Calcium in PDB 3a7q: Structural Basis For Specific Recognition of Reelin By Its Receptors

The structure of Structural Basis For Specific Recognition of Reelin By Its Receptors, PDB code: 3a7q was solved by N.Yasui, T.Nogi, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.93 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.980, 93.844, 73.456, 90.00, 107.41, 90.00
R / Rfree (%)	22.3 / 29.6

The structure of Structural Basis For Specific Recognition of Reelin By Its Receptors also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Structural Basis For Specific Recognition of Reelin By Its Receptors (pdb code 3a7q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structural Basis For Specific Recognition of Reelin By Its Receptors, PDB code: 3a7q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structural Basis For Specific Recognition of Reelin By Its Receptors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Basis For Specific Recognition of Reelin By Its Receptors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4001 b:52.4 occ:1.00 O A:SER1995 2.3 57.2 1.0 OD2 A:ASP1963 2.4 53.2 1.0 O A:THR1961 2.4 54.2 1.0 OD1 A:ASP2125 2.5 50.5 1.0 OD2 A:ASP2125 2.6 56.8 1.0 CG A:ASP2125 2.9 53.5 1.0 C A:SER1995 3.5 57.2 1.0 OD1 A:ASN2126 3.5 60.9 1.0 C A:THR1961 3.5 54.0 1.0 CG A:ASP1963 3.6 56.7 1.0 N A:SER1995 4.0 58.4 1.0 N A:ASP1994 4.2 59.3 1.0 CA A:SER1995 4.2 57.5 1.0 CA A:THR1961 4.2 54.2 1.0 CB A:ASP2125 4.4 56.1 1.0 CB A:ASP1963 4.4 56.6 1.0 CB A:THR1961 4.4 54.2 1.0 CG A:ASN2126 4.5 59.1 1.0 OD1 A:ASP1963 4.5 55.8 1.0 N A:ALA1996 4.5 56.6 1.0 N A:PHE1962 4.6 54.0 1.0 CB A:SER1995 4.6 57.5 1.0 C A:ASP1994 4.7 59.1 1.0 C A:PHE1962 4.7 54.7 1.0 N A:ASP1963 4.7 55.4 1.0 CA A:ALA1996 4.7 56.1 1.0 CA A:ASP1963 4.7 56.6 1.0 CB A:PHE1962 4.8 53.0 1.0 N A:ASN2126 4.9 57.4 1.0 CA A:PHE1962 4.9 53.9 1.0 ND2 A:ASN2126 4.9 59.5 1.0

Calcium binding site 2 out of 5 in the Structural Basis For Specific Recognition of Reelin By Its Receptors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Basis For Specific Recognition of Reelin By Its Receptors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4002 b:56.2 occ:1.00 O A:HOH6001 2.2 34.7 1.0 OD1 A:ASP2310 2.3 55.8 1.0 OD2 A:ASP2310 2.3 55.8 1.0 O A:ASN2202 2.3 61.0 1.0 OE2 A:GLU2175 2.5 55.7 1.0 O A:ASP2173 2.6 56.5 1.0 CG A:ASP2310 2.6 56.1 1.0 C A:ASN2202 3.5 60.7 1.0 CD A:GLU2175 3.6 57.4 1.0 C A:ASP2173 3.7 56.6 1.0 CB A:ASP2310 4.2 55.9 1.0 N A:ASN2202 4.2 62.1 1.0 O A:GLY2201 4.3 62.8 1.0 C A:GLY2201 4.3 63.0 1.0 CG A:GLU2175 4.4 56.7 1.0 CA A:ASP2173 4.4 56.8 1.0 CA A:ASN2202 4.4 61.3 1.0 N A:ASN2203 4.5 59.7 1.0 OE1 A:GLU2175 4.5 59.0 1.0 CA A:ASN2203 4.6 59.1 1.0 N A:GLN2311 4.7 56.9 1.0 CG A:GLN2311 4.8 59.3 1.0 CB A:ASP2173 4.8 57.0 1.0 NE2 A:GLN2311 4.8 62.8 1.0 N A:PHE2174 4.8 56.4 1.0 CB A:PHE2174 5.0 55.6 1.0 CB A:ASN2203 5.0 59.0 1.0

Calcium binding site 3 out of 5 in the Structural Basis For Specific Recognition of Reelin By Its Receptors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Basis For Specific Recognition of Reelin By Its Receptors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4003 b:55.4 occ:1.00 O A:HOH6002 2.3 54.5 1.0 O A:ASP2353 2.3 55.3 1.0 OD2 A:ASP2474 2.3 55.5 1.0 O A:THR2351 2.3 55.9 1.0 O A:ASP2327 2.4 57.1 1.0 OD1 A:ASP2474 2.4 54.1 1.0 CG A:ASP2474 2.7 54.1 1.0 C A:ASP2353 3.5 55.6 1.0 C A:ASP2327 3.5 57.9 1.0 C A:THR2351 3.6 56.5 1.0 N A:ASP2353 4.0 54.8 1.0 C A:GLY2352 4.2 54.9 1.0 CA A:ASP2327 4.2 57.8 1.0 CB A:ASP2474 4.2 53.3 1.0 OD1 A:ASN2475 4.3 53.9 1.0 CB A:ASP2327 4.3 57.5 1.0 CA A:ASP2353 4.4 55.4 1.0 N A:ALA2354 4.4 56.0 1.0 CA A:GLY2352 4.5 55.6 1.0 N A:GLY2352 4.5 56.2 1.0 N A:PHE2328 4.6 58.1 1.0 CA A:THR2351 4.6 57.1 1.0 O A:GLY2352 4.6 54.1 1.0 CA A:ALA2354 4.6 56.2 1.0 N A:THR2351 4.8 57.4 1.0 CB A:THR2351 4.8 57.6 1.0 CB A:PHE2328 4.8 58.1 1.0 O A:PHE2328 4.9 58.9 1.0 C A:PHE2328 4.9 58.7 1.0 CG A:ASN2475 4.9 53.7 1.0 N A:ASN2475 4.9 54.2 1.0 CA A:PHE2328 5.0 58.4 1.0 CG A:ASP2327 5.0 57.4 1.0

Calcium binding site 4 out of 5 in the Structural Basis For Specific Recognition of Reelin By Its Receptors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Basis For Specific Recognition of Reelin By Its Receptors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4004 b:53.5 occ:1.00 O A:ASN2522 2.3 56.8 1.0 O A:SER2549 2.3 53.4 1.0 O A:HOH6003 2.3 52.1 1.0 OD2 A:ASP2657 2.3 53.1 1.0 OD1 A:ASP2657 2.4 52.8 1.0 O A:LEU2551 2.4 51.9 1.0 CG A:ASP2657 2.7 51.1 1.0 OD1 A:ASN2524 3.0 63.5 1.0 C A:SER2549 3.5 53.5 1.0 C A:LEU2551 3.5 52.1 1.0 C A:ASN2522 3.5 58.5 1.0 N A:LEU2551 4.0 52.1 1.0 OD1 A:ASN2658 4.0 53.1 1.0 O A:PHE2523 4.1 61.7 1.0 C A:GLY2550 4.2 52.0 1.0 CG A:ASN2524 4.2 63.8 1.0 C A:PHE2523 4.2 61.1 1.0 N A:SER2549 4.2 54.6 1.0 CB A:ASP2657 4.2 52.6 1.0 N A:GLY2550 4.3 52.9 1.0 OG A:SER2549 4.3 55.5 1.0 CA A:LEU2551 4.3 52.1 1.0 CB A:PHE2523 4.4 59.8 1.0 O A:HOH6016 4.4 46.3 1.0 CA A:GLY2550 4.4 52.3 1.0 N A:ALA2552 4.4 52.2 1.0 CA A:SER2549 4.4 54.1 1.0 N A:PHE2523 4.4 59.0 1.0 CA A:ASN2522 4.5 58.5 1.0 CA A:PHE2523 4.5 60.1 1.0 CA A:ALA2552 4.6 52.4 1.0 N A:ASN2524 4.6 62.1 1.0 O A:GLY2550 4.7 51.6 1.0 CB A:ASN2522 4.8 58.5 1.0 ND2 A:ASN2524 4.8 62.8 1.0 N A:ASN2658 4.9 53.4 1.0

Calcium binding site 5 out of 5 in the Structural Basis For Specific Recognition of Reelin By Its Receptors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Basis For Specific Recognition of Reelin By Its Receptors within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5001 b:55.6 occ:1.00 O B:TRP64 2.2 57.8 1.0 OE2 B:GLU78 2.3 55.4 1.0 OD2 B:ASP77 2.3 55.5 1.0 O B:ASP69 2.3 56.7 1.0 OD2 B:ASP71 2.3 55.1 1.0 OD2 B:ASP67 2.3 56.3 1.0 CG B:ASP67 3.3 56.1 1.0 CD B:GLU78 3.4 55.7 1.0 C B:TRP64 3.4 57.6 1.0 CG B:ASP77 3.4 55.5 1.0 C B:ASP69 3.5 57.0 1.0 CG B:ASP71 3.5 54.6 1.0 OD1 B:ASP67 3.7 55.9 1.0 CG B:GLU78 3.8 55.7 1.0 CB B:ASP77 4.1 54.9 1.0 N B:ASP67 4.1 57.3 1.0 CB B:ASP71 4.1 55.0 1.0 N B:ASP71 4.1 55.9 1.0 N B:ASP69 4.1 57.2 1.0 CA B:ASP69 4.2 57.2 1.0 N B:CYS66 4.2 58.0 1.0 CB B:ASP69 4.3 57.4 1.0 CA B:TRP64 4.3 57.3 1.0 CB B:TRP64 4.3 57.1 1.0 N B:ARG65 4.3 57.7 1.0 O B:ASP77 4.3 55.2 1.0 CA B:ARG65 4.4 58.1 1.0 OE1 B:GLU78 4.4 55.9 1.0 OD1 B:ASP77 4.4 56.1 1.0 CB B:ASP67 4.4 56.6 1.0 NZ A:LYS2467 4.4 52.5 1.0 N B:ASP70 4.5 56.9 1.0 OD1 B:ASP71 4.5 52.4 1.0 C B:ARG65 4.6 58.0 1.0 CA B:ASP67 4.6 56.8 1.0 C B:ASP77 4.7 55.4 1.0 CA B:ASP70 4.7 56.6 1.0 CA B:ASP71 4.7 55.3 1.0 N B:GLU68 4.8 56.8 1.0 C B:ASP70 4.8 56.2 1.0 C B:ASP67 4.8 56.7 1.0

N.Yasui, T.Nogi, J.Takagi. Structural Basis For Specific Recognition of Reelin By Its Receptors Structure V. 18 320 2010.
ISSN: ISSN 0969-2126
PubMed: 20223215
DOI: 10.1016/J.STR.2010.01.010