Calcium in PDB 6khp: Crystal Structure of Oryza Sativa Tdc with Plp and Tryptamine

The structure of Crystal Structure of Oryza Sativa Tdc with Plp and Tryptamine, PDB code: 6khp 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)	28.14 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	155.769, 155.769, 102.094, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 19.8

The binding sites of Calcium atom in the Crystal Structure of Oryza Sativa Tdc with Plp and Tryptamine (pdb code 6khp). 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 Tryptamine, PDB code: 6khp:
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 Tryptamine


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 Tryptamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:40.3 occ:1.00 OD1 A:ASP408 2.3 32.0 1.0 O A:HOH738 2.3 37.1 1.0 O A:HOH715 2.4 30.9 1.0 O A:HOH791 2.4 35.8 1.0 O A:HOH727 2.4 29.7 1.0 O A:HOH853 2.5 37.0 1.0 O A:HOH746 2.6 43.6 1.0 CG A:ASP408 3.3 36.0 1.0 OD2 A:ASP408 3.6 34.0 1.0 CE A:MET411 4.3 37.4 1.0 O A:HOH869 4.3 33.8 1.0 O A:GLN493 4.3 41.5 1.0 O A:GLY489 4.3 30.8 1.0 ND1 A:HIS404 4.4 35.3 1.0 OG A:SER407 4.5 41.0 1.0 O A:SER491 4.6 39.5 1.0 O A:SER490 4.6 36.6 1.0 CB A:ASP408 4.6 33.5 1.0 O A:HIS404 4.7 36.3 1.0 CA A:GLY489 4.8 33.9 1.0 C A:GLY489 4.8 33.3 1.0 CE1 A:HIS404 4.8 33.0 1.0 N A:ASP408 4.9 35.8 1.0 CA A:ASP408 4.9 38.3 1.0

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


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 Tryptamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:78.5 occ:1.00 O A:HOH871 2.6 43.8 1.0 O A:HOH876 2.7 46.8 1.0 O A:HOH892 2.7 48.8 1.0 O A:SER365 4.0 37.5 1.0 O A:HOH744 4.4 38.2 1.0 O A:HOH851 4.4 31.8 1.0 O A:HOH713 4.6 45.2 1.0 O A:HOH730 4.8 37.2 1.0 OE1 A:GLU354 4.9 42.7 1.0 C A:SER365 4.9 31.8 1.0

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


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 Tryptamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:31.8 occ:1.00 O B:HOH747 2.4 28.3 1.0 OD1 B:ASP408 2.4 24.7 1.0 O B:HOH708 2.4 26.7 1.0 O B:HOH768 2.4 34.3 1.0 O B:HOH761 2.4 27.0 1.0 O B:HOH791 2.5 28.5 1.0 O B:HOH803 2.6 38.0 1.0 CG B:ASP408 3.4 28.1 1.0 OD2 B:ASP408 3.7 27.1 1.0 O B:GLN493 4.3 31.7 1.0 CE B:MET411 4.3 34.2 1.0 O B:HOH711 4.3 32.3 1.0 O B:GLY489 4.4 26.2 1.0 ND1 B:HIS404 4.4 32.0 1.0 OG B:SER407 4.4 32.5 1.0 O B:SER491 4.4 31.3 1.0 O B:SER490 4.6 28.4 1.0 CB B:ASP408 4.7 29.0 1.0 O B:HIS404 4.7 27.0 1.0 CE1 B:HIS404 4.8 29.8 1.0 C B:GLY489 4.9 29.3 1.0 CA B:GLY489 4.9 26.0 1.0 N B:ASP408 4.9 26.5 1.0 CA B:ASP408 4.9 29.8 1.0

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


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 Tryptamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:66.2 occ:1.00 O A:HOH701 2.5 46.9 1.0 O B:HOH703 2.5 47.9 1.0 O A:HOH885 2.6 59.3 1.0 O B:HOH882 2.7 51.6 1.0 OD1 A:ASP64 3.7 42.3 1.0 NH2 B:ARG159 4.4 44.6 1.0 OE1 B:GLU162 4.6 41.1 1.0 CG A:ASP64 4.7 39.1 1.0 O B:GLU162 4.8 46.1 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