Fluorine in PDB 5vsr: Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1

Enzymatic activity of Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1

All present enzymatic activity of Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1:
3.1.3.16;

Protein crystallography data

The structure of Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1, PDB code: 5vsr was solved by M.-J.Cao, Y.-L.Zhang, X.Liu, H.Huang, X.E.Zhou, W.-L.Wang, A.Zeng, C.-Z.Zhao, T.Si, J.-M.Du, W.-W.Wu, F.-X.Wang, H.X.Xu, J.-K.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.62 / 2.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.210, 64.380, 144.830, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 27.5

Other elements in 5vsr:

The structure of Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1 also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1 (pdb code 5vsr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1, PDB code: 5vsr:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5vsr

Go back to Fluorine Binding Sites List in 5vsr
Fluorine binding site 1 out of 4 in the Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:65.9
occ:1.00
 F1 A:AF0300 0.0 65.9 1.0
C5 A:AF0300 1.3 63.5 1.0
C6 A:AF0300 2.4 56.5 1.0
C2 A:AF0300 2.4 61.6 1.0
F2 A:AF0300 2.7 72.2 1.0
C17 A:AF0300 2.8 59.2 1.0
CG1 A:VAL169 3.3 36.2 1.0
C7 A:AF0300 3.6 56.7 1.0
C1 A:AF0300 3.7 58.5 1.0
OH A:TYR124 3.8 55.7 1.0
CG2 A:VAL170 4.0 46.7 1.0
CB A:VAL169 4.0 39.1 1.0
C3 A:AF0300 4.1 58.6 1.0
CZ A:TYR124 4.2 41.5 1.0
N A:VAL170 4.5 42.3 1.0
CG1 A:VAL166 4.6 45.1 1.0
ND2 A:ASN173 4.6 49.4 1.0
CE1 A:TYR124 4.6 38.1 1.0
F4 A:AF0300 4.7 73.2 1.0
CE2 A:TYR124 4.8 43.5 1.0
C A:VAL169 4.8 38.9 1.0
O A:VAL166 4.8 45.1 1.0
CA A:VAL170 4.9 40.9 1.0
C4 A:AF0300 4.9 67.4 1.0
CG2 A:VAL169 5.0 34.2 1.0

Fluorine binding site 2 out of 4 in 5vsr

Go back to Fluorine Binding Sites List in 5vsr
Fluorine binding site 2 out of 4 in the Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:72.2
occ:1.00
 F2 A:AF0300 0.0 72.2 1.0
C2 A:AF0300 1.3 61.6 1.0
C5 A:AF0300 2.4 63.5 1.0
C1 A:AF0300 2.4 58.5 1.0
F1 A:AF0300 2.7 65.9 1.0
C4 A:AF0300 2.9 67.4 1.0
ND2 A:ASN173 3.1 49.4 1.0
C6 A:AF0300 3.6 56.5 1.0
C3 A:AF0300 3.7 58.6 1.0
O1 A:AF0300 4.0 77.4 1.0
NZ A:LYS64 4.0 70.2 1.0
S A:AF0300 4.1 87.2 1.0
C7 A:AF0300 4.1 56.7 1.0
CG1 A:VAL169 4.2 36.2 1.0
CE A:LYS64 4.2 65.2 1.0
CG A:ASN173 4.3 42.8 1.0
CD A:LYS64 4.4 60.7 1.0
F3 A:AF0300 4.8 63.2 1.0
OH A:TYR124 4.8 55.7 1.0
C17 A:AF0300 4.9 59.2 1.0

Fluorine binding site 3 out of 4 in 5vsr

Go back to Fluorine Binding Sites List in 5vsr
Fluorine binding site 3 out of 4 in the Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:63.2
occ:1.00
 F3 A:AF0300 0.0 63.2 1.0
C3 A:AF0300 1.3 58.6 1.0
C7 A:AF0300 2.4 56.7 1.0
C1 A:AF0300 2.4 58.5 1.0
OE2 A:GLU98 2.6 61.7 1.0
F4 A:AF0300 2.8 73.2 1.0
C4 A:AF0300 2.9 67.4 1.0
CD A:GLU98 3.0 58.5 1.0
N2 A:AF0300 3.1 58.0 1.0
C12 A:AF0300 3.2 57.7 1.0
S A:AF0300 3.5 87.2 1.0
C10 A:AF0300 3.5 61.6 1.0
OE1 A:GLU98 3.6 59.7 1.0
C6 A:AF0300 3.6 56.5 1.0
CG A:GLU98 3.6 48.5 1.0
C2 A:AF0300 3.7 61.6 1.0
CG2 A:VAL114 3.8 44.0 1.0
CE2 A:PHE112 3.8 41.9 1.0
OG A:SER96 3.9 46.5 1.0
C5 A:AF0300 4.1 63.5 1.0
O3 A:AF0300 4.2 75.9 1.0
C13 A:AF0300 4.3 55.5 1.0
CZ A:PHE112 4.4 41.7 1.0
O1 A:AF0300 4.7 77.4 1.0
CD2 A:TYR124 4.7 42.6 1.0
CE2 A:TYR124 4.7 43.5 1.0
F2 A:AF0300 4.8 72.2 1.0
C11 A:AF0300 4.8 53.1 1.0
C15 A:AF0300 4.8 45.6 1.0
CB A:SER96 4.8 45.7 1.0
C17 A:AF0300 4.9 59.2 1.0
CD2 A:PHE112 4.9 52.1 1.0

Fluorine binding site 4 out of 4 in 5vsr

Go back to Fluorine Binding Sites List in 5vsr
Fluorine binding site 4 out of 4 in the Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Aba-Mimicking Ligand AMF4 in Complex with Aba Receptor PYL2 and PP2C HAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:73.2
occ:1.00
 F4 A:AF0300 0.0 73.2 1.0
C7 A:AF0300 1.3 56.7 1.0
C6 A:AF0300 2.4 56.5 1.0
C3 A:AF0300 2.4 58.6 1.0
F3 A:AF0300 2.8 63.2 1.0
C17 A:AF0300 2.9 59.2 1.0
CG2 A:VAL114 3.3 44.0 1.0
CD2 A:TYR124 3.5 42.6 1.0
C5 A:AF0300 3.6 63.5 1.0
C1 A:AF0300 3.7 58.5 1.0
CG A:TYR124 3.8 37.3 1.0
C15 A:AF0300 3.9 45.6 1.0
CE2 A:TYR124 3.9 43.5 1.0
C12 A:AF0300 3.9 57.7 1.0
C18 A:AF0300 4.1 52.1 1.0
C2 A:AF0300 4.1 61.6 1.0
C13 A:AF0300 4.2 55.5 1.0
CB A:TYR124 4.2 30.8 1.0
CD1 A:TYR124 4.5 38.2 1.0
CZ A:TYR124 4.5 41.5 1.0
CB A:VAL114 4.6 43.9 1.0
CD1 A:LEU121 4.7 44.3 1.0
F1 A:AF0300 4.7 65.9 1.0
CE1 A:TYR124 4.8 38.1 1.0
OG A:SER96 4.8 46.5 1.0
CB A:LEU121 4.9 49.6 1.0
C10 A:AF0300 4.9 61.6 1.0
C4 A:AF0300 4.9 67.4 1.0
OE2 A:GLU98 5.0 61.7 1.0

Reference:

M.J.Cao, Y.L.Zhang, X.Liu, H.Huang, X.E.Zhou, W.L.Wang, A.Zeng, C.Z.Zhao, T.Si, J.Du, W.W.Wu, F.X.Wang, H.E.Xu, J.K.Zhu. Combining Chemical and Genetic Approaches to Increase Drought Resistance in Plants. Nat Commun V. 8 1183 2017.
ISSN: ESSN 2041-1723
PubMed: 29084945
DOI: 10.1038/S41467-017-01239-3
Page generated: Sun Dec 13 12:41:05 2020

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