Zinc 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:

Cobalt

(Co)

2 atoms

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Oryza Sativa Hppd (pdb code 9kp0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Oryza Sativa Hppd, PDB code: 9kp0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:46.6 occ:1.00 O A:HOH684 1.8 39.5 1.0 O A:HOH744 2.2 47.4 1.0 NE2 A:HIS30 2.3 36.2 1.0 O A:HOH823 2.7 29.9 1.0 O A:HOH841 2.7 46.7 1.0 CD2 A:HIS30 3.0 36.6 1.0 CE1 A:HIS30 3.4 37.8 1.0 CG A:HIS30 4.3 34.5 1.0 O A:PHE416 4.4 30.8 1.0 ND1 A:HIS30 4.4 36.9 1.0 N A:LYS418 4.5 30.6 1.0 CB A:LYS418 4.8 35.5 1.0 CA A:GLY417 4.8 30.3 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:37.8 occ:1.00 O A:HOH813 1.8 31.1 1.0 OD1 A:ASP367 2.0 29.4 1.0 O A:HOH818 2.5 44.9 1.0 CG A:ASP367 2.9 30.2 1.0 OD2 A:ASP367 3.2 31.8 1.0 O A:HOH823 3.2 29.9 1.0 O A:HOH845 3.6 46.4 1.0 O A:HOH803 4.1 44.3 1.0 N A:GLY419 4.1 25.1 1.0 NH2 A:ARG346 4.1 38.5 1.0 O A:ARG368 4.2 36.8 1.0 CA A:GLY419 4.2 24.4 1.0 CB A:ASP367 4.3 29.5 1.0 N A:ARG368 4.5 31.5 1.0 NE A:ARG346 4.5 42.2 1.0 CZ A:ARG346 4.7 40.0 1.0 CA A:ASP367 4.7 28.2 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:50.7 occ:1.00 OD2 A:ASP185 2.0 38.3 1.0 NE2 A:HIS136 2.3 28.1 1.0 O A:HOH616 2.4 33.9 1.0 O A:HOH840 2.7 38.2 1.0 CE1 A:HIS136 2.9 28.0 1.0 CG A:ASP185 2.9 33.5 1.0 OD1 A:ASP185 3.2 40.5 1.0 CD2 A:HIS136 3.5 28.2 1.0 OD2 A:ASP135 3.7 35.8 1.0 O A:HOH736 4.0 42.1 1.0 ND1 A:HIS136 4.1 26.0 1.0 O A:HOH639 4.2 28.7 1.0 CB A:ASP185 4.2 27.9 1.0 CB A:ASP135 4.3 29.3 1.0 CG A:HIS136 4.4 26.0 1.0 CG A:ASP135 4.4 32.5 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:27.1 occ:1.00 O A:HOH829 2.1 22.8 1.0 OD2 A:ASP152 2.1 26.9 1.0 CG A:ASP152 2.8 27.7 1.0 OD1 A:ASP152 2.9 28.6 1.0 O A:HOH851 3.9 16.1 1.0 CB A:ASP152 4.3 26.5 1.0 O A:HOH843 4.3 40.8 1.0 O A:HOH706 4.6 19.7 1.0 O A:HOH819 4.7 48.3 1.0 NH2 A:ARG155 5.0 31.5 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:29.2 occ:1.00 OD1 A:ASP149 1.9 24.2 1.0 O A:HOH774 2.1 29.0 1.0 CG A:ASP149 2.7 23.9 1.0 OD2 A:ASP149 3.0 24.4 1.0 O A:HOH729 4.0 35.1 1.0 O A:HOH808 4.0 32.2 1.0 CB A:ASP149 4.2 23.6 1.0 O A:HOH662 4.2 25.8 1.0 CB A:ALA151 4.5 24.9 1.0 OG A:SER192 4.5 19.8 1.0 N A:ALA150 4.6 23.3 1.0 N A:ALA151 4.6 24.2 1.0 CA A:ASP149 4.7 23.9 1.0 O A:HOH706 4.8 19.7 1.0 C A:ASP149 5.0 23.8 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:39.4 occ:1.00 ND1 A:HIS283 2.0 27.2 1.0 O A:HOH816 2.4 30.4 1.0 CE1 A:HIS283 3.0 26.2 1.0 CG A:HIS283 3.0 27.7 1.0 CB A:HIS283 3.4 28.4 1.0 O A:HOH787 3.8 36.6 1.0 O A:HOH849 3.9 39.8 1.0 NE2 A:HIS283 4.1 25.8 1.0 CD2 A:HIS283 4.1 27.7 1.0 CA A:HIS283 4.1 27.9 1.0 O A:HOH713 4.6 34.4 1.0 N A:GLY284 4.9 33.9 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:75.4 occ:1.00 NE2 A:HIS297 2.0 30.6 1.0 CE1 A:HIS297 2.3 30.6 1.0 O A:HOH606 2.5 46.6 1.0 O A:HOH836 3.0 41.1 1.0 CD2 A:HIS297 3.4 29.7 1.0 ND1 A:HIS297 3.6 28.6 1.0 CG A:HIS297 4.1 27.6 1.0 NH1 A:ARG288 4.2 46.1 1.0 NH2 A:ARG288 4.6 45.5 1.0 CZ A:ARG288 4.9 45.9 1.0 CD2 B:LEU79 4.9 34.6 1.0 OXT A:ACY502 4.9 27.9 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:54.8 occ:1.00 O B:HOH685 1.8 40.4 1.0 O B:HOH779 2.3 39.7 1.0 NE2 B:HIS30 2.3 38.1 1.0 CD2 B:HIS30 3.0 37.3 1.0 CE1 B:HIS30 3.5 37.6 1.0 CG B:HIS30 4.2 35.4 1.0 O B:PHE416 4.4 36.3 1.0 ND1 B:HIS30 4.5 34.9 1.0 CB B:LYS418 4.8 44.0 1.0 N B:LYS418 4.8 38.4 1.0 O B:HOH789 5.0 33.0 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:44.8 occ:1.00 OD1 B:ASP367 2.1 35.0 1.0 O B:HOH804 2.2 33.6 1.0 O B:HOH788 2.8 36.0 1.0 O B:HOH729 2.8 32.7 1.0 CG B:ASP367 3.0 32.8 1.0 OD2 B:ASP367 3.4 29.2 1.0 NH2 B:ARG346 4.0 43.9 1.0 CA B:GLY419 4.2 29.4 1.0 CB B:ASP367 4.3 30.6 1.0 N B:GLY419 4.3 30.9 1.0 NE B:ARG346 4.3 49.6 1.0 O B:ARG368 4.4 37.7 1.0 N B:ARG368 4.5 34.1 1.0 CA B:ASP367 4.5 30.4 1.0 CZ B:ARG346 4.6 44.9 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Oryza Sativa Hppd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Oryza Sativa Hppd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:24.8 occ:1.00 NE2 B:HIS136 1.9 24.0 1.0 OD2 B:ASP185 2.0 27.2 1.0 O B:HOH626 2.1 26.3 1.0 CE1 B:HIS136 2.8 23.8 1.0 CG B:ASP185 2.9 24.0 1.0 CD2 B:HIS136 3.0 22.9 1.0 OD1 B:ASP185 3.2 23.9 1.0 CD2 B:PHE132 3.8 19.4 1.0 ND1 B:HIS136 4.0 23.0 1.0 OD2 B:ASP135 4.0 21.3 1.0 CG B:HIS136 4.1 22.8 1.0 CB B:ASP185 4.1 23.6 1.0 CE2 B:PHE132 4.2 19.9 1.0 O B:HOH693 4.2 22.6 1.0 CB B:ASP135 4.3 22.7 1.0 O B:HOH714 4.3 22.9 1.0 O B:HOH746 4.3 33.3 1.0 O B:HOH657 4.6 21.9 1.0 CG B:ASP135 4.6 22.2 1.0 CG B:PHE132 4.7 20.6 1.0 CA B:PHE132 4.9 21.4 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