Calcium in PDB 5b3p: NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form

All present enzymatic activity of NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form:
1.6.5.11;

The structure of NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form, PDB code: 5b3p was solved by Y.Hanazono, K.Takeda, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.50 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.264, 42.185, 70.095, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.9

The binding sites of Calcium atom in the NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form (pdb code 5b3p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form, PDB code: 5b3p:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:28.3 occ:1.00 O A:HOH360 2.3 39.5 1.0 O A:HOH369 2.4 29.2 1.0 OD2 A:ASP51 2.4 21.7 1.0 O A:HOH356 2.6 33.1 1.0 OD1 A:ASP51 2.7 19.5 1.0 CG A:ASP51 2.9 17.7 1.0 CG2 A:VAL53 4.0 21.7 1.0 CA A:CA203 4.4 18.3 1.0 CB A:ASP51 4.4 16.1 1.0 O A:HOH415 4.7 31.7 1.0 O A:ILE52 4.8 21.1 1.0

Calcium binding site 2 out of 3 in the NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:25.6 occ:1.00 OE2 A:GLU73 2.4 19.9 1.0 O A:HOH403 2.8 32.5 1.0 CD A:GLU73 3.1 20.4 1.0 OE1 A:GLU73 3.2 20.2 1.0 CA A:CA203 3.6 18.3 1.0 NH1 A:ARG87 4.4 43.5 1.0 CZ A:ARG87 4.5 50.9 1.0 CG A:GLU73 4.6 15.1 1.0 NE A:ARG87 4.7 52.6 1.0 CD A:ARG87 4.8 49.4 1.0

Calcium binding site 3 out of 3 in the NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of NQO5 of the Trypsin-Resistant Fragment (1-134) in P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:18.3 occ:1.00 OD2 A:ASP51 2.3 21.7 1.0 OE1 A:GLU73 2.4 20.2 1.0 CG A:ASP51 3.2 17.7 1.0 CB A:ASP51 3.3 16.1 1.0 CD A:GLU73 3.5 20.4 1.0 CA A:CA202 3.6 25.6 1.0 O A:HOH360 3.8 39.5 1.0 OE2 A:GLU73 4.0 19.9 1.0 CA A:CA201 4.4 28.3 1.0 OD1 A:ASP51 4.4 19.5 1.0 CG A:GLU73 4.7 15.1 1.0 CB A:GLU73 4.7 12.3 1.0 CA A:ASP51 4.8 14.8 1.0

Y.Hanazono, K.Takeda, K.Miki. Characterization of the NQO5 Subunit of Bacterial Complex I in the Isolated State Febs Open Bio V. 6 687 2016.
ISSN: ESSN 2211-5463
PubMed: 27398308
DOI: 10.1002/2211-5463.12070