Calcium in PDB 6ljd: Crystal Structure of Fragmin F2-F3 Domains (Calcium Condition)

The structure of Crystal Structure of Fragmin F2-F3 Domains (Calcium Condition), PDB code: 6ljd was solved by S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.83 / 2.15
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	115.830, 115.830, 42.110, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 21.9

The structure of Crystal Structure of Fragmin F2-F3 Domains (Calcium Condition) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Fragmin F2-F3 Domains (Calcium Condition) (pdb code 6ljd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Fragmin F2-F3 Domains (Calcium Condition), PDB code: 6ljd:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Fragmin F2-F3 Domains (Calcium Condition)


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 F2-F3 Domains (Calcium Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:37.9 occ:1.00 O C:HOH516 2.1 35.6 1.0 O C:GLY192 2.3 38.1 1.0 OD1 C:ASP193 2.4 34.7 1.0 OD2 C:ASP267 2.4 35.3 1.0 OE1 C:GLU215 2.5 37.4 1.0 O C:HOH608 2.6 37.2 1.0 OE2 C:GLU215 2.7 35.9 1.0 OD1 C:ASP267 2.7 37.6 1.0 CG C:ASP267 2.9 36.8 1.0 CD C:GLU215 2.9 33.8 1.0 C C:GLY192 3.3 49.1 1.0 CG C:ASP193 3.6 37.9 1.0 CA C:ASP193 3.9 41.6 1.0 N C:ASP193 4.0 38.5 1.0 O C:HOH513 4.2 52.2 1.0 CA C:GLY192 4.2 41.5 1.0 CB C:ASP193 4.3 41.5 1.0 O C:HOH571 4.3 42.1 1.0 NZ C:LYS172 4.3 38.9 1.0 N C:GLY212 4.4 41.0 1.0 O C:HOH618 4.4 55.9 1.0 CB C:ASP267 4.4 35.2 1.0 CG C:GLU215 4.4 33.0 1.0 O C:HOH606 4.5 50.5 1.0 OD2 C:ASP193 4.6 37.3 1.0 O C:LYS210 4.6 46.0 1.0 CG C:LYS172 4.7 36.3 1.0 CA C:ALA211 4.9 43.6 1.0 O C:GLY173 4.9 38.1 1.0 N C:GLY173 5.0 37.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Fragmin F2-F3 Domains (Calcium Condition)


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 F2-F3 Domains (Calcium Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:44.6 occ:1.00 O C:HOH626 2.3 49.7 1.0 O C:HOH563 2.4 38.1 1.0 O C:ASN308 2.4 43.1 1.0 O C:HOH564 2.4 40.3 1.0 OD1 C:ASP309 2.5 40.9 1.0 OE2 C:GLU331 2.5 39.1 1.0 OE1 C:GLU331 2.5 39.2 1.0 CD C:GLU331 2.9 40.4 1.0 CG C:ASP309 3.5 40.5 1.0 C C:ASN308 3.6 49.8 1.0 OG C:SER283 3.9 38.0 1.0 CA C:ASP309 4.0 37.0 1.0 N C:SER328 4.1 45.0 1.0 N C:ASP309 4.2 40.3 1.0 OD2 C:ASP309 4.3 41.2 1.0 CB C:ASP309 4.3 33.1 1.0 CG C:GLU331 4.4 32.6 1.0 OD1 C:ASP284 4.5 46.3 1.0 O C:HOH552 4.5 49.5 1.0 CB C:SER328 4.5 40.6 1.0 OG C:SER328 4.5 41.6 1.0 CA C:ALA327 4.6 44.0 1.0 CA C:ASN308 4.6 40.6 1.0 CB C:ASN308 4.6 45.6 1.0 O C:HIS326 4.7 46.6 1.0 C C:ALA327 4.9 45.8 1.0 N C:ASP284 4.9 42.7 1.0 CB C:SER283 4.9 31.5 1.0 CA C:SER328 4.9 47.8 1.0 CB C:ALA285 4.9 53.1 1.0 O C:HOH661 4.9 45.6 1.0 CA C:SER283 5.0 38.3 1.0 N C:ALA285 5.0 49.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Fragmin F2-F3 Domains (Calcium Condition)


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 Fragmin F2-F3 Domains (Calcium Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:44.6 occ:1.00 O C:HOH627 2.3 34.6 1.0 OD1 C:ASP371 2.4 44.3 1.0 O C:ASP368 2.4 33.1 1.0 OE2 C:GLU221 2.6 37.7 1.0 OD1 C:ASP368 2.6 38.5 1.0 O C:ASP371 2.7 46.7 1.0 C C:ASP371 3.1 45.8 1.0 CG C:ASP368 3.3 35.6 1.0 C C:ASP368 3.5 34.8 1.0 OXT C:ASP371 3.5 44.4 1.0 CG C:ASP371 3.6 51.9 1.0 O C:HOH530 3.7 31.0 1.0 CD C:GLU221 3.8 38.1 1.0 OD2 C:ASP368 3.8 38.0 1.0 CA C:ASP368 3.9 34.3 1.0 CA C:ASP371 4.0 40.0 1.0 N C:ASP371 4.1 37.4 1.0 CD C:LYS218 4.2 38.3 1.0 CB C:GLU221 4.2 32.7 1.0 CB C:ASP368 4.2 31.6 1.0 CB C:ASP371 4.3 36.7 1.0 OD2 C:ASP371 4.5 43.9 1.0 CG C:GLU221 4.6 35.2 1.0 NZ C:LYS218 4.6 36.4 1.0 N C:PHE369 4.7 31.6 1.0 OE1 C:GLU221 4.7 38.0 1.0 O C:HOH630 4.8 56.4 1.0 CE C:LYS218 4.9 37.4 1.0 C C:PHE369 4.9 38.0 1.0 O C:HOH592 5.0 44.4 1.0 CA C:PHE369 5.0 35.1 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