Calcium in PDB 8jqo: Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole

The structure of Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole, PDB code: 8jqo was solved by R.Fukushima, N.Katsuki, S.Fushinobu, N.Takaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.45 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.26, 67.389, 128.234, 90, 90.67, 90
R / Rfree (%)	22.3 / 24.7

The binding sites of Calcium atom in the Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole (pdb code 8jqo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole, PDB code: 8jqo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:17.1 occ:0.50 OD2 A:ASP134 2.4 19.1 1.0 O A:HOH566 2.5 28.0 1.0 OD1 A:ASP134 2.7 21.9 1.0 CG A:ASP134 2.9 21.4 1.0 CB A:ASP134 4.4 19.6 1.0 NH1 A:ARG138 4.4 24.1 1.0 O A:HOH567 4.6 28.2 1.0 OD2 A:ASP135 4.7 26.9 1.0 N A:ASP135 5.0 19.7 1.0

Calcium binding site 2 out of 4 in the Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:22.2 occ:0.50 O B:HOH672 2.4 33.0 1.0 O B:HOH656 2.4 31.4 1.0 OD1 B:ASP237 2.5 22.8 1.0 OD2 B:ASP237 2.6 25.9 1.0 CG B:ASP237 2.9 24.3 1.0 O B:HOH502 3.9 32.0 1.0 CB B:ASP237 4.4 19.1 1.0 O B:ASP237 4.7 22.5 1.0 CB B:SER241 4.9 23.5 1.0

Calcium binding site 3 out of 4 in the Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca404 b:35.6 occ:0.50 OD2 C:ASP232 2.2 30.8 1.0 O C:HOH626 2.4 46.0 1.0 O B:HOH553 2.4 43.4 1.0 O C:HOH560 2.7 37.4 1.0 O C:HOH504 2.9 36.6 1.0 O C:HOH589 3.1 46.1 1.0 CG C:ASP232 3.3 27.7 1.0 OD1 C:ASP232 4.0 29.6 1.0 CD B:ARG138 4.3 29.7 1.0 OD1 C:ASP230 4.4 22.2 1.0 CB C:ASP232 4.4 22.2 1.0 OE1 B:GLU149 4.6 39.7 1.0 OE2 B:GLU149 4.6 36.9 1.0 OD2 C:ASP230 4.7 25.9 1.0 CG C:ASP230 5.0 23.0 1.0 NE B:ARG138 5.0 27.3 1.0

Calcium binding site 4 out of 4 in the Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Protocatecuate Hydroxylase From Xylophilus Ampelinus Complexed with Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca403 b:34.3 occ:0.50 OD2 D:ASP232 2.3 24.0 1.0 O D:HOH568 2.4 46.9 1.0 O D:HOH521 2.5 31.6 1.0 O D:HOH509 2.8 31.8 1.0 O D:HOH531 3.0 39.8 1.0 CG D:ASP232 3.3 24.0 1.0 OD1 D:ASP232 3.9 23.9 1.0 O D:HOH563 3.9 35.4 1.0 OD1 D:ASP230 4.4 17.6 1.0 CB D:ASP232 4.4 17.2 1.0 OD2 D:ASP230 4.7 17.0 1.0 CG D:ASP230 5.0 16.8 1.0

N.Katsuki, R.Fukushima, Y.Doi, S.Masuo, T.Arakawa, C.Yamada, S.Fushinobu, N.Takaya. Protocatechuate Hydroxylase Is A Novel Group A Flavoprotein Monooxygenase with A Unique Substrate Recognition Mechanism. J.Biol.Chem. 05508 2023.
ISSN: ESSN 1083-351X
PubMed: 38029967
DOI: 10.1016/J.JBC.2023.105508