Calcium in PDB 6khn: Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin

The structure of Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin, PDB code: 6khn was solved by Y.Z.Zhou, L.J.Liao, X.K.Liu, Y.Guo, Y.C.Zhao, Z.X.Zeng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.88 / 2.29
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.274, 156.274, 102.392, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20.2

The binding sites of Calcium atom in the Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin (pdb code 6khn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin, PDB code: 6khn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:44.2 occ:1.00 OD1 A:ASP408 2.3 38.4 1.0 O A:HOH727 2.3 42.0 1.0 O A:HOH701 2.3 41.0 1.0 O A:HOH837 2.4 41.8 1.0 O A:HOH713 2.5 32.5 1.0 O A:HOH806 2.5 42.2 1.0 O A:HOH734 3.0 50.8 1.0 CG A:ASP408 3.3 41.9 1.0 OD2 A:ASP408 3.6 39.4 1.0 ND1 A:HIS404 4.1 42.8 1.0 O A:HOH844 4.1 40.0 1.0 CE A:MET411 4.1 45.5 1.0 O A:GLY489 4.3 33.5 1.0 O A:GLN493 4.3 44.6 1.0 CE1 A:HIS404 4.4 41.4 1.0 O A:SER490 4.5 39.6 1.0 OG A:SER407 4.5 47.4 1.0 CB A:ASP408 4.7 35.7 1.0 O A:HIS404 4.7 39.8 1.0 O A:SER491 4.8 45.5 1.0 C A:GLY489 4.8 38.1 1.0 CA A:GLY489 4.8 39.6 1.0 N A:ASP408 4.9 41.1 1.0 CA A:ASP408 4.9 42.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:80.7 occ:1.00 O A:HOH852 2.4 54.8 1.0 O A:HOH863 2.5 58.3 1.0 O A:HOH864 2.8 50.0 1.0 OE1 A:GLU354 4.1 57.1 1.0 O A:HOH762 4.4 34.4 1.0 O A:SER365 4.5 38.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:38.0 occ:1.00 O B:HOH750 2.4 30.7 1.0 O B:HOH718 2.4 32.3 1.0 O B:HOH788 2.5 30.9 1.0 OD1 B:ASP408 2.5 32.7 1.0 O B:HOH850 2.5 46.4 1.0 O B:HOH723 2.6 34.4 1.0 CG B:ASP408 3.5 32.7 1.0 OD2 B:ASP408 3.8 35.0 1.0 CE B:MET411 4.2 36.1 1.0 O B:GLN493 4.3 39.1 1.0 O B:HOH743 4.3 35.3 1.0 O B:GLY489 4.4 31.0 1.0 ND1 B:HIS404 4.4 35.0 1.0 OG B:SER407 4.5 40.2 1.0 O B:SER491 4.5 35.0 1.0 O B:SER490 4.6 32.3 1.0 O B:HIS404 4.7 32.6 1.0 CB B:ASP408 4.8 32.6 1.0 CA B:GLY489 4.9 30.5 1.0 C B:GLY489 4.9 32.7 1.0 CE1 B:HIS404 4.9 31.4 1.0 N B:ASP408 5.0 31.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Oryza Sativa Tdc with Plp and Serotonin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:74.7 occ:1.00 O B:HOH847 2.4 58.4 1.0 O B:HOH711 2.5 57.5 1.0 O A:HOH702 2.7 52.0 1.0 O A:HOH860 2.8 61.6 1.0 OD1 A:ASP64 3.8 48.5 1.0 NH2 B:ARG159 4.5 48.8 1.0 OE1 B:GLU162 4.5 48.1 1.0 CG A:ASP64 4.7 43.8 1.0 O B:GLU162 5.0 51.3 1.0

Y.Zhou, L.Liao, X.Liu, B.Liu, X.Chen, Y.Guo, C.Huang, Y.Zhao, Z.Zeng. Crystal Structure Oforyza Sativatdc Reveals the Substrate Specificity For Tdc-Mediated Melatonin Biosynthesis. J Adv Res V. 24 501 2020.
ISSN: ISSN 2090-1232
PubMed: 32595985
DOI: 10.1016/J.JARE.2020.06.004