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Fluorine in PDB 1a08: C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine)

Enzymatic activity of C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine)

All present enzymatic activity of C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine):
2.7.1.112;

Protein crystallography data

The structure of C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine), PDB code: 1a08 was solved by L.Shewchuk, S.Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.900, 67.400, 75.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / n/a

Fluorine Binding Sites:

The binding sites of Fluorine atom in the C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine) (pdb code 1a08). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine), PDB code: 1a08:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1a08

Go back to Fluorine Binding Sites List in 1a08
Fluorine binding site 1 out of 4 in the C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:23.5
occ:1.00
 F1 C:FTY101 0.0 23.5 1.0
C1 C:FTY101 1.4 13.1 1.0
HG A:SER180 1.8 0.0 1.0
F2 C:FTY101 2.1 17.9 1.0
CZ C:FTY101 2.4 12.9 1.0
OG A:SER180 2.6 26.8 1.0
P C:FTY101 2.6 13.4 1.0
HG1 A:THR183 2.8 0.0 1.0
O2P C:FTY101 2.9 20.9 1.0
O1P C:FTY101 2.9 14.9 1.0
CE1 C:FTY101 3.0 9.1 1.0
H A:THR183 3.4 0.0 1.0
H A:THR182 3.5 0.0 1.0
CE2 C:FTY101 3.6 12.5 1.0
OG1 A:THR183 3.6 34.4 1.0
CB A:SER180 3.7 17.1 1.0
O3P C:FTY101 3.8 10.0 1.0
HZ2 A:LYS206 3.8 0.0 1.0
CE A:LYS206 3.8 20.8 1.0
CG2 A:THR182 3.9 33.5 1.0
CB A:THR182 3.9 30.3 1.0
H2 C:HOH517 4.1 0.0 1.0
H A:GLU181 4.1 0.0 1.0
N A:THR183 4.2 30.3 1.0
NZ A:LYS206 4.3 23.4 1.0
OE1 B:GLU160 4.3 62.2 1.0
CA A:SER180 4.3 20.9 1.0
CB A:THR183 4.3 30.5 1.0
CD1 C:FTY101 4.3 16.0 1.0
N A:THR182 4.3 30.4 1.0
HZ1 A:LYS206 4.4 0.0 1.0
N A:GLU181 4.5 29.2 1.0
HH12 A:ARG178 4.6 0.0 1.0
CA A:THR182 4.6 29.9 1.0
C A:SER180 4.7 27.0 1.0
CD2 C:FTY101 4.7 13.6 1.0
C A:THR182 4.8 31.6 1.0
HH21 A:ARG158 4.8 0.0 1.0
CA A:THR183 4.9 30.1 1.0
HH22 A:ARG178 4.9 0.0 1.0
CG A:LYS206 4.9 12.4 1.0
CD A:LYS206 5.0 16.8 1.0
O C:HOH517 5.0 39.0 1.0

Fluorine binding site 2 out of 4 in 1a08

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Fluorine binding site 2 out of 4 in the C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:17.9
occ:1.00
 F2 C:FTY101 0.0 17.9 1.0
C1 C:FTY101 1.4 13.1 1.0
F1 C:FTY101 2.1 23.5 1.0
HG A:SER180 2.3 0.0 1.0
CZ C:FTY101 2.3 12.9 1.0
CE2 C:FTY101 2.6 12.5 1.0
P C:FTY101 2.7 13.4 1.0
O1P C:FTY101 2.9 14.9 1.0
OG A:SER180 3.2 26.8 1.0
O3P C:FTY101 3.2 10.0 1.0
CB A:CYS188 3.4 11.4 1.0
SG A:CYS188 3.6 13.1 1.0
CE1 C:FTY101 3.6 9.1 1.0
HH22 A:ARG178 3.6 0.0 1.0
CB A:SER180 3.7 17.1 1.0
HH12 A:ARG178 3.7 0.0 1.0
O2P C:FTY101 3.8 20.9 1.0
CA A:SER180 3.9 20.9 1.0
CD2 C:FTY101 3.9 13.6 1.0
H A:GLU181 4.2 0.0 1.0
NH2 A:ARG178 4.2 12.8 1.0
NH1 A:ARG178 4.2 12.9 1.0
O A:TYR187 4.3 6.3 1.0
HH21 A:ARG158 4.4 0.0 1.0
CZ A:ARG178 4.6 18.7 1.0
CA A:CYS188 4.6 6.7 1.0
CD1 C:FTY101 4.6 16.0 1.0
CE A:LYS206 4.7 20.8 1.0
HG1 A:THR183 4.7 0.0 1.0
H A:THR182 4.7 0.0 1.0
CG C:FTY101 4.8 16.5 1.0
CG A:LYS206 4.8 12.4 1.0
C A:TYR187 4.8 4.7 1.0
N A:GLU181 4.8 29.2 1.0
C A:SER180 4.8 27.0 1.0
HH21 A:ARG178 4.8 0.0 1.0
HH11 A:ARG178 4.9 0.0 1.0
H A:THR183 4.9 0.0 1.0
N A:SER180 5.0 19.4 1.0
CA A:LYS206 5.0 11.7 1.0

Fluorine binding site 3 out of 4 in 1a08

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Fluorine binding site 3 out of 4 in the C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F101

b:34.9
occ:1.00
 F1 D:FTY101 0.0 34.9 1.0
C1 D:FTY101 1.4 30.2 1.0
F2 D:FTY101 2.2 30.5 1.0
CZ D:FTY101 2.4 29.7 1.0
OG B:SER180 2.6 52.6 1.0
CE1 D:FTY101 2.7 26.0 1.0
P D:FTY101 2.7 35.3 1.0
O2P D:FTY101 2.8 38.0 1.0
HG B:SER180 2.9 0.0 1.0
H B:THR183 3.1 0.0 1.0
O1P D:FTY101 3.1 37.5 1.0
H B:THR182 3.5 0.0 1.0
CE2 D:FTY101 3.6 28.1 1.0
HZ2 B:LYS206 3.7 0.0 1.0
CB B:SER180 3.7 49.4 1.0
CE B:LYS206 3.7 31.8 1.0
CB B:THR182 3.7 68.6 1.0
O3P D:FTY101 3.9 33.1 1.0
OG1 B:THR183 3.9 74.2 1.0
HG1 B:THR182 3.9 0.0 1.0
N B:THR183 4.0 65.9 1.0
CD1 D:FTY101 4.0 26.2 1.0
OG1 B:THR182 4.2 71.4 1.0
NZ B:LYS206 4.2 39.1 1.0
CA B:SER180 4.2 52.9 1.0
N B:THR182 4.3 66.8 1.0
H B:GLU181 4.3 0.0 1.0
CB B:THR183 4.4 70.8 1.0
HZ1 B:LYS206 4.5 0.0 1.0
CA B:THR182 4.5 68.2 1.0
C B:SER180 4.6 57.3 1.0
HG1 B:THR183 4.6 0.0 1.0
N B:GLU181 4.6 60.5 1.0
CG2 B:THR182 4.7 71.2 1.0
CD2 D:FTY101 4.7 27.6 1.0
HH12 B:ARG178 4.7 0.0 1.0
CG D:FTY101 4.8 21.3 1.0
C B:THR182 4.9 67.2 1.0
HH21 B:ARG158 4.9 0.0 1.0
CD B:LYS206 4.9 26.2 1.0
CA B:THR183 4.9 66.7 1.0
CG B:LYS206 4.9 18.0 1.0

Fluorine binding site 4 out of 4 in 1a08

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Fluorine binding site 4 out of 4 in the C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of C-Src (SH2 Domain) Complexed with Ace-Difluoro Phosphotyr-Glu-(N,N- Dipentyl Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F101

b:30.5
occ:1.00
 F2 D:FTY101 0.0 30.5 1.0
C1 D:FTY101 1.4 30.2 1.0
F1 D:FTY101 2.2 34.9 1.0
CZ D:FTY101 2.4 29.7 1.0
P D:FTY101 2.7 35.3 1.0
CE2 D:FTY101 2.8 28.1 1.0
O1P D:FTY101 2.9 37.5 1.0
OG B:SER180 3.0 52.6 1.0
O3P D:FTY101 3.3 33.1 1.0
CB B:SER180 3.3 49.4 1.0
CB B:CYS188 3.4 8.8 1.0
CA B:SER180 3.4 52.9 1.0
HH12 B:ARG178 3.5 0.0 1.0
CE1 D:FTY101 3.5 26.0 1.0
HG B:SER180 3.7 0.0 1.0
SG B:CYS188 3.8 13.5 1.0
O2P D:FTY101 3.8 38.0 1.0
HH22 B:ARG178 3.8 0.0 1.0
H B:GLU181 4.0 0.0 1.0
NH1 B:ARG178 4.0 18.7 1.0
CD2 D:FTY101 4.1 27.6 1.0
O B:TYR187 4.3 12.4 1.0
NH2 B:ARG178 4.3 15.8 1.0
C B:SER180 4.4 57.3 1.0
H B:THR182 4.4 0.0 1.0
CA B:CYS188 4.4 16.1 1.0
CZ B:ARG178 4.4 17.5 1.0
HH21 B:ARG158 4.5 0.0 1.0
N B:GLU181 4.5 60.5 1.0
N B:SER180 4.6 47.9 1.0
HH11 B:ARG178 4.6 0.0 1.0
H B:THR183 4.6 0.0 1.0
CD1 D:FTY101 4.6 26.2 1.0
C B:TYR187 4.7 17.7 1.0
CE B:LYS206 4.7 31.8 1.0
N B:CYS188 4.8 14.3 1.0
CG D:FTY101 4.9 21.3 1.0
CG B:LYS206 4.9 18.0 1.0

Reference:

P.S.Charifson, L.M.Shewchuk, W.Rocque, C.W.Hummel, S.R.Jordan, C.Mohr, G.J.Pacofsky, M.R.Peel, M.Rodriguez, D.D.Sternbach, T.G.Consler. Peptide Ligands of PP60(C-Src) SH2 Domains: A Thermodynamic and Structural Study. Biochemistry V. 36 6283 1997.
ISSN: ISSN 0006-2960
PubMed: 9174343
DOI: 10.1021/BI970019N
Page generated: Wed Jul 31 10:45:31 2024

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