Cobalt in PDB 6d3i: FTV7 Dioxygenase with 2,4-D Bound

The structure of FTV7 Dioxygenase with 2,4-D Bound, PDB code: 6d3i 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)	49.70 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.927, 109.980, 116.145, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 27.3

The structure of FTV7 Dioxygenase with 2,4-D Bound also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Cobalt atom in the FTV7 Dioxygenase with 2,4-D Bound (pdb code 6d3i). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the FTV7 Dioxygenase with 2,4-D Bound, PDB code: 6d3i:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the FTV7 Dioxygenase with 2,4-D Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of FTV7 Dioxygenase with 2,4-D Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:45.9 occ:1.00 NE2 A:HIS270 2.1 45.3 1.0 NE2 A:HIS111 2.1 61.8 1.0 OD1 A:ASP113 2.3 51.0 1.0 O1 A:AKG302 2.4 56.0 1.0 CE1 A:HIS111 2.6 58.3 1.0 C1 A:AKG302 2.7 73.0 1.0 CD2 A:HIS270 2.7 47.7 1.0 C2 A:AKG302 2.9 69.1 1.0 CG A:ASP113 3.0 58.4 1.0 OD2 A:ASP113 3.1 63.0 1.0 O5 A:AKG302 3.2 63.6 1.0 CE1 A:HIS270 3.2 50.3 1.0 CD2 A:HIS111 3.3 56.0 1.0 O2 A:AKG302 3.6 73.5 1.0 ND1 A:HIS111 3.8 56.8 1.0 C3 A:AKG302 3.8 59.8 1.0 CG A:HIS270 4.0 50.2 1.0 ND1 A:HIS270 4.2 43.6 1.0 CG A:HIS111 4.2 55.5 1.0 CZ2 A:TRP263 4.2 51.7 1.0 CH2 A:TRP263 4.2 47.3 1.0 CB A:ASP113 4.4 56.8 1.0 NH1 A:ARG285 4.8 65.9 1.0 CA A:ASP113 5.0 61.9 1.0

Cobalt binding site 2 out of 4 in the FTV7 Dioxygenase with 2,4-D Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of FTV7 Dioxygenase with 2,4-D Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Co301 b:52.4 occ:1.00 O2 G:AKG302 1.5 38.3 1.0 NE2 G:HIS270 1.7 32.4 1.0 C1 G:AKG302 2.3 39.0 1.0 OD1 G:ASP113 2.3 42.9 1.0 O5 G:AKG302 2.4 43.2 1.0 NE2 G:HIS111 2.5 40.4 1.0 CD2 G:HIS270 2.6 33.5 1.0 C2 G:AKG302 2.7 43.5 1.0 CE1 G:HIS270 2.8 35.4 1.0 CG G:ASP113 3.0 39.1 1.0 OD2 G:ASP113 3.1 45.5 1.0 CE1 G:HIS111 3.1 41.4 1.0 O1 G:AKG302 3.3 32.6 1.0 CD2 G:HIS111 3.6 35.2 1.0 CG G:HIS270 3.8 39.8 1.0 ND1 G:HIS270 3.9 39.1 1.0 C3 G:AKG302 4.2 35.5 1.0 ND1 G:HIS111 4.2 31.9 1.0 CB G:ASP113 4.4 29.4 1.0 O1' G:CFA303 4.4 59.4 1.0 CZ2 G:TRP263 4.5 25.8 1.0 CG G:HIS111 4.5 28.3 1.0 NH1 G:ARG285 4.7 37.8 1.0 CH2 G:TRP263 4.7 31.7 1.0 CA G:ASP113 4.7 34.7 1.0 C1 G:CFA303 4.8 56.6 1.0 O2 G:CFA303 4.9 41.8 1.0 C4 G:AKG302 4.9 33.8 1.0 N G:ASP113 5.0 31.3 1.0 CA G:GLY107 5.0 38.2 1.0 C2 G:CFA303 5.0 56.2 1.0

Cobalt binding site 3 out of 4 in the FTV7 Dioxygenase with 2,4-D Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of FTV7 Dioxygenase with 2,4-D Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Co301 b:40.9 occ:1.00 O2 D:AKG302 1.6 44.8 1.0 NE2 D:HIS270 1.9 35.3 1.0 O5 D:AKG302 2.3 58.1 1.0 OD1 D:ASP113 2.4 50.1 1.0 NE2 D:HIS111 2.4 52.0 1.0 C1 D:AKG302 2.4 44.8 1.0 C2 D:AKG302 2.7 56.8 1.0 CE1 D:HIS270 2.8 46.2 1.0 CD2 D:HIS270 3.0 38.4 1.0 CD2 D:HIS111 3.0 51.6 1.0 CG D:ASP113 3.1 45.2 1.0 OD2 D:ASP113 3.4 42.8 1.0 CE1 D:HIS111 3.5 45.6 1.0 O1 D:AKG302 3.6 44.6 1.0 ND1 D:HIS270 3.9 45.1 1.0 CG D:HIS270 4.0 43.4 1.0 O1' D:CFA303 4.1 70.1 1.0 C3 D:AKG302 4.2 48.9 1.0 CG D:HIS111 4.3 47.3 1.0 CZ2 D:TRP263 4.3 29.4 1.0 CB D:ASP113 4.4 43.0 1.0 C1' D:CFA303 4.4 79.0 1.0 ND1 D:HIS111 4.5 46.1 1.0 NH1 D:ARG285 4.6 46.0 1.0 CA D:ASP113 4.6 50.7 1.0 CH2 D:TRP263 4.6 33.0 1.0 C2 D:CFA303 4.7 64.7 1.0 N D:ASP113 4.7 42.4 1.0 C6' D:CFA303 4.8 74.8 1.0 C2' D:CFA303 4.9 89.2 1.0

Cobalt binding site 4 out of 4 in the FTV7 Dioxygenase with 2,4-D Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of FTV7 Dioxygenase with 2,4-D Bound within 5.0Å range: probe atom residue distance (Å) B Occ J:Co301 b:41.0 occ:1.00 O2 J:AKG302 1.8 47.6 1.0 OD1 J:ASP113 1.8 48.3 1.0 NE2 J:HIS270 1.9 39.3 1.0 NE2 J:HIS111 2.1 40.3 1.0 C1 J:AKG302 2.4 37.1 1.0 O5 J:AKG302 2.7 37.8 1.0 CG J:ASP113 2.9 39.5 1.0 CD2 J:HIS270 2.9 38.7 1.0 CE1 J:HIS270 2.9 42.2 1.0 CE1 J:HIS111 3.0 49.3 1.0 C2 J:AKG302 3.0 35.5 1.0 CD2 J:HIS111 3.1 33.3 1.0 OD2 J:ASP113 3.3 35.9 1.0 O1 J:AKG302 3.3 32.6 1.0 ND1 J:HIS270 4.0 38.4 1.0 CG J:HIS270 4.0 34.2 1.0 ND1 J:HIS111 4.1 39.2 1.0 CG J:HIS111 4.1 29.9 1.0 CB J:ASP113 4.2 34.9 1.0 CZ2 J:TRP263 4.4 32.8 1.0 CA J:ASP113 4.4 34.6 1.0 C3 J:AKG302 4.5 44.9 1.0 CH2 J:TRP263 4.6 36.3 1.0 N J:ASP113 4.8 29.3 1.0 NH1 J:ARG285 5.0 51.2 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