Cobalt in PDB 6d3j: FT_T Dioxygenase Holoenzyme

The structure of FT_T Dioxygenase Holoenzyme, PDB code: 6d3j 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)	119.00 / 3.00
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	137.413, 137.413, 76.261, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 27.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cobalt atom in the FT_T Dioxygenase Holoenzyme (pdb code 6d3j). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the FT_T Dioxygenase Holoenzyme, PDB code: 6d3j:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 12 in the FT_T Dioxygenase Holoenzyme


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 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:83.4 occ:1.00 O2 A:AKG302 1.6 0.2 1.0 OD2 A:ASP113 2.2 87.6 1.0 O A:HOH401 2.2 70.8 1.0 NE2 A:HIS111 2.2 67.0 1.0 C1 A:AKG302 2.2 0.3 1.0 NE2 A:HIS270 2.3 75.6 1.0 O5 A:AKG302 2.4 0.5 1.0 C2 A:AKG302 2.5 0.6 1.0 CG A:ASP113 3.0 79.9 1.0 CE1 A:HIS111 3.1 69.5 1.0 OD1 A:ASP113 3.2 78.9 1.0 CD2 A:HIS111 3.2 68.0 1.0 CD2 A:HIS270 3.2 73.9 1.0 O1 A:AKG302 3.2 0.8 1.0 CE1 A:HIS270 3.3 78.3 1.0 C3 A:AKG302 3.9 0.9 1.0 ND1 A:HIS111 4.2 68.0 1.0 CG A:HIS111 4.3 70.9 1.0 ND1 A:HIS270 4.4 77.8 1.0 CG A:HIS270 4.4 72.4 1.0 CB A:ASP113 4.4 76.0 1.0 CZ2 A:TRP263 4.8 73.0 1.0 CA A:ASP113 4.9 73.3 1.0 C4 A:AKG302 4.9 0.9 1.0

Cobalt binding site 2 out of 12 in the FT_T Dioxygenase Holoenzyme


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 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co303 b:0.9 occ:1.00 OD2 A:ASP16 2.4 0.8 1.0 CG A:ASP16 3.5 0.4 1.0 OD1 A:ASP16 4.0 0.1 1.0 CB A:ASP16 4.8 0.9 1.0 N A:ASP16 5.0 0.1 1.0

Cobalt binding site 3 out of 12 in the FT_T Dioxygenase Holoenzyme


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 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co304 b:0.6 occ:1.00 OE1 A:GLU35 2.3 0.2 1.0 CD A:GLU35 3.3 0.2 1.0 OE2 A:GLU35 3.7 0.3 1.0 CG A:GLU35 4.7 0.9 1.0 CD A:PRO36 4.8 0.7 1.0 CA A:GLU35 4.9 0.9 1.0 O A:ARG34 4.9 0.7 1.0 CB A:GLU35 4.9 0.9 1.0

Cobalt binding site 4 out of 12 in the FT_T Dioxygenase Holoenzyme


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 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co305 b:0.4 occ:1.00 OE2 A:GLU65 3.1 0.8 1.0 CD A:GLU65 4.3 1.0 1.0 OE1 A:GLU65 4.9 0.5 1.0 OH A:TYR89 5.0 0.2 1.0

Cobalt binding site 5 out of 12 in the FT_T Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of FT_T Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co306 b:1.0 occ:0.50 N A:VAL77 3.5 88.0 1.0 O A:VAL77 3.9 98.3 1.0 CA A:PRO76 4.1 80.0 1.0 CB A:PRO76 4.1 79.2 1.0 C A:PRO76 4.3 80.4 1.0 CD A:ARG72 4.3 81.7 1.0 NE A:ARG72 4.4 85.1 1.0 CA A:VAL77 4.4 89.9 1.0 C A:VAL77 4.4 93.6 1.0 CB A:VAL77 4.5 92.9 1.0

Cobalt binding site 6 out of 12 in the FT_T Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of FT_T Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co307 b:0.5 occ:1.00 OD1 A:ASP118 2.7 92.7 1.0 OD2 A:ASP118 3.0 98.0 1.0 CG A:ASP118 3.3 91.0 1.0 O A:GLU198 3.3 0.8 1.0 C A:GLU198 4.5 97.8 1.0 CB A:THR199 4.7 92.7 1.0 CB A:ASP118 4.8 83.8 1.0 CA A:THR199 4.9 89.4 1.0 OG1 A:THR199 5.0 94.0 1.0

Cobalt binding site 7 out of 12 in the FT_T Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of FT_T Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co308 b:0.0 occ:1.00 OD2 A:ASP230 3.1 89.0 1.0 OD1 A:ASP230 3.6 93.0 1.0 CG A:ASP230 3.7 88.7 1.0

Cobalt binding site 8 out of 12 in the FT_T Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of FT_T Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co309 b:0.7 occ:1.00 OE2 A:GLU242 2.8 76.8 1.0 OE1 A:GLU242 2.8 98.2 1.0 CD A:GLU242 3.1 88.2 1.0 OG1 A:THR245 3.8 79.2 1.0 CO A:CO312 3.8 0.5 0.5 CG A:GLU242 4.5 78.5 1.0 CO A:CO313 4.6 0.5 1.0 CB A:THR245 4.7 71.7 1.0 CG2 A:THR245 4.8 72.6 1.0 CA A:GLU242 4.9 68.3 1.0

Cobalt binding site 9 out of 12 in the FT_T Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of FT_T Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co310 b:0.5 occ:1.00 OE2 A:GLU27 2.8 0.1 1.0 CD A:GLU27 3.9 0.7 1.0 OE1 A:GLU27 4.4 96.5 1.0 NE2 A:GLN18 4.6 0.1 1.0

Cobalt binding site 10 out of 12 in the FT_T Dioxygenase Holoenzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of FT_T Dioxygenase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Co311 b:0.1 occ:1.00 OD2 A:ASP108 2.8 0.9 1.0 OD2 A:ASP109 3.3 0.8 1.0 CG A:ASP108 3.4 0.5 1.0 OD1 A:ASP108 3.4 0.1 1.0 OD1 A:ASP109 3.5 1.0 1.0 CG A:ASP109 3.7 0.3 1.0 N A:ASP109 4.7 98.7 1.0 C A:ASP108 4.8 0.3 1.0 CB A:ASP108 4.8 0.1 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