Calcium in PDB 5nm8: Structure of Pipy, the COG0325 Family Member of Synechococcus Elongatus PCC7942, with Plp Bound

The structure of Structure of Pipy, the COG0325 Family Member of Synechococcus Elongatus PCC7942, with Plp Bound, PDB code: 5nm8 was solved by L.Tremino, A.Forcada-Nadal, A.Contreras, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.60 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.627, 98.937, 103.737, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.8

The binding sites of Calcium atom in the Structure of Pipy, the COG0325 Family Member of Synechococcus Elongatus PCC7942, with Plp Bound (pdb code 5nm8). 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 Structure of Pipy, the COG0325 Family Member of Synechococcus Elongatus PCC7942, with Plp Bound, PDB code: 5nm8:

Calcium binding site 1 out of 1 in the Structure of Pipy, the COG0325 Family Member of Synechococcus Elongatus PCC7942, with Plp Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Pipy, the COG0325 Family Member of Synechococcus Elongatus PCC7942, with Plp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:38.4 occ:1.00 O B:HOH452 2.3 44.6 1.0 O B:HOH429 2.4 39.4 1.0 O B:PRO63 2.4 36.7 1.0 O B:HOH433 2.5 36.2 1.0 O B:HOH408 2.5 35.9 1.0 C B:PRO63 3.6 36.8 1.0 O B:HOH432 4.3 37.0 1.0 O B:HOH457 4.4 54.6 1.0 CA B:ASP64 4.4 36.2 1.0 O B:HOH454 4.5 48.0 1.0 N B:ASP64 4.5 36.7 1.0 CA B:PRO63 4.6 38.6 1.0 OD1 B:ASP64 4.6 40.6 1.0 CB B:PRO63 4.9 38.5 1.0 O B:HOH431 5.0 60.0 1.0 O B:LEU65 5.0 33.9 1.0

L.Tremino, A.Forcada-Nadal, A.Contreras, V.Rubio. Studies on Cyanobacterial Protein Pipy Shed Light on Structure, Potential Functions, and Vitamin B6 -Dependent Epilepsy. Febs Lett. V. 591 3431 2017.
ISSN: ISSN 1873-3468
PubMed: 28914444
DOI: 10.1002/1873-3468.12841