Cobalt in PDB 6d3h: FT_T Dioxygenase with Bound Dichlorprop

The structure of FT_T Dioxygenase with Bound Dichlorprop, PDB code: 6d3h was solved by T.J.Rydel, C.E.Halls, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.60 / 2.03
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	138.161, 138.161, 148.518, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 21.1

The structure of FT_T Dioxygenase with Bound Dichlorprop also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Cobalt atom in the FT_T Dioxygenase with Bound Dichlorprop (pdb code 6d3h). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the FT_T Dioxygenase with Bound Dichlorprop, PDB code: 6d3h:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the FT_T Dioxygenase with Bound Dichlorprop


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of FT_T Dioxygenase with Bound Dichlorprop within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:21.1 occ:1.00 OD2 A:ASP113 2.0 21.3 1.0 O1 A:AKG303 2.0 20.7 1.0 NE2 A:HIS270 2.1 19.6 1.0 NE2 A:HIS111 2.2 17.2 1.0 O5 A:AKG303 2.2 21.8 1.0 C1 A:AKG303 2.8 21.7 1.0 C2 A:AKG303 2.9 23.2 1.0 CE1 A:HIS270 2.9 18.3 1.0 CG A:ASP113 3.0 20.5 1.0 CE1 A:HIS111 3.1 19.9 1.0 CD2 A:HIS270 3.1 20.5 1.0 CD2 A:HIS111 3.1 18.6 1.0 OD1 A:ASP113 3.3 19.8 1.0 O2 A:AKG303 3.9 24.0 1.0 ND1 A:HIS270 4.1 20.7 1.0 ND1 A:HIS111 4.2 17.6 1.0 CG A:HIS270 4.2 20.9 1.0 C1 A:FTV301 4.2 26.2 1.0 CG A:HIS111 4.2 18.3 1.0 C5 A:FTV301 4.3 27.6 1.0 CB A:ASP113 4.3 18.9 1.0 CZ2 A:TRP263 4.4 16.7 1.0 C3 A:AKG303 4.4 22.5 1.0 NH1 A:ARG285 4.4 16.8 1.0 CA A:ASP113 4.7 19.0 1.0 C6 A:FTV301 4.7 28.6 1.0 CH2 A:TRP263 4.8 20.4 1.0 C3 A:FTV301 4.8 27.1 1.0 N A:ASP113 4.9 19.5 1.0 C8 A:FTV301 4.9 27.4 1.0 C2 A:FTV301 5.0 29.9 1.0

Cobalt binding site 2 out of 4 in the FT_T Dioxygenase with Bound Dichlorprop


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of FT_T Dioxygenase with Bound Dichlorprop within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:20.0 occ:1.00 O2 B:AKG303 2.0 19.3 1.0 NE2 B:HIS270 2.0 16.7 1.0 NE2 B:HIS111 2.1 18.1 1.0 OD2 B:ASP113 2.1 19.5 1.0 O5 B:AKG303 2.4 19.9 1.0 C1 B:AKG303 2.9 19.2 1.0 CE1 B:HIS270 3.0 18.0 1.0 C2 B:AKG303 3.0 24.6 1.0 CD2 B:HIS111 3.0 17.8 1.0 CE1 B:HIS111 3.1 16.6 1.0 CG B:ASP113 3.1 19.0 1.0 CD2 B:HIS270 3.1 16.9 1.0 OD1 B:ASP113 3.4 19.3 1.0 O1 B:AKG303 4.0 20.6 1.0 ND1 B:HIS270 4.1 15.7 1.0 C1 B:FTV301 4.1 27.3 1.0 ND1 B:HIS111 4.2 16.4 1.0 CG B:HIS111 4.2 19.8 1.0 CG B:HIS270 4.2 16.3 1.0 C5 B:FTV301 4.3 26.7 1.0 CZ2 B:TRP263 4.3 17.0 1.0 NH1 B:ARG285 4.4 16.7 1.0 CB B:ASP113 4.4 16.5 1.0 C3 B:AKG303 4.5 20.3 1.0 C3 B:FTV301 4.6 26.0 1.0 C6 B:FTV301 4.7 26.3 1.0 CA B:ASP113 4.7 16.5 1.0 CH2 B:TRP263 4.7 20.0 1.0 N B:ASP113 4.8 16.8 1.0 C8 B:FTV301 4.9 21.6 1.0 C2 B:FTV301 5.0 27.2 1.0

Cobalt binding site 3 out of 4 in the FT_T Dioxygenase with Bound Dichlorprop


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of FT_T Dioxygenase with Bound Dichlorprop within 5.0Å range: probe atom residue distance (Å) B Occ I:Co302 b:19.7 occ:1.00 NE2 I:HIS270 2.0 18.4 1.0 O1 I:AKG303 2.0 18.1 1.0 OD2 I:ASP113 2.1 19.1 1.0 NE2 I:HIS111 2.1 15.8 1.0 O5 I:AKG303 2.3 21.4 1.0 C1 I:AKG303 2.8 20.1 1.0 C2 I:AKG303 2.9 22.5 1.0 CE1 I:HIS270 2.9 17.7 1.0 CD2 I:HIS270 3.1 18.1 1.0 CE1 I:HIS111 3.1 16.6 1.0 CD2 I:HIS111 3.1 18.1 1.0 CG I:ASP113 3.1 18.6 1.0 OD1 I:ASP113 3.4 20.1 1.0 O2 I:AKG303 4.0 19.4 1.0 ND1 I:HIS270 4.1 16.6 1.0 ND1 I:HIS111 4.2 14.9 1.0 C1 I:FTV301 4.2 26.0 1.0 CG I:HIS270 4.2 17.7 1.0 CG I:HIS111 4.2 18.6 1.0 CZ2 I:TRP263 4.3 14.2 1.0 C5 I:FTV301 4.3 25.2 1.0 NH1 I:ARG285 4.4 16.6 1.0 C3 I:AKG303 4.5 19.1 1.0 CB I:ASP113 4.5 16.8 1.0 C3 I:FTV301 4.7 23.5 1.0 C6 I:FTV301 4.7 27.1 1.0 CA I:ASP113 4.7 16.9 1.0 CH2 I:TRP263 4.8 19.4 1.0 N I:ASP113 4.8 17.0 1.0 C8 I:FTV301 4.9 22.2 1.0

Cobalt binding site 4 out of 4 in the FT_T Dioxygenase with Bound Dichlorprop


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of FT_T Dioxygenase with Bound Dichlorprop within 5.0Å range: probe atom residue distance (Å) B Occ M:Co302 b:21.0 occ:1.00 OD2 M:ASP113 1.9 21.9 1.0 O2 M:AKG303 2.0 20.6 1.0 NE2 M:HIS270 2.1 19.5 1.0 NE2 M:HIS111 2.1 17.4 1.0 O5 M:AKG303 2.3 21.0 1.0 C1 M:AKG303 2.8 23.0 1.0 C2 M:AKG303 2.9 25.7 1.0 CG M:ASP113 3.0 20.8 1.0 CE1 M:HIS270 3.0 17.6 1.0 CE1 M:HIS111 3.0 18.3 1.0 CD2 M:HIS270 3.1 21.4 1.0 CD2 M:HIS111 3.1 18.2 1.0 OD1 M:ASP113 3.3 19.2 1.0 O1 M:AKG303 4.0 24.3 1.0 ND1 M:HIS270 4.1 18.4 1.0 C1 M:FTV301 4.1 27.4 1.0 ND1 M:HIS111 4.1 17.9 1.0 CG M:HIS270 4.2 20.5 1.0 CG M:HIS111 4.2 19.1 1.0 C5 M:FTV301 4.3 30.4 1.0 CB M:ASP113 4.3 19.2 1.0 CZ2 M:TRP263 4.3 17.8 1.0 NH1 M:ARG285 4.4 17.1 1.0 C3 M:AKG303 4.4 24.2 1.0 C6 M:FTV301 4.7 27.3 1.0 CA M:ASP113 4.7 19.0 1.0 CH2 M:TRP263 4.7 18.6 1.0 C3 M:FTV301 4.8 29.7 1.0 N M:ASP113 4.9 20.0 1.0 C8 M:FTV301 4.9 30.7 1.0 O3 M:FTV301 5.0 24.2 1.0 C2 M:FTV301 5.0 29.5 1.0

C.T.Larue, M.Goley, L.Shi, A.G.Evdokimov, O.C.Sparks, C.Ellis, A.M.Wollacott, T.J.Rydel, C.E.Halls, B.Van Scoyoc, X.Fu, J.R.Nageotte, A.M.Adio, M.Zheng, E.J.Sturman, G.S.Garvey, M.J.Varagona. Development of Enzymes For Robust Aryloxyphenoxypropionate and Synthetic Auxin Herbicide Tolerance Traits in Maize and Soybean Crops. Pest Manag. Sci. V. 75 2086 2019.
ISSN: ISSN 1526-4998
PubMed: 30828945
DOI: 10.1002/PS.5393