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Fluorine in PDB 1xxv: Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites

Enzymatic activity of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites

All present enzymatic activity of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites:
3.1.3.48;

Protein crystallography data

The structure of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites, PDB code: 1xxv was solved by M.I.Ivanov, J.A.Stuckey, H.L.Schubert, M.A.Saper, J.B.Bliska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.130, 47.170, 71.820, 104.45, 115.05, 89.97
R / Rfree (%) 17.8 / 22.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites (pdb code 1xxv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites, PDB code: 1xxv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 1xxv

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Fluorine binding site 1 out of 8 in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F105

b:36.8
occ:1.00
 F1 C:FTY105 0.0 36.8 1.0
C1 C:FTY105 1.4 35.8 1.0
F2 C:FTY105 2.1 36.6 1.0
CZ C:FTY105 2.5 39.8 1.0
P C:FTY105 2.5 31.8 1.0
O3P C:FTY105 2.8 29.3 1.0
CE2 C:FTY105 2.9 42.3 1.0
O1P C:FTY105 2.9 31.0 1.0
O A:HOH632 3.3 15.6 1.0
CB A:ASP356 3.4 34.0 1.0
N A:GLN357 3.5 34.0 1.0
CE1 C:FTY105 3.7 42.1 1.0
O2P C:FTY105 3.7 27.0 1.0
CG A:GLN357 3.8 43.0 1.0
NH2 A:ARG409 3.9 16.2 1.0
CA A:ASP356 4.1 31.7 1.0
C A:ASP356 4.2 32.4 1.0
CD2 C:FTY105 4.3 44.8 1.0
CA A:GLN357 4.3 36.5 1.0
CG A:ASP356 4.3 37.6 1.0
OD1 A:ASP356 4.3 38.2 1.0
NE A:ARG409 4.4 14.8 1.0
CZ A:ARG409 4.5 15.4 1.0
CB A:GLN357 4.6 39.1 1.0
CD1 C:FTY105 4.8 45.1 1.0
OE1 A:GLN446 4.9 37.9 1.0
CD A:GLN357 5.0 45.3 1.0
NE2 A:GLN446 5.0 37.5 1.0
O A:HOH785 5.0 24.6 1.0

Fluorine binding site 2 out of 8 in 1xxv

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Fluorine binding site 2 out of 8 in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F105

b:36.6
occ:1.00
 F2 C:FTY105 0.0 36.6 1.0
C1 C:FTY105 1.4 35.8 1.0
F1 C:FTY105 2.1 36.8 1.0
CZ C:FTY105 2.3 39.8 1.0
P C:FTY105 2.6 31.8 1.0
O A:HOH632 2.7 15.6 1.0
CE1 C:FTY105 2.8 42.1 1.0
O3P C:FTY105 3.0 29.3 1.0
O2P C:FTY105 3.1 27.0 1.0
OE1 A:GLN446 3.5 37.9 1.0
CE2 C:FTY105 3.5 42.3 1.0
CD A:GLN446 3.6 35.3 1.0
NE2 A:GLN446 3.6 37.5 1.0
O1P C:FTY105 3.8 31.0 1.0
CA A:GLY408 3.9 14.8 1.0
N A:GLY408 4.1 15.4 1.0
CD1 C:FTY105 4.1 45.1 1.0
CG A:GLN357 4.2 43.0 1.0
CB A:GLN446 4.2 26.8 1.0
N A:GLN357 4.3 34.0 1.0
CG A:GLN446 4.5 32.1 1.0
CG2 A:VAL407 4.5 15.7 1.0
CA A:GLN357 4.5 36.5 1.0
CD2 C:FTY105 4.7 44.8 1.0
N A:ARG409 4.9 14.7 1.0
CG C:FTY105 4.9 47.1 1.0
CB A:GLN357 5.0 39.1 1.0
C A:GLY408 5.0 14.4 1.0

Fluorine binding site 3 out of 8 in 1xxv

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Fluorine binding site 3 out of 8 in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F5

b:27.7
occ:1.00
 F1 D:FTY5 0.0 27.7 1.0
C1 D:FTY5 1.4 26.5 1.0
F2 D:FTY5 2.1 26.4 1.0
CZ D:FTY5 2.4 27.5 1.0
P D:FTY5 2.5 24.6 1.0
O1P D:FTY5 2.7 25.1 1.0
O3P D:FTY5 3.0 20.3 1.0
CE1 D:FTY5 3.0 28.2 1.0
NZ A:LYS342 3.4 20.9 1.0
CE2 D:FTY5 3.4 27.5 1.0
CE A:LYS342 3.6 17.7 1.0
OE2 D:GLU4 3.7 42.1 1.0
O2P D:FTY5 3.7 24.1 1.0
CD D:GLU4 4.0 41.3 1.0
CD A:LYS342 4.1 18.9 1.0
CD1 D:FTY5 4.3 29.1 1.0
OE1 D:GLU4 4.4 41.2 1.0
CD2 D:FTY5 4.6 29.2 1.0
CG D:GLU4 4.6 39.5 1.0
CG D:FTY5 5.0 29.2 1.0

Fluorine binding site 4 out of 8 in 1xxv

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Fluorine binding site 4 out of 8 in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F5

b:26.4
occ:1.00
 F2 D:FTY5 0.0 26.4 1.0
C1 D:FTY5 1.4 26.5 1.0
F1 D:FTY5 2.1 27.7 1.0
CZ D:FTY5 2.4 27.5 1.0
P D:FTY5 2.6 24.6 1.0
CE2 D:FTY5 2.6 27.5 1.0
O3P D:FTY5 2.8 20.3 1.0
O2P D:FTY5 3.3 24.1 1.0
CA A:SER388 3.3 15.1 1.0
CB A:SER388 3.6 13.1 1.0
CE1 D:FTY5 3.7 28.2 1.0
O1P D:FTY5 3.7 25.1 1.0
OG A:SER388 3.8 4.5 1.0
N A:SER388 4.0 15.0 1.0
CD2 D:FTY5 4.0 29.2 1.0
O A:LYS386 4.2 15.9 1.0
N A:SER389 4.3 20.1 1.0
C A:SER388 4.3 17.1 1.0
O A:GLY387 4.4 14.6 1.0
C A:GLY387 4.4 13.8 1.0
CD1 D:FTY5 4.8 29.1 1.0
OE1 D:GLU4 4.9 41.2 1.0
CB A:LYS386 4.9 15.7 1.0
CG D:FTY5 4.9 29.2 1.0
CD D:GLU4 4.9 41.3 1.0
C A:LYS386 5.0 15.4 1.0

Fluorine binding site 5 out of 8 in 1xxv

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Fluorine binding site 5 out of 8 in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F105

b:43.9
occ:1.00
 F1 E:FTY105 0.0 43.9 1.0
C1 E:FTY105 1.4 43.6 1.0
F2 E:FTY105 2.1 44.6 1.0
P E:FTY105 2.5 41.2 1.0
CZ E:FTY105 2.5 44.2 1.0
O3P E:FTY105 2.8 41.1 1.0
O1P E:FTY105 2.9 41.6 1.0
CE2 E:FTY105 2.9 45.2 1.0
O E:HOH783 3.3 27.5 1.0
CB B:ASP356 3.4 34.2 1.0
N B:GLN357 3.6 33.2 1.0
CE1 E:FTY105 3.7 44.9 1.0
O2P E:FTY105 3.7 39.9 1.0
NH2 B:ARG409 3.8 14.8 1.0
O B:HOH532 3.9 35.1 1.0
CG B:GLN357 3.9 41.6 1.0
CA B:ASP356 4.1 32.0 1.0
CD2 E:FTY105 4.3 45.9 1.0
CG B:ASP356 4.3 38.4 1.0
C B:ASP356 4.3 31.8 1.0
OD1 B:ASP356 4.3 41.6 1.0
NE B:ARG409 4.3 15.5 1.0
CZ B:ARG409 4.4 15.3 1.0
CA B:GLN357 4.4 35.2 1.0
CB B:GLN357 4.8 37.3 1.0
CD1 E:FTY105 4.8 45.8 1.0

Fluorine binding site 6 out of 8 in 1xxv

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Fluorine binding site 6 out of 8 in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F105

b:44.6
occ:1.00
 F2 E:FTY105 0.0 44.6 1.0
C1 E:FTY105 1.4 43.6 1.0
F1 E:FTY105 2.1 43.9 1.0
CZ E:FTY105 2.3 44.2 1.0
P E:FTY105 2.6 41.2 1.0
O E:HOH783 2.7 27.5 1.0
CE1 E:FTY105 2.8 44.9 1.0
O3P E:FTY105 2.9 41.1 1.0
O2P E:FTY105 3.1 39.9 1.0
OE1 B:GLN446 3.5 38.1 1.0
CE2 E:FTY105 3.5 45.2 1.0
NE2 B:GLN446 3.6 35.4 1.0
CD B:GLN446 3.6 34.5 1.0
O1P E:FTY105 3.8 41.6 1.0
CA B:GLY408 4.0 14.3 1.0
CG B:GLN357 4.1 41.6 1.0
CD1 E:FTY105 4.1 45.8 1.0
N B:GLY408 4.2 14.2 1.0
N B:GLN357 4.3 33.2 1.0
CB B:GLN446 4.3 26.9 1.0
CA B:GLN357 4.5 35.2 1.0
CG B:GLN446 4.5 31.4 1.0
CG2 B:VAL407 4.6 13.7 1.0
CD2 E:FTY105 4.6 45.9 1.0
CG E:FTY105 4.9 46.7 1.0
CB B:GLN357 4.9 37.3 1.0
CD B:GLN357 5.0 45.0 1.0

Fluorine binding site 7 out of 8 in 1xxv

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Fluorine binding site 7 out of 8 in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F5

b:28.4
occ:1.00
 F1 F:FTY5 0.0 28.4 1.0
C1 F:FTY5 1.4 26.2 1.0
F2 F:FTY5 2.1 24.5 1.0
CZ F:FTY5 2.4 26.9 1.0
P F:FTY5 2.4 24.9 1.0
O1P F:FTY5 2.7 25.9 1.0
O3P F:FTY5 2.9 23.0 1.0
CE1 F:FTY5 3.2 28.1 1.0
CE2 F:FTY5 3.3 27.2 1.0
NZ B:LYS342 3.6 22.1 1.0
O2P F:FTY5 3.7 22.9 1.0
CE B:LYS342 3.8 21.1 1.0
OE1 F:GLU4 4.0 40.8 1.0
CD F:GLU4 4.2 40.2 1.0
CD B:LYS342 4.3 21.4 1.0
OE2 F:GLU4 4.4 40.1 1.0
CD1 F:FTY5 4.4 28.6 1.0
CD2 F:FTY5 4.5 27.7 1.0
CG F:GLU4 5.0 38.8 1.0

Fluorine binding site 8 out of 8 in 1xxv

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Fluorine binding site 8 out of 8 in the Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Yersinia Yoph (Residues 163-468) Binds Phosphonodifluoromethyl-Phe Containing Hexapeptide at Two Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F5

b:24.5
occ:1.00
 F2 F:FTY5 0.0 24.5 1.0
C1 F:FTY5 1.4 26.2 1.0
F1 F:FTY5 2.1 28.4 1.0
CZ F:FTY5 2.4 26.9 1.0
P F:FTY5 2.6 24.9 1.0
CE2 F:FTY5 2.6 27.2 1.0
O3P F:FTY5 2.7 23.0 1.0
CA B:SER388 3.1 14.9 1.0
O2P F:FTY5 3.2 22.9 1.0
CB B:SER388 3.4 11.9 1.0
OG B:SER388 3.6 5.3 1.0
CE1 F:FTY5 3.7 28.1 1.0
O1P F:FTY5 3.7 25.9 1.0
N B:SER388 3.8 16.6 1.0
CD2 F:FTY5 4.0 27.7 1.0
N B:SER389 4.2 18.7 1.0
C B:SER388 4.2 17.2 1.0
O B:LYS386 4.2 18.2 1.0
O B:GLY387 4.3 17.4 1.0
C B:GLY387 4.3 15.7 1.0
CD1 F:FTY5 4.7 28.6 1.0
OE1 F:GLU4 4.8 40.8 1.0
CB B:LYS386 4.8 15.7 1.0
CG F:FTY5 4.9 28.3 1.0
C B:LYS386 4.9 16.6 1.0

Reference:

M.I.Ivanov, J.A.Stuckey, H.L.Schubert, M.A.Saper, J.B.Bliska. Two Substrate-Targeting Sites in the Yersinia Protein Tyrosine Phosphatase Co-Operate to Promote Bacterial Virulence Mol.Microbiol. V. 55 1346 2005.
ISSN: ISSN 0950-382X
PubMed: 15720545
DOI: 10.1111/J.1365-2958.2005.04477.X
Page generated: Wed Jul 31 13:28:58 2024

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