Cobalt in PDB 9kp0: Crystal Structure of Oryza Sativa Hppd

The structure of Crystal Structure of Oryza Sativa Hppd, PDB code: 9kp0 was solved by T.Nishio, N.Nishijima, T.Kubota, Y.Furuhata, Y.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.94 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.11, 64.59, 73.16, 101.39, 107.96, 97
R / Rfree (%)	19.4 / 22.7

The structure of Crystal Structure of Oryza Sativa Hppd also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

The binding sites of Cobalt atom in the Crystal Structure of Oryza Sativa Hppd (pdb code 9kp0). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Oryza Sativa Hppd, PDB code: 9kp0:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:20.3 occ:1.00 OE2 A:GLU391 1.8 21.6 1.0 NE2 A:HIS223 2.1 19.3 1.0 NE2 A:HIS305 2.1 22.7 1.0 O A:HOH839 2.2 24.7 1.0 CD A:GLU391 2.9 22.6 1.0 CD2 A:HIS223 3.0 19.4 1.0 CE1 A:HIS305 3.0 22.0 1.0 CD2 A:HIS305 3.1 21.4 1.0 CE1 A:HIS223 3.1 19.7 1.0 OE1 A:GLU391 3.4 24.1 1.0 CE1 A:PHE378 4.0 32.4 1.0 CG A:HIS223 4.1 18.9 1.0 ND1 A:HIS305 4.2 19.8 1.0 CG A:GLU391 4.2 22.1 1.0 ND1 A:HIS223 4.2 19.6 1.0 CG A:HIS305 4.2 20.9 1.0 NE2 A:GLN376 4.2 29.8 1.0 CZ A:PHE378 4.3 36.1 1.0 CB A:ALA307 4.3 22.1 1.0 CG2 A:VAL225 4.4 19.0 1.0 CB A:GLU391 4.4 22.3 1.0 CE2 A:PHE416 4.8 26.7 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ B:Co501 b:19.7 occ:1.00 OE2 B:GLU391 1.8 23.7 1.0 NE2 B:HIS223 2.0 17.1 1.0 NE2 B:HIS305 2.1 21.3 1.0 CD B:GLU391 2.9 23.0 1.0 CE1 B:HIS223 3.0 18.6 1.0 CE1 B:HIS305 3.1 20.8 1.0 CD2 B:HIS223 3.1 18.5 1.0 CD2 B:HIS305 3.1 20.9 1.0 OE1 B:GLU391 3.4 25.1 1.0 CZ B:PHE378 3.8 46.7 1.0 CE2 B:PHE378 4.0 45.0 1.0 ND1 B:HIS223 4.1 18.5 1.0 CG B:GLU391 4.2 22.7 1.0 CG B:HIS223 4.2 18.3 1.0 NE2 B:GLN376 4.2 29.4 1.0 ND1 B:HIS305 4.2 20.3 1.0 CG B:HIS305 4.3 21.8 1.0 CB B:ALA307 4.3 21.7 1.0 CG2 B:VAL225 4.3 19.6 1.0 CB B:GLU391 4.5 22.5 1.0 CE2 B:PHE416 4.8 28.1 1.0

T.Nishio, N.Nishijima, T.Kubota, Y.Furuhata, Y.Nanao, H.Permana, T.Furuhashi, Y.Kato. Mechanism of Herbicidal Action and Rice Selectivity of Iptriazopyrid: A Novel Azole Carboxamide-Based Inhibitor of 4-Hydroxyphenylpyruvate Dioxygenase. J.Agric.Food Chem. 2025.
ISSN: ESSN 1520-5118
PubMed: 40495343
DOI: 10.1021/ACS.JAFC.4C11831