Calcium in PDB 7lyu: Reelin Repeat 8

The structure of Reelin Repeat 8, PDB code: 7lyu was solved by L.S.Turk, D.Comoletti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.12 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.171, 104.059, 67.615, 90, 104.11, 90
R / Rfree (%)	22.7 / 26.4

The binding sites of Calcium atom in the Reelin Repeat 8 (pdb code 7lyu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Reelin Repeat 8, PDB code: 7lyu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Reelin Repeat 8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Reelin Repeat 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3501 b:105.0 occ:1.00 OG A:SER3091 2.4 122.3 1.0 OD1 A:ASP3224 2.4 88.5 1.0 O A:THR3062 2.5 86.4 1.0 CG A:ASP3224 3.2 83.6 1.0 OD2 A:ASP3224 3.2 88.3 1.0 CB A:SER3091 3.3 119.2 1.0 O A:PHE3092 3.4 76.3 1.0 C A:THR3062 3.5 89.1 1.0 CB A:THR3062 3.6 99.5 1.0 CA A:THR3062 3.9 91.2 1.0 OG1 A:THR3062 4.1 97.9 1.0 N A:PHE3092 4.4 92.2 1.0 C A:PHE3092 4.4 79.2 1.0 N A:HIS3225 4.5 69.3 1.0 CB A:HIS3225 4.6 91.1 1.0 CA A:SER3091 4.6 120.5 1.0 CB A:ASP3224 4.6 64.2 1.0 C A:SER3091 4.7 111.5 1.0 N A:PHE3063 4.7 78.3 1.0 CA A:HIS3225 4.8 77.2 1.0 ND1 A:HIS3225 4.9 88.4 1.0 CG2 A:THR3062 4.9 100.5 1.0 CA A:PHE3092 5.0 80.4 1.0

Calcium binding site 2 out of 4 in the Reelin Repeat 8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Reelin Repeat 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3502 b:78.7 occ:1.00 OD2 A:ASP3422 2.2 67.7 1.0 O A:HIS3304 2.4 77.5 1.0 O A:ASN3273 2.5 70.4 1.0 OD1 A:ASP3422 2.7 68.3 1.0 CG A:ASP3422 2.8 66.8 1.0 O A:ASP3306 3.0 86.0 1.0 OE2 A:GLU3275 3.5 111.8 1.0 C A:ASN3273 3.6 67.4 1.0 C A:HIS3304 3.6 79.0 1.0 C A:ASP3306 3.9 83.1 1.0 C A:GLY3305 4.1 81.1 1.0 CB A:ASN3273 4.1 70.3 1.0 CA A:ASN3273 4.2 71.2 1.0 N A:ASP3306 4.2 87.4 1.0 CB A:ASP3422 4.3 66.3 1.0 CA A:GLY3305 4.3 73.6 1.0 CD A:GLU3275 4.4 117.1 1.0 CG A:GLU3275 4.4 108.1 1.0 O A:GLY3305 4.4 88.7 1.0 N A:GLY3305 4.5 73.3 1.0 N A:HIS3304 4.5 73.0 1.0 CE1 A:HIS3423 4.5 75.3 1.0 ND1 A:HIS3423 4.6 75.8 1.0 O A:PHE3274 4.7 82.6 1.0 N A:PHE3274 4.7 63.3 1.0 N A:SER3307 4.7 71.5 1.0 CA A:HIS3304 4.7 77.4 1.0 CA A:ASP3306 4.7 83.2 1.0 ND1 A:HIS3304 4.8 81.9 1.0 C A:PHE3274 4.8 77.7 1.0 CA A:SER3307 4.9 64.2 1.0 CE1 A:HIS3304 4.9 76.3 1.0 CB A:PHE3274 5.0 66.9 1.0

Calcium binding site 3 out of 4 in the Reelin Repeat 8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Reelin Repeat 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3501 b:68.0 occ:1.00 OD2 B:ASP3422 2.5 59.9 1.0 O B:HIS3304 2.6 65.9 1.0 OD1 B:ASP3422 2.6 57.2 1.0 O B:ASP3306 2.6 77.0 0.5 O B:ASP3306 2.6 68.0 0.5 CG B:ASP3422 2.9 58.1 1.0 OE2 B:GLU3275 3.4 90.8 1.0 N B:PHE3274 3.4 50.6 1.0 CG B:GLU3275 3.6 76.0 1.0 CB B:ASN3273 3.6 58.5 1.0 CD B:GLU3275 3.7 87.6 1.0 C B:HIS3304 3.8 74.0 1.0 C B:ASP3306 3.8 77.5 0.5 C B:ASP3306 3.8 94.2 0.5 C B:ASN3273 3.9 51.8 1.0 CA B:ASN3273 3.9 47.0 1.0 C B:GLY3305 4.0 72.2 1.0 N B:ASP3306 4.1 72.0 0.5 N B:ASP3306 4.1 78.5 0.5 O B:GLY3305 4.2 74.7 1.0 CA B:GLY3305 4.3 74.1 1.0 CB B:ASP3422 4.4 51.5 1.0 CA B:PHE3274 4.4 55.5 1.0 C B:PHE3274 4.4 59.5 1.0 N B:GLY3305 4.5 76.9 1.0 N B:GLU3275 4.5 58.2 1.0 CA B:ASP3306 4.6 72.1 0.5 CA B:ASP3306 4.6 72.1 0.5 NE2 B:HIS3423 4.6 72.1 1.0 CD2 B:HIS3423 4.7 67.1 1.0 CG B:ASN3273 4.7 68.4 1.0 OE1 B:GLU3275 4.7 95.2 1.0 N B:HIS3304 4.7 73.6 1.0 N B:SER3307 4.7 66.5 1.0 O B:ASN3273 4.8 61.2 1.0 CB B:GLU3275 4.8 68.3 1.0 O B:PHE3274 4.8 64.0 1.0 CB B:PHE3274 4.8 48.9 1.0 ND1 B:HIS3304 4.9 85.3 1.0 CA B:SER3307 4.9 56.6 1.0 CA B:HIS3304 4.9 73.9 1.0

Calcium binding site 4 out of 4 in the Reelin Repeat 8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Reelin Repeat 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3502 b:74.1 occ:1.00 OD1 B:ASP3224 2.3 63.6 1.0 OG B:SER3091 2.3 87.1 1.0 O B:THR3062 2.5 69.4 1.0 OD2 B:ASP3224 2.8 75.3 1.0 CG B:ASP3224 2.9 65.7 1.0 O B:PHE3092 2.9 88.3 1.0 CB B:SER3091 3.1 80.7 1.0 C B:THR3062 3.6 67.7 1.0 OD1 B:ASP3064 3.9 93.2 1.0 OD2 B:ASP3064 3.9 88.1 1.0 C B:PHE3092 4.0 85.6 1.0 CD2 B:HIS3225 4.0 86.7 1.0 CA B:THR3062 4.0 63.6 1.0 N B:PHE3092 4.0 95.6 1.0 CB B:THR3062 4.1 64.2 1.0 CG B:ASP3064 4.2 96.9 1.0 C B:SER3091 4.2 92.3 1.0 CA B:SER3091 4.3 84.4 1.0 NE2 B:HIS3225 4.3 84.8 1.0 CB B:ASP3224 4.3 50.5 1.0 N B:HIS3225 4.4 64.9 1.0 CG B:HIS3225 4.6 73.8 1.0 CA B:PHE3092 4.6 85.2 1.0 N B:PHE3063 4.7 67.9 1.0 CD2 B:PHE3063 4.8 61.7 1.0 O B:SER3091 4.9 89.4 1.0 CB B:PHE3063 5.0 64.2 1.0 CA B:ASP3224 5.0 51.0 1.0 N B:HIS3093 5.0 76.5 1.0

L.S.Turk, M.J.Currie, R.C.J.Dobson, D.Comoletti. Structure of Reelin Repeat 8 and the Adjacent C-Terminal Region. Biophys.J. V. 121 2526 2022.
ISSN: ESSN 1542-0086
PubMed: 35659645
DOI: 10.1016/J.BPJ.2022.06.002