Calcium in PDB 6kwz: Crystal Structure of Fragmin F3 Domain with Calcium Ion

The structure of Crystal Structure of Fragmin F3 Domain with Calcium Ion, PDB code: 6kwz was solved by S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.60 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.648, 55.076, 69.890, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.6

The binding sites of Calcium atom in the Crystal Structure of Fragmin F3 Domain with Calcium Ion (pdb code 6kwz). 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 Fragmin F3 Domain with Calcium Ion, PDB code: 6kwz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Fragmin F3 Domain with Calcium Ion


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 Fragmin F3 Domain with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:17.7 occ:1.00 O A:ASN308 2.3 17.0 1.0 OE2 A:GLU331 2.4 16.9 1.0 OD1 A:ASP309 2.4 20.2 1.0 O A:HOH598 2.4 20.1 1.0 O A:HOH564 2.4 20.2 1.0 OE1 A:GLU331 2.5 15.4 1.0 O A:HOH555 2.5 18.6 1.0 CD A:GLU331 2.8 15.9 1.0 C A:ASN308 3.4 20.7 1.0 CG A:ASP309 3.6 17.2 1.0 CA A:ASP309 3.9 17.4 1.0 OG A:SER283 4.0 18.8 1.0 N A:ASP309 4.1 18.0 1.0 N A:SER328 4.2 17.3 1.0 CG A:GLU331 4.3 16.4 1.0 CB A:ASP309 4.3 18.9 1.0 O A:HOH563 4.4 25.9 1.0 O A:HOH620 4.5 26.1 0.4 CB A:ASN308 4.5 16.8 1.0 OD2 A:ASP309 4.5 21.9 1.0 CA A:ASN308 4.5 21.8 1.0 OD1 A:ASP284 4.5 20.2 1.0 O A:HOH625 4.5 35.9 1.0 OG A:SER328 4.5 15.6 1.0 CA A:ALA327 4.5 16.9 1.0 CB A:SER328 4.6 17.4 1.0 CB A:ALA285 4.7 19.9 1.0 O A:HIS326 4.7 19.5 1.0 N A:ALA285 4.8 16.6 1.0 C A:ALA327 4.9 20.2 1.0 N A:ASP284 4.9 18.8 1.0 CB A:SER283 4.9 17.3 1.0 CA A:SER283 5.0 18.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Fragmin F3 Domain with Calcium Ion


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 Fragmin F3 Domain with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:18.9 occ:1.00 O B:ASN308 2.3 20.2 1.0 OD1 B:ASP309 2.4 17.9 1.0 O B:HOH512 2.4 20.8 1.0 O B:HOH556 2.4 20.7 1.0 OE1 B:GLU331 2.5 18.8 1.0 OE2 B:GLU331 2.5 19.8 1.0 O B:HOH594 2.5 20.3 1.0 CD B:GLU331 2.8 16.9 1.0 C B:ASN308 3.5 19.2 1.0 CG B:ASP309 3.5 20.9 1.0 CA B:ASP309 3.9 15.0 1.0 OG B:SER283 4.0 20.4 1.0 N B:SER328 4.2 20.3 1.0 N B:ASP309 4.2 16.2 1.0 CB B:ASP309 4.3 18.6 1.0 CG B:GLU331 4.3 20.2 1.0 OD2 B:ASP309 4.3 20.0 1.0 CA B:ALA327 4.4 16.5 1.0 OD1 B:ASP284 4.4 27.4 1.0 O B:HOH510 4.4 30.9 1.0 CA B:ASN308 4.5 18.2 1.0 CB B:ASN308 4.5 18.1 1.0 O B:HOH631 4.6 41.8 1.0 CB B:SER328 4.6 17.4 1.0 O B:HIS326 4.7 21.2 1.0 O B:HOH624 4.7 29.8 1.0 C B:ALA327 4.8 20.9 1.0 OG B:SER328 4.8 21.5 1.0 CB B:ALA285 4.9 29.0 1.0 N B:ASP284 4.9 20.3 1.0 CB B:SER283 4.9 20.4 1.0 N B:ALA285 4.9 19.3 1.0 CA B:SER283 5.0 16.0 1.0

S.Takeda, I.Fujiwara, Y.Sugimoto, T.Oda, A.Narita, Y.Maeda. Novel Inter-Domain CA2+-Binding Site in the Gelsolin Superfamily Protein Fragmin. J.Muscle Res.Cell.Motil. 2019.
ISSN: ISSN 0142-4319
PubMed: 31863323
DOI: 10.1007/S10974-019-09571-5