Calcium in PDB 5d9v: Crystal Structure of Oxidized Dehydroascorbate Reductase (Osdhar) From Oryza Sativa L. Japonica

The structure of Crystal Structure of Oxidized Dehydroascorbate Reductase (Osdhar) From Oryza Sativa L. Japonica, PDB code: 5d9v was solved by H.Do, J.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.18 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.966, 47.905, 51.900, 90.00, 107.24, 90.00
R / Rfree (%)	19.8 / 25.5

The binding sites of Calcium atom in the Crystal Structure of Oxidized Dehydroascorbate Reductase (Osdhar) From Oryza Sativa L. Japonica (pdb code 5d9v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Oxidized Dehydroascorbate Reductase (Osdhar) From Oryza Sativa L. Japonica, PDB code: 5d9v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Oxidized Dehydroascorbate Reductase (Osdhar) From Oryza Sativa L. Japonica


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 Oxidized Dehydroascorbate Reductase (Osdhar) From Oryza Sativa L. Japonica within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:28.8 occ:1.00 N A:LYS200 3.3 24.6 1.0 CG A:LYS200 3.5 22.3 1.0 NZ A:LYS197 3.6 28.4 1.0 CB A:LYS200 3.9 22.5 1.0 CA A:ALA199 4.0 20.5 1.0 CD A:LYS200 4.1 21.1 1.0 C A:ALA199 4.2 21.8 1.0 CA A:LYS200 4.2 21.8 1.0 O A:HOH423 4.3 31.9 1.0 CE A:LYS200 4.3 24.5 1.0 OE1 A:GLU201 4.5 29.5 1.0 OH A:TYR159 4.5 33.8 1.0 CB A:ALA199 4.5 23.9 1.0 O A:ALA198 4.9 23.6 1.0 CE A:LYS197 4.9 27.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Oxidized Dehydroascorbate Reductase (Osdhar) From Oryza Sativa L. Japonica


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 Oxidized Dehydroascorbate Reductase (Osdhar) From Oryza Sativa L. Japonica within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:41.1 occ:1.00 N A:ASP15 3.1 26.1 1.0 OG1 A:THR16 3.3 30.0 1.0 C A:HIS13 3.5 29.5 1.0 CA A:ASP15 3.7 28.2 1.0 N A:PRO14 3.7 29.5 1.0 CB A:ASP15 3.7 43.9 1.0 CA A:HIS13 3.7 29.2 1.0 CB A:HIS13 3.7 27.7 1.0 N A:THR16 3.7 24.5 1.0 C A:ASP15 3.7 26.5 1.0 O A:HIS13 3.8 24.1 1.0 CD A:PRO14 3.9 34.7 1.0 CB A:THR16 4.1 27.4 1.0 C A:PRO14 4.2 26.5 1.0 O A:ASP15 4.4 29.7 1.0 CG A:HIS13 4.5 32.5 1.0 CD2 A:HIS13 4.5 35.8 1.0 CA A:THR16 4.5 25.1 1.0 CA A:PRO14 4.5 27.1 1.0 CG A:PRO14 4.6 35.6 1.0 OD2 A:ASP15 4.6 69.8 1.0 CG A:ASP15 4.7 61.8 1.0

H.Do, I.S.Kim, B.W.Jeon, C.W.Lee, A.K.Park, A.R.Wi, S.C.Shin, H.Park, Y.S.Kim, H.S.Yoon, H.W.Kim, J.H.Lee. Structural Understanding of the Recycling of Oxidized Ascorbate By Dehydroascorbate Reductase (Osdhar) From Oryza Sativa L. Japonica Sci Rep V. 6 19498 2016.
ISSN: ESSN 2045-2322
PubMed: 26775680
DOI: 10.1038/SREP19498