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Fluorine in PDB 1qz0: Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide

Enzymatic activity of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide

All present enzymatic activity of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide, PDB code: 1qz0 was solved by J.Phan, K.Lee, S.Cherry, J.E.Tropea, T.R.Burke Jr, D.S.Waugh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.292, 53.450, 69.066, 109.61, 104.75, 89.98
R / Rfree (%) 18.8 / 20.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide (pdb code 1qz0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide, PDB code: 1qz0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 1qz0

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Fluorine binding site 1 out of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide


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 the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F505

b:22.6
occ:1.00
 F1 C:FTY505 0.0 22.6 1.0
C1 C:FTY505 1.4 19.6 1.0
CZ C:FTY505 2.2 20.8 1.0
F2 C:FTY505 2.3 22.0 1.0
CE2 C:FTY505 2.6 19.7 1.0
P C:FTY505 2.7 18.2 1.0
NE2 A:GLN357 3.0 35.3 1.0
O1P C:FTY505 3.1 16.8 1.0
O2P C:FTY505 3.1 17.1 1.0
CB A:ASP356 3.4 26.5 1.0
O C:HOH61 3.4 18.4 1.0
CE1 C:FTY505 3.5 21.4 1.0
N A:GLN357 3.8 26.1 1.0
O3P C:FTY505 3.9 16.9 1.0
CD2 C:FTY505 4.0 20.7 1.0
NH2 A:ARG409 4.0 13.5 1.0
CD A:GLN357 4.1 34.0 1.0
CA A:ASP356 4.1 24.1 1.0
OD2 A:ASP356 4.3 31.7 1.0
CG A:GLN357 4.3 32.0 1.0
CG A:ASP356 4.4 29.7 1.0
C A:ASP356 4.4 25.1 1.0
CD1 C:FTY505 4.6 22.1 1.0
NE A:ARG409 4.6 11.4 1.0
CA A:GLN357 4.6 26.8 1.0
CZ A:ARG409 4.6 11.7 1.0
NE2 A:GLN446 4.7 28.6 1.0
CG C:FTY505 4.8 21.5 1.0

Fluorine binding site 2 out of 8 in 1qz0

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Fluorine binding site 2 out of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide


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 the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F505

b:22.0
occ:1.00
 F2 C:FTY505 0.0 22.0 1.0
C1 C:FTY505 1.4 19.6 1.0
CZ C:FTY505 2.2 20.8 1.0
F1 C:FTY505 2.3 22.6 1.0
CE1 C:FTY505 2.6 21.4 1.0
P C:FTY505 2.7 18.2 1.0
O C:HOH61 3.0 18.4 1.0
NE2 A:GLN446 3.0 28.6 1.0
O2P C:FTY505 3.1 17.1 1.0
O3P C:FTY505 3.2 16.9 1.0
NE2 A:GLN357 3.3 35.3 1.0
CE2 C:FTY505 3.5 19.7 1.0
CD A:GLN446 3.9 28.8 1.0
O1P C:FTY505 3.9 16.8 1.0
CA A:GLY408 3.9 11.0 1.0
CD1 C:FTY505 4.0 22.1 1.0
N A:GLY408 4.0 10.4 1.0
CG2 A:VAL407 4.3 13.2 1.0
CB A:GLN446 4.3 22.2 1.0
CD A:GLN357 4.4 34.0 1.0
CG A:GLN446 4.5 25.3 1.0
OE1 A:GLN446 4.6 32.3 1.0
N A:GLN357 4.6 26.1 1.0
CD2 C:FTY505 4.6 20.7 1.0
CG C:FTY505 4.8 21.5 1.0
CA A:GLN357 4.9 26.8 1.0

Fluorine binding site 3 out of 8 in 1qz0

Go back to Fluorine Binding Sites List in 1qz0
Fluorine binding site 3 out of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide


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 the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F605

b:23.0
occ:1.00
 F1 D:FTY605 0.0 23.0 1.0
C1 D:FTY605 1.4 18.6 1.0
CZ D:FTY605 2.2 17.4 1.0
F2 D:FTY605 2.3 18.8 1.0
P D:FTY605 2.7 16.2 1.0
CE2 D:FTY605 2.7 16.6 1.0
O1P D:FTY605 2.9 17.4 1.0
OE1 D:GLU604 3.0 23.4 1.0
O A:HOH524 3.2 22.3 1.0
O2P D:FTY605 3.3 16.1 1.0
NZ A:LYS342 3.4 24.3 1.0
CE1 D:FTY605 3.4 15.8 1.0
O3P D:FTY605 3.9 13.6 1.0
CD D:GLU604 4.0 23.7 1.0
CD2 D:FTY605 4.0 16.9 1.0
O D:HOH610 4.2 28.8 1.0
O A:HOH690 4.3 29.7 1.0
CD1 D:FTY605 4.5 15.1 1.0
OE2 D:GLU604 4.7 23.4 1.0
CE A:LYS342 4.8 23.4 1.0
CG D:GLU604 4.8 20.7 1.0
CG D:FTY605 4.8 13.4 1.0
NH2 A:ARG278 4.9 13.7 1.0

Fluorine binding site 4 out of 8 in 1qz0

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Fluorine binding site 4 out of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide


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 the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F605

b:18.8
occ:1.00
 F2 D:FTY605 0.0 18.8 1.0
C1 D:FTY605 1.4 18.6 1.0
CZ D:FTY605 2.3 17.4 1.0
F1 D:FTY605 2.3 23.0 1.0
CE1 D:FTY605 2.6 15.8 1.0
P D:FTY605 2.7 16.2 1.0
O2P D:FTY605 3.0 16.1 1.0
CA A:SER388 3.2 13.8 1.0
O3P D:FTY605 3.4 13.6 1.0
CE2 D:FTY605 3.6 16.6 1.0
CB A:SER388 3.6 13.0 1.0
N A:SER388 3.8 13.4 1.0
O1P D:FTY605 3.9 17.4 1.0
OG A:SER388 4.0 13.4 1.0
CD1 D:FTY605 4.0 15.1 1.0
O A:GLY387 4.1 14.1 1.0
C A:GLY387 4.2 13.9 1.0
O A:LYS386 4.3 15.0 1.0
N A:SER389 4.3 15.3 1.0
C A:SER388 4.3 15.0 1.0
OE1 D:GLU604 4.5 23.4 1.0
CD2 D:FTY605 4.7 16.9 1.0
O D:HOH610 4.8 28.8 1.0
CG D:FTY605 4.9 13.4 1.0
O D:HOH615 4.9 33.5 1.0
C A:LYS386 4.9 14.8 1.0
CD D:GLU604 5.0 23.7 1.0

Fluorine binding site 5 out of 8 in 1qz0

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Fluorine binding site 5 out of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide


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 the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F505

b:23.8
occ:1.00
 F1 E:FTY505 0.0 23.8 1.0
C1 E:FTY505 1.4 20.4 1.0
CZ E:FTY505 2.3 21.6 1.0
F2 E:FTY505 2.3 22.7 1.0
CE2 E:FTY505 2.7 20.6 1.0
P E:FTY505 2.7 18.6 1.0
NE2 B:GLN357 3.0 36.5 1.0
O1P E:FTY505 3.1 17.3 1.0
O2P E:FTY505 3.1 16.1 1.0
CB B:ASP356 3.4 27.1 1.0
O E:HOH138 3.4 19.7 1.0
CE1 E:FTY505 3.5 21.9 1.0
N B:GLN357 3.7 27.9 1.0
O3P E:FTY505 3.9 16.4 1.0
NH2 B:ARG409 4.0 13.9 1.0
CD2 E:FTY505 4.0 21.6 1.0
CD B:GLN357 4.1 34.7 1.0
CA B:ASP356 4.1 25.3 1.0
OD2 B:ASP356 4.2 32.5 1.0
CG B:GLN357 4.2 33.4 1.0
CG B:ASP356 4.3 30.8 1.0
C B:ASP356 4.3 26.6 1.0
CA B:GLN357 4.6 28.0 1.0
NE B:ARG409 4.6 11.5 1.0
CD1 E:FTY505 4.6 23.2 1.0
CZ B:ARG409 4.6 12.8 1.0
NE2 B:GLN446 4.7 28.6 1.0
CG E:FTY505 4.8 21.9 1.0

Fluorine binding site 6 out of 8 in 1qz0

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Fluorine binding site 6 out of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide


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 the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F505

b:22.7
occ:1.00
 F2 E:FTY505 0.0 22.7 1.0
C1 E:FTY505 1.4 20.4 1.0
CZ E:FTY505 2.3 21.6 1.0
F1 E:FTY505 2.3 23.8 1.0
CE1 E:FTY505 2.6 21.9 1.0
P E:FTY505 2.7 18.6 1.0
O E:HOH138 2.9 19.7 1.0
NE2 B:GLN446 3.0 28.6 1.0
O2P E:FTY505 3.1 16.1 1.0
O3P E:FTY505 3.2 16.4 1.0
NE2 B:GLN357 3.3 36.5 1.0
CE2 E:FTY505 3.5 20.6 1.0
O1P E:FTY505 3.9 17.3 1.0
CD B:GLN446 3.9 29.1 1.0
CA B:GLY408 3.9 12.1 1.0
CD1 E:FTY505 4.0 23.2 1.0
N B:GLY408 4.1 11.4 1.0
CG2 B:VAL407 4.3 12.0 1.0
CB B:GLN446 4.3 22.5 1.0
CD B:GLN357 4.4 34.7 1.0
N B:GLN357 4.5 27.9 1.0
CG B:GLN446 4.6 26.4 1.0
OE1 B:GLN446 4.6 33.3 1.0
CD2 E:FTY505 4.7 21.6 1.0
CG E:FTY505 4.8 21.9 1.0
CA B:GLN357 4.9 28.0 1.0

Fluorine binding site 7 out of 8 in 1qz0

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Fluorine binding site 7 out of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide


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 the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F605

b:22.8
occ:1.00
 F1 F:FTY605 0.0 22.8 1.0
C1 F:FTY605 1.4 18.8 1.0
CZ F:FTY605 2.2 16.6 1.0
F2 F:FTY605 2.3 19.7 1.0
P F:FTY605 2.7 17.7 1.0
CE2 F:FTY605 2.7 16.4 1.0
O1P F:FTY605 2.9 17.4 1.0
OE1 F:GLU604 3.0 24.2 1.0
O B:HOH534 3.1 22.0 1.0
O2P F:FTY605 3.3 17.8 1.0
NZ B:LYS342 3.4 25.5 1.0
CE1 F:FTY605 3.4 14.8 1.0
O3P F:FTY605 3.9 15.8 1.0
CD F:GLU604 4.0 23.6 1.0
CD2 F:FTY605 4.0 16.5 1.0
O F:HOH210 4.0 23.3 1.0
O F:HOH519 4.4 28.2 1.0
CD1 F:FTY605 4.5 14.4 1.0
OE2 F:GLU604 4.7 23.8 1.0
CE B:LYS342 4.7 22.0 1.0
CG F:GLU604 4.8 21.6 1.0
CG F:FTY605 4.8 14.2 1.0
NH2 B:ARG278 4.9 14.5 1.0
CG B:LYS342 4.9 16.8 1.0
CD B:LYS342 5.0 20.3 1.0

Fluorine binding site 8 out of 8 in 1qz0

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Fluorine binding site 8 out of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F605

b:19.7
occ:1.00
 F2 F:FTY605 0.0 19.7 1.0
C1 F:FTY605 1.4 18.8 1.0
CZ F:FTY605 2.3 16.6 1.0
F1 F:FTY605 2.3 22.8 1.0
CE1 F:FTY605 2.6 14.8 1.0
P F:FTY605 2.7 17.7 1.0
O2P F:FTY605 3.0 17.8 1.0
CA B:SER388 3.2 13.9 1.0
O3P F:FTY605 3.4 15.8 1.0
CE2 F:FTY605 3.6 16.4 1.0
CB B:SER388 3.6 13.2 1.0
O1P F:FTY605 3.9 17.4 1.0
N B:SER388 3.9 13.4 1.0
OG B:SER388 4.0 13.3 1.0
CD1 F:FTY605 4.0 14.4 1.0
O B:GLY387 4.2 14.5 1.0
C B:GLY387 4.3 13.7 1.0
N B:SER389 4.3 15.8 1.0
C B:SER388 4.3 14.9 1.0
O B:LYS386 4.4 15.4 1.0
OE1 F:GLU604 4.4 24.2 1.0
O F:HOH210 4.5 23.3 1.0
CD2 F:FTY605 4.7 16.5 1.0
CG F:FTY605 4.9 14.2 1.0
CD F:GLU604 5.0 23.6 1.0

Reference:

J.Phan, K.Lee, S.Cherry, J.E.Tropea, T.R.Burke Jr, D.S.Waugh. High-Resolution Structure of the Yersinia Pestis Protein Tyrosine Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide Biochemistry V. 42 13113 2003.
ISSN: ISSN 0006-2960
PubMed: 14609321
DOI: 10.1021/BI030156M
Page generated: Sun Dec 13 11:32:18 2020

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