Cobalt in PDB 6d0o: Rdpa Dioxygenase Holoenzyme

All present enzymatic activity of Rdpa Dioxygenase Holoenzyme:
1.14.11.44;

The structure of Rdpa Dioxygenase Holoenzyme, PDB code: 6d0o was solved by T.J.Rydel, E.J.Sturman, M.Zheng, A.Evdokimov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	153.014, 153.014, 156.845, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.8

The binding sites of Cobalt atom in the Rdpa Dioxygenase Holoenzyme (pdb code 6d0o). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Rdpa Dioxygenase Holoenzyme, PDB code: 6d0o:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Rdpa Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Rdpa Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:28.5 occ:1.00 O1 A:AKG402 1.9 42.0 1.0 NE2 A:HIS111 2.1 24.5 1.0 NE2 A:HIS270 2.2 22.1 1.0 O5 A:AKG402 2.2 39.6 1.0 OD1 A:ASP113 2.2 28.2 1.0 O A:HOH591 2.2 36.8 1.0 C1 A:AKG402 2.6 73.7 1.0 C2 A:AKG402 2.6 72.8 1.0 CD2 A:HIS111 3.1 25.0 1.0 CE1 A:HIS111 3.1 25.0 1.0 CD2 A:HIS270 3.1 22.4 1.0 CE1 A:HIS270 3.1 25.2 1.0 CG A:ASP113 3.3 35.4 1.0 OD2 A:ASP113 3.6 36.3 1.0 O2 A:AKG402 3.8 78.4 1.0 O A:HOH502 4.0 69.5 1.0 C3 A:AKG402 4.1 79.3 1.0 ND1 A:HIS111 4.2 30.6 1.0 CG A:HIS111 4.2 29.0 1.0 ND1 A:HIS270 4.2 25.9 1.0 CG A:HIS270 4.2 22.3 1.0 N A:GLY107 4.6 0.7 1.0 CB A:ASP113 4.6 31.7 1.0 C4 A:AKG402 4.7 76.1 1.0 O A:HOH529 4.7 35.6 1.0 CZ2 A:TRP263 4.9 28.7 1.0 CA A:ASP113 4.9 26.0 1.0 O A:HOH653 5.0 46.9 1.0

Cobalt binding site 2 out of 4 in the Rdpa Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Rdpa Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:31.6 occ:1.00 C1 B:AKG402 1.7 70.2 1.0 O2 B:AKG402 2.0 37.6 1.0 NE2 B:HIS270 2.1 25.3 1.0 NE2 B:HIS111 2.1 27.9 1.0 OD1 B:ASP113 2.1 31.5 1.0 O5 B:AKG402 2.2 40.5 1.0 C2 B:AKG402 2.3 59.8 1.0 O1 B:AKG402 2.3 36.4 1.0 CE1 B:HIS270 3.0 26.6 1.0 CD2 B:HIS270 3.1 23.7 1.0 CD2 B:HIS111 3.1 27.2 1.0 CE1 B:HIS111 3.1 25.1 1.0 CG B:ASP113 3.2 34.5 1.0 OD2 B:ASP113 3.6 38.2 1.0 C3 B:AKG402 3.7 64.2 1.0 ND1 B:HIS270 4.2 23.4 1.0 CG B:HIS270 4.2 22.8 1.0 ND1 B:HIS111 4.2 31.5 1.0 CG B:HIS111 4.2 29.3 1.0 C4 B:AKG402 4.3 52.9 1.0 CB B:ASP113 4.6 32.7 1.0 CA B:ASP113 4.9 28.6 1.0 O B:HOH506 4.9 38.2 1.0 CZ2 B:TRP263 4.9 27.9 1.0

Cobalt binding site 3 out of 4 in the Rdpa Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Rdpa Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:33.2 occ:1.00 O2 C:AKG402 1.9 34.9 1.0 NE2 C:HIS270 2.0 30.9 1.0 OD1 C:ASP113 2.1 34.0 1.0 O C:HOH542 2.1 47.0 1.0 O5 C:AKG402 2.2 36.0 1.0 NE2 C:HIS111 2.2 27.1 1.0 C1 C:AKG402 2.7 41.9 1.0 C2 C:AKG402 2.8 33.9 1.0 CE1 C:HIS270 3.0 32.1 1.0 CD2 C:HIS270 3.1 27.4 1.0 CG C:ASP113 3.1 35.0 1.0 CD2 C:HIS111 3.1 26.4 1.0 CE1 C:HIS111 3.2 28.3 1.0 OD2 C:ASP113 3.4 35.1 1.0 O1 C:AKG402 3.9 41.0 1.0 O C:HOH622 4.1 57.1 1.0 ND1 C:HIS270 4.1 27.9 1.0 CG C:HIS270 4.2 29.6 1.0 ND1 C:HIS111 4.3 30.3 1.0 CG C:HIS111 4.3 29.8 1.0 C3 C:AKG402 4.3 35.2 1.0 CB C:ASP113 4.4 33.0 1.0 NH1 C:ARG285 4.6 45.0 1.0 O C:HOH527 4.6 31.6 1.0 CZ2 C:TRP263 4.7 31.4 1.0 CA C:ASP113 4.8 36.3 1.0 N C:ASP113 4.9 28.6 1.0 CA C:GLY107 5.0 45.9 1.0

Cobalt binding site 4 out of 4 in the Rdpa Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Rdpa Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Co401 b:44.1 occ:1.00 O5 D:AKG402 2.0 37.0 1.0 NE2 D:HIS270 2.0 38.0 1.0 O1 D:AKG402 2.1 61.0 1.0 OD1 D:ASP113 2.1 48.5 1.0 O D:HOH548 2.2 57.0 1.0 NE2 D:HIS111 2.3 40.8 1.0 C2 D:AKG402 2.8 45.4 1.0 C1 D:AKG402 2.8 53.8 1.0 CE1 D:HIS270 3.0 40.6 1.0 CD2 D:HIS270 3.1 34.1 1.0 CG D:ASP113 3.1 47.4 1.0 CD2 D:HIS111 3.2 39.4 1.0 CE1 D:HIS111 3.2 40.2 1.0 OD2 D:ASP113 3.4 51.2 1.0 O2 D:AKG402 4.1 49.3 1.0 ND1 D:HIS270 4.1 37.4 1.0 CG D:HIS270 4.1 32.0 1.0 O D:HOH603 4.3 61.4 1.0 C3 D:AKG402 4.3 48.0 1.0 ND1 D:HIS111 4.3 42.5 1.0 CG D:HIS111 4.3 36.3 1.0 CB D:ASP113 4.5 44.8 1.0 NH1 D:ARG285 4.5 73.4 1.0 CZ2 D:TRP263 4.6 36.2 1.0 O D:HOH518 4.6 46.2 1.0 CA D:ASP113 4.8 38.3 1.0 N D:ASP113 5.0 42.1 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