Calcium in PDB 2e26: Crystal Structure of Two Repeat Fragment of Reelin

The structure of Crystal Structure of Two Repeat Fragment of Reelin, PDB code: 2e26 was solved by N.Yasui, T.Nogi, T.Kitao, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.29 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.008, 70.953, 94.769, 90.00, 93.61, 90.00
R / Rfree (%)	17.9 / 21.9

The structure of Crystal Structure of Two Repeat Fragment of Reelin also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Two Repeat Fragment of Reelin (pdb code 2e26). 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 Two Repeat Fragment of Reelin, PDB code: 2e26:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Two Repeat Fragment of Reelin


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 Two Repeat Fragment of Reelin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:26.4 occ:1.00 O A:LEU2551 2.3 27.9 1.0 O A:ASN2522 2.3 31.4 1.0 O A:SER2549 2.4 28.9 1.0 OD1 A:ASP2657 2.4 27.5 1.0 O A:HOH2707 2.5 24.5 1.0 OD1 A:ASN2524 2.7 36.6 1.0 OD2 A:ASP2657 2.8 26.0 1.0 CG A:ASP2657 3.0 28.0 1.0 C A:LEU2551 3.5 27.8 1.0 C A:ASN2522 3.5 31.5 1.0 C A:SER2549 3.6 29.0 1.0 CG A:ASN2524 3.7 36.3 1.0 OD1 A:ASN2658 3.9 25.4 1.0 N A:LEU2551 4.0 28.2 1.0 ND2 A:ASN2524 4.2 36.4 1.0 C A:GLY2550 4.2 28.7 1.0 C A:PHE2523 4.2 33.0 1.0 O A:PHE2523 4.2 33.3 1.0 O A:HOH2706 4.2 21.6 1.0 N A:SER2549 4.3 28.8 1.0 CA A:LEU2551 4.3 28.1 1.0 CB A:PHE2523 4.4 32.4 1.0 CA A:ASN2522 4.4 31.1 1.0 N A:PHE2523 4.5 31.9 1.0 CB A:ASP2657 4.5 27.7 1.0 OG A:SER2549 4.5 30.2 1.0 N A:ASN2524 4.5 33.3 1.0 N A:ALA2552 4.5 27.7 1.0 CA A:SER2549 4.5 29.0 1.0 N A:GLY2550 4.5 29.0 1.0 CA A:PHE2523 4.6 32.6 1.0 CB A:ASN2522 4.6 31.4 1.0 CA A:GLY2550 4.6 29.0 1.0 O A:GLY2550 4.6 28.4 1.0 CA A:ALA2552 4.7 27.8 1.0 CB A:LEU2551 4.9 27.6 1.0 CB A:ASN2524 4.9 34.5 1.0 CA A:ASN2524 4.9 34.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Two Repeat Fragment of Reelin


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 Two Repeat Fragment of Reelin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:24.3 occ:1.00 O A:ASN2202 2.2 22.9 1.0 O A:ASP2173 2.3 22.0 1.0 O A:HOH2724 2.3 20.6 1.0 OD1 A:ASP2310 2.4 22.6 1.0 OE2 A:GLU2175 2.4 34.0 1.0 OD2 A:ASP2310 2.8 24.3 1.0 OE1 A:GLN2311 2.8 34.0 1.0 CG A:ASP2310 3.0 22.3 1.0 CD A:GLU2175 3.4 32.1 1.0 C A:ASN2202 3.4 23.5 1.0 C A:ASP2173 3.5 22.8 1.0 CD A:GLN2311 4.0 32.0 1.0 OE1 A:GLU2175 4.0 33.7 1.0 N A:ASN2202 4.1 25.4 1.0 CA A:ASP2173 4.1 23.1 1.0 CB A:ASP2173 4.3 22.9 1.0 C A:GLY2201 4.3 26.6 1.0 CG A:GLU2175 4.3 28.4 1.0 N A:ASN2203 4.3 22.0 1.0 CA A:ASN2202 4.4 24.6 1.0 CA A:ASN2203 4.4 21.6 1.0 CB A:ASP2310 4.5 19.9 1.0 N A:PHE2174 4.6 22.9 1.0 CD1 A:LEU2198 4.6 33.1 1.0 O A:GLY2201 4.6 26.2 1.0 CA A:GLY2201 4.7 27.5 1.0 CG A:GLN2311 4.7 25.8 1.0 CB A:PHE2174 4.7 22.4 1.0 N A:GLN2311 4.8 20.6 1.0 O A:SER2200 4.8 30.5 1.0 C A:PHE2174 4.9 23.1 1.0 CA A:PHE2174 4.9 23.0 1.0 N A:GLU2175 5.0 23.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Two Repeat Fragment of Reelin


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 Two Repeat Fragment of Reelin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:21.5 occ:1.00 O A:ASP2327 2.3 22.1 1.0 O A:HOH2996 2.3 20.1 1.0 O A:ASP2353 2.4 20.2 1.0 O A:THR2351 2.4 22.1 1.0 O A:HOH2849 2.4 24.3 1.0 OD1 A:ASP2474 2.5 21.5 1.0 OD2 A:ASP2474 2.5 19.8 1.0 CG A:ASP2474 2.8 21.3 1.0 C A:ASP2327 3.4 22.8 1.0 C A:ASP2353 3.6 20.6 1.0 C A:THR2351 3.6 22.0 1.0 N A:ASP2353 4.0 21.2 1.0 C A:GLY2352 4.0 21.7 1.0 CA A:ASP2327 4.1 23.0 1.0 CB A:ASP2327 4.2 23.4 1.0 OG1 A:THR2351 4.2 21.7 0.5 CA A:GLY2352 4.3 21.7 1.0 O A:HOH2924 4.3 43.6 1.0 CB A:ASP2474 4.4 21.1 1.0 N A:GLY2352 4.4 21.8 1.0 CA A:ASP2353 4.4 21.2 1.0 O A:GLY2352 4.4 21.5 1.0 OD1 A:ASN2475 4.4 23.8 1.0 N A:PHE2328 4.5 22.5 1.0 N A:ALA2354 4.5 20.4 1.0 CA A:THR2351 4.6 22.2 0.5 CA A:THR2351 4.6 22.1 0.5 CB A:THR2351 4.7 22.0 0.5 CB A:PHE2328 4.7 23.0 1.0 CA A:ALA2354 4.7 20.5 1.0 CB A:THR2351 4.8 21.9 0.5 O A:HOH2906 4.8 41.0 1.0 CA A:PHE2328 4.9 23.3 1.0 C A:PHE2328 4.9 23.8 1.0 O A:HOH2745 4.9 37.6 1.0 CG A:ASP2327 4.9 25.0 1.0 N A:THR2351 4.9 22.1 1.0 N A:ASN2475 5.0 21.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Two Repeat Fragment of Reelin


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 Two Repeat Fragment of Reelin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:24.8 occ:1.00 O A:HOH3084 2.1 23.1 1.0 O A:SER1995 2.2 25.6 1.0 O A:THR1961 2.3 25.8 1.0 O A:GLU1993 2.4 34.6 1.0 OD1 A:ASP1963 2.4 32.2 1.0 OD1 A:ASP2125 2.5 19.7 1.0 OD2 A:ASP2125 2.5 21.0 1.0 CG A:ASP2125 2.8 21.8 1.0 CG A:ASP1963 3.4 34.9 1.0 C A:SER1995 3.4 26.4 1.0 C A:GLU1993 3.5 35.2 1.0 C A:THR1961 3.5 26.3 1.0 OD2 A:ASP1963 3.7 36.9 1.0 N A:SER1995 4.1 28.7 1.0 CA A:GLU1993 4.1 36.9 1.0 CA A:SER1995 4.2 27.5 1.0 O A:HOH3107 4.2 45.2 1.0 OD1 A:ASN2126 4.2 25.9 1.0 CA A:THR1961 4.2 25.6 1.0 C A:ASP1994 4.3 29.9 1.0 CB A:ASP2125 4.3 22.2 1.0 CB A:THR1961 4.4 25.9 1.0 N A:ALA1996 4.5 25.2 1.0 N A:ASP1994 4.5 33.2 1.0 N A:ASP1963 4.5 31.8 1.0 N A:PHE1962 4.5 26.7 1.0 C A:PHE1962 4.5 29.4 1.0 CB A:ASP1963 4.6 34.3 1.0 CB A:SER1995 4.6 27.5 1.0 CB A:PHE1962 4.6 26.7 1.0 CB A:GLU1993 4.7 37.5 1.0 O A:ASP1994 4.7 29.5 1.0 CA A:ALA1996 4.7 24.8 1.0 CA A:ASP1963 4.7 34.5 1.0 CG A:ASN2126 4.7 25.6 1.0 CA A:ASP1994 4.7 31.5 1.0 ND2 A:ASN2126 4.8 28.1 1.0 CA A:PHE1962 4.8 27.8 1.0 N A:ASN2126 4.9 22.4 1.0 O A:PHE1962 4.9 29.3 1.0 OE2 A:GLU1993 4.9 45.4 1.0

N.Yasui, T.Nogi, T.Kitao, Y.Nakano, M.Hattori, J.Takagi. Structure of A Receptor-Binding Fragment of Reelin and Mutational Analysis Reveal A Recognition Mechanism Similar to Endocytic Receptors. Proc.Natl.Acad.Sci.Usa V. 104 9988 2007.
ISSN: ISSN 0027-8424
PubMed: 17548821
DOI: 10.1073/PNAS.0700438104