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Fluorine in PDB 5bkd: Crystal Structure of Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate

Enzymatic activity of Crystal Structure of Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate

All present enzymatic activity of Crystal Structure of Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate:
1.14.11.44;

Protein crystallography data

The structure of Crystal Structure of Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate, PDB code: 5bkd was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.74 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.531, 97.421, 69.804, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.8

Other elements in 5bkd:

The structure of Crystal Structure of Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate (pdb code 5bkd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate, PDB code: 5bkd:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5bkd

Go back to Fluorine Binding Sites List in 5bkd
Fluorine binding site 1 out of 2 in the Crystal Structure of Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate


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 Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:33.3
occ:1.00
F06 A:RCF503 0.0 33.3 1.0
C05 A:RCF503 1.4 25.1 1.0
C07 A:RCF503 2.4 24.5 1.0
C04 A:RCF503 2.4 28.8 1.0
O10 A:RCF503 2.6 27.6 1.0
OD1 A:ASP108 2.9 32.4 1.0
N A:ASP109 3.0 21.3 1.0
CB A:ASP109 3.1 21.6 1.0
O A:HOH609 3.2 37.0 1.0
N A:ASP108 3.3 16.9 1.0
CA A:ASP109 3.6 19.0 1.0
C A:ASP108 3.6 21.9 1.0
C08 A:RCF503 3.6 25.4 1.0
C03 A:RCF503 3.7 28.2 1.0
OD2 A:ASP109 3.7 33.3 1.0
CG A:ASP109 3.7 35.1 1.0
C A:GLY107 3.8 19.2 1.0
C11 A:RCF503 4.0 23.6 1.0
CA A:ASP108 4.0 21.4 1.0
CA A:GLY107 4.0 16.8 1.0
CG A:ASP108 4.1 28.5 1.0
C09 A:RCF503 4.1 27.9 1.0
CG2 A:VAL220 4.2 16.0 1.0
O A:ASP109 4.2 15.3 1.0
N A:GLY107 4.3 18.4 1.0
C A:ASP109 4.4 17.0 1.0
O A:ASP108 4.4 21.9 1.0
O A:GLY107 4.5 18.4 1.0
C16 A:RCF503 4.6 20.6 1.0
CB A:ASP108 4.7 27.1 1.0
OD1 A:ASP109 4.7 42.5 1.0
C02 A:RCF503 4.9 35.1 1.0
O A:HOH841 5.0 36.3 1.0

Fluorine binding site 2 out of 2 in 5bkd

Go back to Fluorine Binding Sites List in 5bkd
Fluorine binding site 2 out of 2 in the Crystal Structure of Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate


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 Aad-1 in Complex with (R)-Cyhalofop, Mn(II), and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:49.2
occ:1.00
F06 B:RCF503 0.0 49.2 1.0
C05 B:RCF503 1.4 45.5 1.0
C04 B:RCF503 2.4 46.5 1.0
C07 B:RCF503 2.4 44.2 1.0
O10 B:RCF503 2.9 47.7 1.0
C11 B:RCF503 2.9 41.4 1.0
C12 B:RCF503 3.3 44.2 1.0
C16 B:RCF503 3.5 33.4 1.0
CG2 B:VAL170 3.6 32.8 1.0
C03 B:RCF503 3.7 45.7 1.0
C08 B:RCF503 3.7 36.3 1.0
CG1 B:VAL170 3.7 42.5 1.0
CB B:VAL170 4.1 42.0 1.0
C13 B:RCF503 4.1 37.1 1.0
C09 B:RCF503 4.1 43.3 1.0
C15 B:RCF503 4.3 35.0 1.0
CA B:VAL170 4.3 41.1 1.0
CG1 B:VAL220 4.4 24.7 1.0
C14 B:RCF503 4.6 35.6 1.0
O B:HOH609 4.6 38.2 1.0
C02 B:RCF503 5.0 48.3 1.0

Reference:

J.R.Chekan, C.Ongpipattanakul, T.R.Wright, B.Zhang, J.M.Bollinger Jr., L.J.Rajakovich, C.Krebs, R.M.Cicchillo, S.K.Nair. Molecular Basis For Enantioselective Herbicide Degradation Imparted By Aryloxyalkanoate Dioxygenases in Transgenic Plants. Proc.Natl.Acad.Sci.Usa V. 116 13299 2019.
ISSN: ESSN 1091-6490
PubMed: 31209034
DOI: 10.1073/PNAS.1900711116
Page generated: Sun Dec 13 12:19:09 2020

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