6 in the Phers in Complex with Compound 4A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Phers in Complex with Compound 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:55.7
occ:1.00
 F1 C:2NM301 0.0 55.7 1.0
C10 C:2NM301 1.3 56.1 1.0
F2 C:2NM301 2.1 61.4 1.0
F C:2NM301 2.2 59.2 1.0
C9 C:2NM301 2.3 48.7 1.0
N C:2NM301 2.7 47.9 1.0
CD2 C:LEU64 3.2 63.3 1.0
C8 C:2NM301 3.7 44.4 1.0
CB C:GLN95 3.8 45.4 1.0
N1 C:2NM301 4.0 47.9 1.0
O C:SER92 4.1 49.4 1.0
CG2 C:VAL96 4.2 40.8 1.0
CB C:SER92 4.4 52.9 1.0
CE C:MET99 4.5 53.2 1.0
CG1 C:VAL211 4.5 47.3 1.0
C7 C:2NM301 4.5 45.7 1.0
N C:VAL96 4.6 41.3 1.0
OE1 C:GLN95 4.6 88.5 1.0
CG C:LEU64 4.6 61.1 1.0
C C:GLN95 4.7 48.0 1.0
CA C:SER92 4.7 46.9 1.0
C C:SER92 4.7 51.7 1.0
CD C:GLN95 4.7 79.2 1.0
CG C:GLN95 4.8 59.0 1.0
CA C:GLN95 4.8 45.8 1.0

Fluorine binding site 4 out of 6 in 4p75

Go back to Fluorine Binding Sites List in 4p75
Fluorine binding site 4 out of 6 in the Phers in Complex with Compound 4A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Phers in Complex with Compound 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:58.7
occ:1.00
 F2 D:2NM301 0.0 58.7 1.0
C10 D:2NM301 1.3 55.8 1.0
F D:2NM301 2.1 63.2 1.0
F1 D:2NM301 2.1 55.5 1.0
C9 D:2NM301 2.3 45.3 1.0
C8 D:2NM301 3.2 41.9 1.0
N D:2NM301 3.2 41.5 1.0
CD1 D:LEU133 3.4 44.4 1.0
CG2 D:VAL207 4.0 45.2 1.0
CB D:ALA226 4.0 41.5 1.0
CD2 D:LEU133 4.2 48.2 1.0
CG1 D:VAL207 4.2 46.7 1.0
N1 D:2NM301 4.3 42.0 1.0
CG D:LEU133 4.3 45.3 1.0
C7 D:2NM301 4.3 41.2 1.0
CB D:GLN95 4.5 53.4 1.0
CG1 D:VAL211 4.6 42.3 1.0
CE D:MET99 4.7 63.1 1.0
CB D:LEU133 4.7 41.8 1.0
CB D:VAL207 4.8 46.4 1.0
SD D:MET99 4.9 65.7 1.0
CD D:GLN95 4.9 83.3 1.0
CD2 D:LEU64 5.0 49.3 1.0

Fluorine binding site 5 out of 6 in 4p75

Go back to Fluorine Binding Sites List in 4p75
Fluorine binding site 5 out of 6 in the Phers in Complex with Compound 4A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Phers in Complex with Compound 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:63.2
occ:1.00
 F D:2NM301 0.0 63.2 1.0
C10 D:2NM301 1.3 55.8 1.0
F2 D:2NM301 2.1 58.7 1.0
F1 D:2NM301 2.1 55.5 1.0
C9 D:2NM301 2.3 45.3 1.0
C8 D:2NM301 3.0 41.9 1.0
CG1 D:VAL211 3.3 42.3 1.0
CD2 D:LEU64 3.4 49.3 1.0
N D:2NM301 3.4 41.5 1.0
CB D:PHE171 3.9 49.3 1.0
CG1 D:VAL207 4.2 46.7 1.0
C7 D:2NM301 4.2 41.2 1.0
O D:PHE171 4.3 51.5 1.0
N1 D:2NM301 4.4 42.0 1.0
CB D:VAL211 4.4 44.0 1.0
CG2 D:VAL211 4.5 43.4 1.0
CG D:PHE171 4.7 49.5 1.0
CG D:LEU64 4.8 49.6 1.0
CE D:MET99 4.8 63.1 1.0
CD1 D:PHE171 4.9 50.0 1.0
CG2 D:VAL207 4.9 45.2 1.0
CA D:PHE171 5.0 48.6 1.0

Fluorine binding site 6 out of 6 in 4p75

Go back to Fluorine Binding Sites List in 4p75
Fluorine binding site 6 out of 6 in the Phers in Complex with Compound 4A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Phers in Complex with Compound 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:55.5
occ:1.00
 F1 D:2NM301 0.0 55.5 1.0
C10 D:2NM301 1.3 55.8 1.0
F2 D:2NM301 2.1 58.7 1.0
F D:2NM301 2.1 63.2 1.0
C9 D:2NM301 2.3 45.3 1.0
N D:2NM301 2.7 41.5 1.0
CD2 D:LEU64 3.3 49.3 1.0
CB D:GLN95 3.7 53.4 1.0
C8 D:2NM301 3.7 41.9 1.0
N1 D:2NM301 4.0 42.0 1.0
O D:SER92 4.1 53.2 1.0
CG2 D:VAL96 4.2 51.0 1.0
CE D:MET99 4.4 63.1 1.0
N D:VAL96 4.5 48.9 1.0
C7 D:2NM301 4.5 41.2 1.0
C D:GLN95 4.5 55.2 1.0
CB D:SER92 4.6 51.2 1.0
CG1 D:VAL211 4.6 42.3 1.0
OE1 D:GLN95 4.6 91.6 1.0
CD D:GLN95 4.7 83.3 1.0
CG D:GLN95 4.7 66.4 1.0
CA D:GLN95 4.7 52.8 1.0
CG D:LEU64 4.7 49.6 1.0
C D:SER92 4.7 53.1 1.0
CA D:SER92 4.8 47.9 1.0
O D:GLN95 5.0 55.6 1.0

Reference:

A.Abibi, A.D.Ferguson, P.R.Fleming, N.Gao, L.I.Hajec, J.Hu, V.A.Laganas, D.C.Mckinney, S.M.Mcleod, D.B.Prince, A.B.Shapiro, E.T.Buurman. The Role of A Novel Auxiliary Pocket in Bacterial Phenylalanyl-Trna Synthetase Druggability. J.Biol.Chem. V. 289 21651 2014.
ISSN: ESSN 1083-351X
PubMed: 24936059
DOI: 10.1074/JBC.M114.574061
Page generated: Thu Aug 1 04:46:12 2024

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