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Fluorine in PDB 2nud: The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide

Protein crystallography data

The structure of The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide, PDB code: 2nud was solved by A.U.Singer, D.Desveaux, A.J.Wu, B.Mcnulty, J.Sondek, J.L.Dangl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.884, 58.166, 119.767, 90.00, 89.92, 90.00
R / Rfree (%) 21 / 26

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide (pdb code 2nud). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide, PDB code: 2nud:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2nud

Go back to Fluorine Binding Sites List in 2nud
Fluorine binding site 1 out of 6 in the The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:50.9
occ:1.00
 F1 A:ETF2001 0.0 50.9 1.0
C1 A:ETF2001 1.3 46.0 1.0
F3 A:ETF2001 2.1 39.7 1.0
F2 A:ETF2001 2.1 49.9 1.0
C2 A:ETF2001 2.4 48.8 1.0
O A:HOH1217 2.7 20.9 1.0
O A:ETF2001 3.1 45.7 1.0
N A:GLY267 3.2 21.1 1.0
CA A:GLY267 3.2 19.8 1.0
CE2 A:PHE113 3.8 15.1 1.0
CZ A:PHE113 4.0 15.3 1.0
N A:TRS1504 4.0 45.2 1.0
C A:GLY267 4.3 18.8 1.0
O C:HOH1118 4.4 29.3 1.0
NE A:ARG266 4.4 24.2 1.0
C A:ARG266 4.4 21.4 1.0
CG A:ARG266 4.5 25.7 1.0
N A:SER268 4.7 18.8 1.0
CD A:ARG266 4.9 25.4 1.0
CD2 A:PHE113 4.9 13.5 1.0
CA A:ARG266 5.0 21.6 1.0
CZ A:ARG266 5.0 26.4 1.0

Fluorine binding site 2 out of 6 in 2nud

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Fluorine binding site 2 out of 6 in the The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:49.9
occ:1.00
 F2 A:ETF2001 0.0 49.9 1.0
C1 A:ETF2001 1.3 46.0 1.0
F1 A:ETF2001 2.1 50.9 1.0
F3 A:ETF2001 2.2 39.7 1.0
C2 A:ETF2001 2.4 48.8 1.0
O C:HOH1118 2.6 29.3 1.0
O A:ETF2001 2.8 45.7 1.0
N A:TRS1504 3.0 45.2 1.0
O A:HOH1217 3.8 20.9 1.0
NE A:ARG266 4.1 24.2 1.0
C A:TRS1504 4.1 44.3 1.0
NH2 A:ARG266 4.2 33.1 1.0
C1 A:TRS1504 4.4 43.1 1.0
C2 A:TRS1504 4.4 44.2 1.0
OH A:TYR131 4.5 28.6 1.0
CZ A:ARG266 4.6 26.4 1.0
O1 A:TRS1504 4.7 41.0 1.0
O2 A:TRS1504 4.8 52.2 1.0
N A:GLY267 4.8 21.1 1.0

Fluorine binding site 3 out of 6 in 2nud

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Fluorine binding site 3 out of 6 in the The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:39.7
occ:1.00
 F3 A:ETF2001 0.0 39.7 1.0
C1 A:ETF2001 1.3 46.0 1.0
F1 A:ETF2001 2.1 50.9 1.0
F2 A:ETF2001 2.2 49.9 1.0
C2 A:ETF2001 2.3 48.8 1.0
NE A:ARG266 2.7 24.2 1.0
O C:HOH1118 2.9 29.3 1.0
CD A:ARG266 3.2 25.4 1.0
N A:GLY267 3.2 21.1 1.0
CG A:ARG266 3.3 25.7 1.0
O A:ETF2001 3.6 45.7 1.0
CZ A:ARG266 3.6 26.4 1.0
NH2 A:ARG266 3.9 33.1 1.0
CA A:ARG266 4.0 21.6 1.0
C A:ARG266 4.1 21.4 1.0
CA A:GLY267 4.1 19.8 1.0
CB A:ARG266 4.2 23.8 1.0
O A:HOH1070 4.3 21.0 1.0
CZ A:PHE113 4.4 15.3 1.0
O A:HOH1217 4.5 20.9 1.0
CE2 A:PHE113 4.6 15.1 1.0
NH1 A:ARG266 4.7 26.3 1.0
OG1 C:THR166 4.8 20.2 1.0
CB C:THR166 5.0 22.3 1.0
N A:TRS1504 5.0 45.2 1.0

Fluorine binding site 4 out of 6 in 2nud

Go back to Fluorine Binding Sites List in 2nud
Fluorine binding site 4 out of 6 in the The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:41.7
occ:1.00
 F1 B:ETF2002 0.0 41.7 1.0
C1 B:ETF2002 1.3 48.0 1.0
F3 B:ETF2002 2.1 53.3 1.0
F2 B:ETF2002 2.1 48.0 1.0
C2 B:ETF2002 2.4 49.5 1.0
NE B:ARG266 3.0 22.8 1.0
O B:ETF2002 3.0 48.7 1.0
O D:HOH1035 3.0 18.2 1.0
N B:GLY267 3.2 18.1 1.0
CD B:ARG266 3.3 23.1 1.0
CG B:ARG266 3.6 24.9 1.0
CA B:ARG266 4.0 18.5 1.0
CA B:GLY267 4.0 17.2 1.0
C B:ARG266 4.0 17.6 1.0
CZ B:ARG266 4.1 25.4 1.0
O B:HOH1053 4.1 20.0 1.0
CB B:ARG266 4.3 19.9 1.0
NH2 B:ARG266 4.4 29.4 1.0
CZ B:PHE113 4.7 13.3 1.0
O B:HOH1082 4.7 33.3 1.0
OG1 D:THR166 4.8 27.1 1.0
CE2 B:PHE113 4.8 13.6 1.0
N B:TRS1502 4.8 42.1 1.0
N B:SER268 4.9 17.5 1.0
C B:GLY267 4.9 16.4 1.0
CB D:THR166 4.9 26.9 1.0

Fluorine binding site 5 out of 6 in 2nud

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Fluorine binding site 5 out of 6 in the The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:48.0
occ:1.00
 F2 B:ETF2002 0.0 48.0 1.0
C1 B:ETF2002 1.3 48.0 1.0
F1 B:ETF2002 2.1 41.7 1.0
F3 B:ETF2002 2.2 53.3 1.0
C2 B:ETF2002 2.4 49.5 1.0
O B:HOH1082 2.9 33.3 1.0
O B:ETF2002 3.6 48.7 1.0
NE B:ARG266 3.9 22.8 1.0
N B:GLY267 3.9 18.1 1.0
CZ B:PHE113 3.9 13.3 1.0
N B:TRS1502 4.0 42.1 1.0
CE2 B:PHE113 4.0 13.6 1.0
CA B:GLY267 4.1 17.2 1.0
O D:HOH1035 4.2 18.2 1.0
NH2 B:ARG266 4.3 29.4 1.0
CZ B:ARG266 4.4 25.4 1.0
CG B:ARG266 4.5 24.9 1.0
CD B:ARG266 4.6 23.1 1.0
O1 B:TRS1502 4.7 46.9 1.0

Fluorine binding site 6 out of 6 in 2nud

Go back to Fluorine Binding Sites List in 2nud
Fluorine binding site 6 out of 6 in the The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Structure of the Type III Effector Avrb Complexed with A High-Affinity RIN4 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:53.3
occ:1.00
 F3 B:ETF2002 0.0 53.3 1.0
C1 B:ETF2002 1.3 48.0 1.0
F1 B:ETF2002 2.1 41.7 1.0
F2 B:ETF2002 2.2 48.0 1.0
C2 B:ETF2002 2.3 49.5 1.0
O D:HOH1035 2.6 18.2 1.0
O B:ETF2002 2.8 48.7 1.0
N B:TRS1502 3.1 42.1 1.0
O1 B:TRS1502 3.3 46.9 1.0
O3 B:TRS1502 3.5 48.5 1.0
C B:TRS1502 4.0 41.1 1.0
OH B:TYR131 4.1 34.6 1.0
C1 B:TRS1502 4.1 40.6 1.0
NE B:ARG266 4.2 22.8 1.0
C3 B:TRS1502 4.3 40.9 1.0
O B:HOH1082 4.7 33.3 1.0
NH2 B:ARG266 4.7 29.4 1.0
N B:GLY267 4.9 18.1 1.0
CZ B:ARG266 5.0 25.4 1.0
O D:HOH1261 5.0 43.4 1.0

Reference:

D.Desveaux, A.U.Singer, A.J.Wu, B.C.Mcnulty, L.Musselwhite, Z.Nimchuk, J.Sondek, J.L.Dangl. Type III Effector Activation Via Nucleotide Binding, Phosphorylation, and Host Target Interaction. Plos Pathog. V. 3 E48 2007.
ISSN: ISSN 1553-7366
PubMed: 17397263
DOI: 10.1371/JOURNAL.PPAT.0030048
Page generated: Wed Jul 31 15:13:46 2024

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