Calcium in PDB 6nf0: Nocturnin with Bound Nadph Substrate

All present enzymatic activity of Nocturnin with Bound Nadph Substrate:
3.1.13.4;

The structure of Nocturnin with Bound Nadph Substrate, PDB code: 6nf0 was solved by M.A.Estrella, J.Du, A.Korennykh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.10 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.888, 62.888, 153.597, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 26.4

The binding sites of Calcium atom in the Nocturnin with Bound Nadph Substrate (pdb code 6nf0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Nocturnin with Bound Nadph Substrate, PDB code: 6nf0:

Calcium binding site 1 out of 1 in the Nocturnin with Bound Nadph Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Nocturnin with Bound Nadph Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:50.8 occ:1.00 O2B A:NDP502 2.3 73.3 1.0 OE2 A:GLU195 2.3 40.4 1.0 O A:HOH608 2.5 37.1 1.0 O A:HOH604 2.6 24.9 1.0 O2X A:NDP502 3.2 46.9 1.0 CD A:GLU195 3.3 41.1 1.0 C1B A:NDP502 3.3 71.1 1.0 C2B A:NDP502 3.3 72.8 1.0 P2B A:NDP502 3.3 54.8 1.0 OE1 A:GLU195 3.5 30.2 1.0 O3B A:NDP502 3.7 68.5 1.0 OD2 A:ASP413 4.1 47.3 1.0 C3B A:NDP502 4.2 69.1 1.0 OD1 A:ASP160 4.2 62.6 1.0 O4B A:NDP502 4.3 58.9 1.0 O1X A:NDP502 4.3 49.3 1.0 N9A A:NDP502 4.3 87.9 1.0 CD1 A:LEU151 4.4 32.0 1.0 O3X A:NDP502 4.4 69.4 1.0 OD2 A:ASP160 4.4 56.6 1.0 OD1 A:ASP413 4.4 37.9 1.0 ND2 A:ASN149 4.5 25.5 1.0 OD1 A:ASN149 4.5 25.3 1.0 NE2 A:HIS414 4.6 31.8 1.0 CG A:GLU195 4.7 35.4 1.0 CG A:ASP160 4.7 64.7 1.0 CG A:ASP413 4.7 43.7 1.0 C8A A:NDP502 4.8 89.4 1.0 CG A:ASN149 4.9 29.8 1.0 C4B A:NDP502 4.9 66.6 1.0 CD2 A:HIS414 5.0 29.7 1.0

M.A.Estrella, J.Du, L.Chen, S.Rath, E.Prangley, A.Chitrakar, T.Aoki, P.Schedl, J.Rabinowitz, A.Korennykh. The Metabolites Nadp+and Nadph Are the Targets of the Circadian Protein Nocturnin (Curled). Nat Commun V. 10 2367 2019.
ISSN: ESSN 2041-1723
PubMed: 31147539
DOI: 10.1038/S41467-019-10125-Z