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Fluorine in PDB 1j97: Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase

Enzymatic activity of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase

All present enzymatic activity of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase:
3.1.3.3;

Protein crystallography data

The structure of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase, PDB code: 1j97 was solved by H.Cho, W.Wang, R.Kim, H.Yokota, S.Damo, S.-H.Kim, D.Wemmer, S.Kustu, D.Yan, Berkeley Structural Genomics Center (Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.836, 69.829, 91.625, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 20.9

Other elements in 1j97:

The structure of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase (pdb code 1j97). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase, PDB code: 1j97:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1j97

Go back to Fluorine Binding Sites List in 1j97
Fluorine binding site 1 out of 6 in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F11

b:10.4
occ:1.00
 F1 A:BFD11 0.0 10.4 1.0
BE A:BFD11 1.5 9.9 1.0
F2 A:BFD11 2.4 10.5 1.0
OD1 A:BFD11 2.4 9.7 1.0
F3 A:BFD11 2.5 9.7 1.0
NZ A:LYS144 2.8 8.0 1.0
N A:GLY100 2.9 8.7 1.0
ND2 A:ASN170 2.9 9.5 1.0
O A:HOH890 3.3 14.5 1.0
CG A:BFD11 3.6 9.5 1.0
CA A:SER99 3.6 9.4 1.0
CE A:LYS144 3.7 8.1 1.0
O A:HOH808 3.7 8.1 1.0
C A:SER99 3.8 10.4 1.0
CG A:ASN170 3.8 10.0 1.0
CA A:GLY100 3.8 9.3 1.0
OD1 A:ASN170 3.8 10.1 1.0
OG A:SER99 4.0 8.2 1.0
MG A:MG220 4.1 9.1 1.0
OD2 A:BFD11 4.2 8.7 1.0
CB A:SER99 4.3 10.6 1.0
O A:VAL98 4.4 10.4 1.0
N A:GLY101 4.5 9.1 1.0
C A:GLY100 4.5 9.6 1.0
O A:HOH817 4.6 10.7 1.0
OD1 A:ASP171 4.6 11.2 1.0
CB A:BFD11 4.7 8.8 1.0
N A:SER99 4.8 8.8 1.0
N A:PHE12 4.8 8.4 1.0
N A:ASP13 4.9 9.3 1.0
O A:SER99 5.0 9.4 1.0
O A:HOH845 5.0 10.9 1.0

Fluorine binding site 2 out of 6 in 1j97

Go back to Fluorine Binding Sites List in 1j97
Fluorine binding site 2 out of 6 in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F11

b:10.5
occ:1.00
 F2 A:BFD11 0.0 10.5 1.0
BE A:BFD11 1.5 9.9 1.0
MG A:MG220 2.0 9.1 1.0
F1 A:BFD11 2.4 10.4 1.0
F3 A:BFD11 2.5 9.7 1.0
OD1 A:BFD11 2.6 9.7 1.0
O A:HOH808 2.9 8.1 1.0
OD2 A:BFD11 2.9 8.7 1.0
O A:ASP13 3.0 10.3 1.0
CG A:BFD11 3.0 9.5 1.0
O A:HOH828 3.2 8.6 1.0
CB A:ASP13 3.3 10.1 1.0
O A:HOH890 3.3 14.5 1.0
N A:ASP13 3.5 9.3 1.0
O A:HOH817 3.5 10.7 1.0
CA A:ASP13 3.6 9.5 1.0
C A:ASP13 3.7 10.4 1.0
OD1 A:ASP167 4.1 9.0 1.0
OD1 A:ASP13 4.3 10.8 1.0
CG A:ASP13 4.3 10.3 1.0
C A:PHE12 4.4 8.9 1.0
OD1 A:ASN170 4.5 10.1 1.0
N A:PHE12 4.5 8.4 1.0
ND2 A:ASN170 4.5 9.5 1.0
CB A:BFD11 4.5 8.8 1.0
NZ A:LYS144 4.6 8.0 1.0
SD A:MET43 4.7 13.5 1.0
OE2 A:GLU20 4.8 12.4 1.0
OG A:SER99 4.9 8.2 1.0
OE1 A:GLU20 4.9 10.7 1.0
CA A:PHE12 5.0 8.4 1.0
CG A:ASN170 5.0 10.0 1.0

Fluorine binding site 3 out of 6 in 1j97

Go back to Fluorine Binding Sites List in 1j97
Fluorine binding site 3 out of 6 in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F11

b:9.7
occ:1.00
 F3 A:BFD11 0.0 9.7 1.0
BE A:BFD11 1.5 9.9 1.0
OD1 A:BFD11 2.5 9.7 1.0
F2 A:BFD11 2.5 10.5 1.0
F1 A:BFD11 2.5 10.4 1.0
OG A:SER99 2.6 8.2 1.0
N A:ASP13 2.8 9.3 1.0
N A:PHE12 3.0 8.4 1.0
CB A:SER99 3.2 10.6 1.0
CB A:PHE12 3.3 8.2 1.0
CG A:BFD11 3.4 9.5 1.0
CA A:PHE12 3.4 8.4 1.0
O A:HOH890 3.5 14.5 1.0
CA A:SER99 3.5 9.4 1.0
C A:PHE12 3.5 8.9 1.0
OD1 A:ASP13 3.5 10.8 1.0
CB A:ASP13 3.7 10.1 1.0
CA A:ASP13 3.8 9.5 1.0
OD2 A:BFD11 3.8 8.7 1.0
N A:GLY100 3.9 8.7 1.0
CG A:ASP13 3.9 10.3 1.0
C A:BFD11 4.1 8.9 1.0
MG A:MG220 4.2 9.1 1.0
C A:SER99 4.2 10.4 1.0
O A:ASP13 4.3 10.3 1.0
NZ A:LYS144 4.3 8.0 1.0
CG A:PHE12 4.4 8.9 1.0
O A:VAL98 4.4 10.4 1.0
N A:GLY101 4.5 9.1 1.0
CA A:BFD11 4.5 8.9 1.0
CB A:BFD11 4.5 8.8 1.0
C A:ASP13 4.6 10.4 1.0
CD2 A:PHE12 4.6 9.3 1.0
N A:SER99 4.6 8.8 1.0
O A:PHE12 4.7 9.0 1.0
C A:VAL98 4.9 8.9 1.0
O A:HOH808 4.9 8.1 1.0
CA A:GLY100 5.0 9.3 1.0

Fluorine binding site 4 out of 6 in 1j97

Go back to Fluorine Binding Sites List in 1j97
Fluorine binding site 4 out of 6 in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F511

b:8.9
occ:1.00
 F1 B:BFD511 0.0 8.9 1.0
BE B:BFD511 1.5 8.2 1.0
F3 B:BFD511 2.5 8.8 1.0
OD1 B:BFD511 2.5 7.7 1.0
F2 B:BFD511 2.5 9.3 1.0
OG B:SER599 2.7 8.5 1.0
N B:ASP513 2.8 8.1 1.0
N B:PHE512 3.1 8.1 1.0
CB B:SER599 3.1 9.6 1.0
CB B:PHE512 3.3 9.3 1.0
CG B:BFD511 3.4 8.0 1.0
CA B:PHE512 3.4 9.2 1.0
CA B:SER599 3.4 8.4 1.0
O B:HOH810 3.5 14.2 1.0
OD2 B:ASP513 3.5 12.0 1.0
C B:PHE512 3.5 8.2 1.0
CB B:ASP513 3.7 10.6 1.0
OD2 B:BFD511 3.8 8.4 1.0
CA B:ASP513 3.8 8.6 1.0
N B:GLY600 3.8 8.6 1.0
CG B:ASP513 3.9 10.1 1.0
C B:SER599 4.1 8.4 1.0
MG B:MG720 4.2 8.9 1.0
C B:BFD511 4.2 8.0 1.0
NZ B:LYS644 4.3 7.5 1.0
O B:VAL598 4.3 9.4 1.0
O B:ASP513 4.4 9.2 1.0
CG B:PHE512 4.4 7.6 1.0
N B:GLY601 4.5 8.7 1.0
CB B:BFD511 4.5 7.4 1.0
CA B:BFD511 4.5 7.4 1.0
N B:SER599 4.6 9.1 1.0
CD2 B:PHE512 4.6 8.7 1.0
C B:ASP513 4.6 8.8 1.0
O B:PHE512 4.7 8.4 1.0
C B:VAL598 4.9 8.6 1.0
O B:HOH809 4.9 8.0 1.0
CA B:GLY600 5.0 9.5 1.0

Fluorine binding site 5 out of 6 in 1j97

Go back to Fluorine Binding Sites List in 1j97
Fluorine binding site 5 out of 6 in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F511

b:9.3
occ:1.00
 F2 B:BFD511 0.0 9.3 1.0
BE B:BFD511 1.5 8.2 1.0
F1 B:BFD511 2.5 8.9 1.0
OD1 B:BFD511 2.5 7.7 1.0
F3 B:BFD511 2.5 8.8 1.0
NZ B:LYS644 2.7 7.5 1.0
N B:GLY600 2.9 8.6 1.0
ND2 B:ASN670 2.9 9.8 1.0
O B:HOH810 3.3 14.2 1.0
CA B:SER599 3.6 8.4 1.0
CG B:BFD511 3.6 8.0 1.0
CE B:LYS644 3.6 8.2 1.0
CG B:ASN670 3.7 11.0 1.0
C B:SER599 3.7 8.4 1.0
O B:HOH809 3.8 8.0 1.0
CA B:GLY600 3.8 9.5 1.0
OD1 B:ASN670 3.8 8.5 1.0
OG B:SER599 4.0 8.5 1.0
MG B:MG720 4.2 8.9 1.0
OD2 B:BFD511 4.2 8.4 1.0
CB B:SER599 4.3 9.6 1.0
O B:VAL598 4.4 9.4 1.0
N B:GLY601 4.5 8.7 1.0
C B:GLY600 4.6 9.3 1.0
O B:HOH833 4.6 10.3 1.0
OD1 B:ASP671 4.6 10.5 1.0
N B:SER599 4.8 9.1 1.0
CB B:BFD511 4.8 7.4 1.0
N B:PHE512 4.9 8.1 1.0
O B:SER599 4.9 9.5 1.0

Fluorine binding site 6 out of 6 in 1j97

Go back to Fluorine Binding Sites List in 1j97
Fluorine binding site 6 out of 6 in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F511

b:8.8
occ:1.00
 F3 B:BFD511 0.0 8.8 1.0
BE B:BFD511 1.5 8.2 1.0
MG B:MG720 2.0 8.9 1.0
F1 B:BFD511 2.5 8.9 1.0
F2 B:BFD511 2.5 9.3 1.0
OD1 B:BFD511 2.6 7.7 1.0
OD2 B:BFD511 2.8 8.4 1.0
O B:HOH809 2.9 8.0 1.0
O B:ASP513 3.0 9.2 1.0
CG B:BFD511 3.1 8.0 1.0
O B:HOH821 3.2 9.7 1.0
CB B:ASP513 3.3 10.6 1.0
O B:HOH810 3.3 14.2 1.0
N B:ASP513 3.5 8.1 1.0
O B:HOH833 3.5 10.3 1.0
CA B:ASP513 3.7 8.6 1.0
C B:ASP513 3.7 8.8 1.0
OD1 B:ASP667 4.1 8.6 1.0
OD2 B:ASP513 4.3 12.0 1.0
CG B:ASP513 4.3 10.1 1.0
OD1 B:ASN670 4.4 8.5 1.0
C B:PHE512 4.4 8.2 1.0
N B:PHE512 4.5 8.1 1.0
ND2 B:ASN670 4.5 9.8 1.0
CB B:BFD511 4.6 7.4 1.0
NZ B:LYS644 4.6 7.5 1.0
SD B:MET543 4.7 12.2 1.0
OE2 B:GLU520 4.8 10.2 1.0
OG B:SER599 4.9 8.5 1.0
OE1 B:GLU520 4.9 10.4 1.0
CG B:ASN670 4.9 11.0 1.0
CA B:PHE512 4.9 9.2 1.0

Reference:

H.Cho, W.Wang, R.Kim, H.Yokota, S.Damo, S.-H.Kim, D.Wemmer, S.Kustu, D.Yan. Bef(3)(-) Acts As A Phosphate Analog in Proteins Phosphorylated on Aspartate: Structure of A Bef(3)(-) Complex with Phosphoserine Phosphatase. Proc.Natl.Acad.Sci.Usa V. 98 8525 2001.
ISSN: ISSN 0027-8424
PubMed: 11438683
DOI: 10.1073/PNAS.131213698
Page generated: Wed Jul 31 11:39:01 2024

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