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

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

Resolution Low / High (Å)	34.09 / 1.85
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	115.590, 115.590, 42.220, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 20.3

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

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Fragmin F2-F3 Domains (Calcium and Magnesium Condition) (pdb code 6ljc). 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 F2-F3 Domains (Calcium and Magnesium Condition), PDB code: 6ljc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Fragmin F2-F3 Domains (Calcium and Magnesium 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 and Magnesium Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:27.3 occ:1.00 O C:GLY192 2.4 26.1 1.0 O C:HOH601 2.4 28.1 1.0 OD1 C:ASP193 2.4 27.7 1.0 OE1 C:GLU215 2.4 25.5 1.0 OD2 C:ASP267 2.5 24.9 1.0 O C:HOH684 2.5 27.9 1.0 OD1 C:ASP267 2.7 27.1 1.0 OE2 C:GLU215 2.7 26.9 1.0 CD C:GLU215 2.9 29.2 1.0 CG C:ASP267 2.9 27.3 1.0 C C:GLY192 3.3 32.8 1.0 CG C:ASP193 3.6 29.5 1.0 CA C:ASP193 3.9 24.4 1.0 O C:HOH505 4.0 48.6 1.0 N C:ASP193 4.0 28.3 1.0 O C:HOH695 4.3 33.6 1.0 NZ C:LYS172 4.3 29.5 1.0 CA C:GLY192 4.3 27.3 1.0 CB C:ASP193 4.3 27.6 1.0 CG C:GLU215 4.4 25.3 1.0 O C:HOH680 4.4 38.9 1.0 CB C:ASP267 4.4 24.1 1.0 O C:HOH595 4.4 32.0 1.0 N C:GLY212 4.5 32.5 1.0 O C:HOH583 4.5 49.9 1.0 OD2 C:ASP193 4.5 29.2 1.0 O C:LYS210 4.7 30.7 1.0 CG C:LYS172 4.8 25.0 1.0 O C:HOH554 4.9 49.8 1.0 CA C:ALA211 4.9 30.1 1.0 O C:GLY173 5.0 27.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Fragmin F2-F3 Domains (Calcium and Magnesium 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 and Magnesium Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:33.9 occ:1.00 O C:ASN308 2.3 30.4 1.0 OD1 C:ASP309 2.4 33.5 1.0 O C:HOH702 2.4 32.5 1.0 O C:HOH625 2.5 32.5 1.0 OE1 C:GLU331 2.5 30.8 1.0 O C:HOH619 2.5 33.4 1.0 OE2 C:GLU331 2.5 31.3 1.0 CD C:GLU331 2.9 34.3 1.0 CG C:ASP309 3.5 38.1 1.0 C C:ASN308 3.5 34.4 1.0 CA C:ASP309 3.9 30.3 1.0 OG C:SER283 4.2 31.7 1.0 N C:SER328 4.2 38.2 1.0 N C:ASP309 4.2 31.8 1.0 CB C:ASP309 4.3 28.1 1.0 OD2 C:ASP309 4.3 31.2 1.0 CG C:GLU331 4.4 28.9 1.0 O C:HOH575 4.5 45.1 1.0 OD1 C:ASP284 4.5 33.5 1.0 OG C:SER328 4.5 35.2 1.0 CA C:ALA327 4.5 29.5 1.0 CA C:ASN308 4.5 34.5 1.0 CB C:ASN308 4.6 31.3 1.0 CB C:SER328 4.6 36.3 1.0 O C:HIS326 4.6 37.2 1.0 O C:HOH787 4.7 49.3 1.0 O C:HOH777 4.8 41.4 1.0 O C:HOH810 4.8 56.0 1.0 C C:ALA327 4.9 37.1 1.0 N C:ASP284 4.9 30.1 1.0 CB C:SER283 5.0 29.6 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