Calcium in PDB 3a8r: The Structure of the N-Terminal Regulatory Domain of A Plant Nadph Oxidase

The structure of The Structure of the N-Terminal Regulatory Domain of A Plant Nadph Oxidase, PDB code: 3a8r was solved by T.Oda, H.Hashimoto, N.Kuwabara, S.Akashi, K.Hayashi, C.Kojima, H.L.Wong, T.Kawasaki, K.Shimamoto, M.Sato, T.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.47 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.418, 72.162, 118.902, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 26.6

The binding sites of Calcium atom in the The Structure of the N-Terminal Regulatory Domain of A Plant Nadph Oxidase (pdb code 3a8r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Structure of the N-Terminal Regulatory Domain of A Plant Nadph Oxidase, PDB code: 3a8r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Structure of the N-Terminal Regulatory Domain of A Plant Nadph Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of the N-Terminal Regulatory Domain of A Plant Nadph Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:42.3 occ:1.00 O A:ARG248 2.2 44.3 1.0 O A:HOH25 2.2 44.5 1.0 OD1 A:ASP242 2.2 43.1 1.0 OD1 A:ASP246 2.3 42.8 1.0 OD1 A:ASN244 2.4 44.7 1.0 OE1 A:GLU253 2.5 46.5 1.0 OE2 A:GLU253 2.7 42.7 1.0 CD A:GLU253 2.9 45.0 1.0 CG A:ASP246 3.3 45.7 1.0 CG A:ASP242 3.3 42.6 1.0 C A:ARG248 3.4 42.8 1.0 CG A:ASN244 3.6 45.7 1.0 OD2 A:ASP246 3.6 42.4 1.0 OD2 A:ASP242 4.1 43.8 1.0 N A:ARG248 4.1 45.4 1.0 CA A:ASP242 4.1 41.4 1.0 ND2 A:ASN244 4.2 41.2 1.0 CA A:ARG248 4.2 44.5 1.0 CB A:ASP242 4.2 40.7 1.0 N A:ASP246 4.3 45.0 1.0 N A:LEU249 4.3 41.7 1.0 C A:ASP242 4.4 42.0 1.0 N A:ASN244 4.4 46.5 1.0 N A:LYS243 4.5 43.7 1.0 CG A:GLU253 4.5 46.8 1.0 CA A:LEU249 4.5 42.8 1.0 CB A:ARG248 4.5 45.9 1.0 CB A:ASP246 4.6 42.0 1.0 O A:HOH13 4.7 46.3 1.0 N A:ALA245 4.8 45.9 1.0 CB A:ASN244 4.8 45.3 1.0 CA A:ASP246 4.8 40.2 1.0 N A:THR250 4.9 40.0 1.0 CD1 A:LEU249 4.9 46.1 1.0 CA A:ASN244 4.9 44.2 1.0 O A:ASP242 4.9 42.9 1.0 C A:ASN244 5.0 46.5 1.0

Calcium binding site 2 out of 2 in the The Structure of the N-Terminal Regulatory Domain of A Plant Nadph Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of the N-Terminal Regulatory Domain of A Plant Nadph Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:53.8 occ:1.00 OD1 B:ASP242 2.2 58.0 1.0 OD1 B:ASN244 2.3 62.5 1.0 O B:HOH68 2.3 56.0 1.0 OD1 B:ASP246 2.4 60.3 1.0 O B:ARG248 2.4 55.7 1.0 OE2 B:GLU253 2.5 57.7 1.0 OE1 B:GLU253 2.6 56.0 1.0 CD B:GLU253 2.9 56.8 1.0 CG B:ASN244 3.3 64.0 1.0 CG B:ASP246 3.3 61.2 1.0 CG B:ASP242 3.5 58.8 1.0 C B:ARG248 3.5 54.1 1.0 OD2 B:ASP246 3.5 57.6 1.0 ND2 B:ASN244 3.6 61.8 1.0 N B:ARG248 4.3 54.3 1.0 CA B:ASP242 4.3 58.9 1.0 N B:ASP246 4.3 56.4 1.0 CB B:ASP242 4.3 56.8 1.0 OD2 B:ASP242 4.3 59.0 1.0 CA B:LEU249 4.3 52.5 1.0 N B:LEU249 4.4 53.9 1.0 CA B:ARG248 4.4 52.8 1.0 CG B:GLU253 4.5 56.0 1.0 C B:ASP242 4.5 58.0 1.0 CB B:ASP246 4.6 56.4 1.0 CB B:ASN244 4.6 58.6 1.0 CG2 B:THR250 4.6 56.9 1.0 N B:ASN244 4.7 60.2 1.0 CD2 B:LEU249 4.7 52.2 1.0 N B:LYS243 4.8 60.9 1.0 CB B:ARG248 4.8 54.8 1.0 N B:THR250 4.8 53.5 1.0 N B:ALA245 4.8 59.3 1.0 CA B:ASP246 4.9 60.9 1.0 O B:ASP242 4.9 56.6 1.0

T.Oda, H.Hashimoto, N.Kuwabara, S.Akashi, K.Hayashi, C.Kojima, H.L.Wong, T.Kawasaki, K.Shimamoto, M.Sato, T.Shimizu. The Structure of the N-Terminal Regulatory Domain of A Plant Nadph Oxidase and Its Functional Implications J.Biol.Chem. V. 285 1435 2010.
ISSN: ISSN 0021-9258
PubMed: 19864426
DOI: 10.1074/JBC.M109.058909