Calcium in PDB 9l2n: Crystal Structure of Cytochalasin D Bound to A Filamentous Conformation Actin

The structure of Crystal Structure of Cytochalasin D Bound to A Filamentous Conformation Actin, PDB code: 9l2n was solved by S.Takeda, Y.Maeda, I.Fujiwara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.21 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.213, 90.806, 114.554, 90, 90, 90
R / Rfree (%)	17.5 / 20.5

The structure of Crystal Structure of Cytochalasin D Bound to A Filamentous Conformation Actin also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Cytochalasin D Bound to A Filamentous Conformation Actin (pdb code 9l2n). 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 Cytochalasin D Bound to A Filamentous Conformation Actin, PDB code: 9l2n:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Cytochalasin D Bound to A Filamentous Conformation Actin


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 Cytochalasin D Bound to A Filamentous Conformation Actin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:14.8 occ:1.00 O B:PRO122 2.3 15.0 1.0 O A:HOH860 2.4 19.9 1.0 OE1 A:GLU167 2.4 18.4 1.0 OD2 B:ASP115 2.4 16.4 1.0 O B:HOH413 2.4 16.5 1.0 O B:GLY120 2.5 16.5 1.0 OD1 B:ASP115 2.5 15.9 1.0 CG B:ASP115 2.8 16.6 1.0 C B:GLY120 3.4 15.0 1.0 CD A:GLU167 3.5 16.4 1.0 C B:PRO122 3.5 14.0 1.0 CA B:GLY120 3.9 14.7 1.0 OE2 A:GLU167 4.0 15.4 1.0 O A:HOH819 4.0 25.8 1.0 N B:PRO122 4.1 13.7 1.0 C B:LEU121 4.2 14.8 1.0 O A:HOH731 4.3 27.4 1.0 CB B:ASP115 4.3 10.2 1.0 CA B:PRO122 4.3 14.9 1.0 O B:HOH313 4.4 22.9 1.0 O A:HOH598 4.4 20.8 1.0 N B:LEU121 4.4 15.2 1.0 O B:LEU121 4.5 14.9 1.0 O B:HOH488 4.5 39.5 1.0 N B:VAL123 4.5 11.1 1.0 CA B:VAL123 4.7 14.2 1.0 CD B:PRO122 4.7 14.3 1.0 CG A:GLU167 4.8 14.8 1.0 CA B:LEU121 4.8 16.6 1.0 NE2 B:GLN124 4.8 16.3 1.0 CB B:PRO122 4.8 14.9 1.0 CB A:GLU167 4.9 14.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Cytochalasin D Bound to A Filamentous Conformation Actin


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 Cytochalasin D Bound to A Filamentous Conformation Actin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:13.7 occ:1.00 OD1 B:ASP70 2.3 13.8 1.0 O B:GLY69 2.3 13.6 1.0 O B:HOH392 2.4 14.0 1.0 O B:VAL152 2.4 14.2 1.0 OE2 B:GLU103 2.4 14.4 1.0 O B:HOH396 2.5 16.0 1.0 OE1 B:GLU103 2.5 13.3 1.0 CD B:GLU103 2.8 14.5 1.0 C B:GLY69 3.3 14.1 1.0 CG B:ASP70 3.5 14.4 1.0 C B:VAL152 3.6 13.6 1.0 N B:VAL152 3.9 15.2 1.0 CA B:ASP70 3.9 11.6 1.0 N B:ASP70 4.0 14.0 1.0 CG2 B:VAL152 4.2 13.1 1.0 O B:HOH318 4.2 13.7 1.0 CA B:GLY69 4.3 15.8 1.0 CA B:VAL152 4.3 14.6 1.0 CB B:ASP70 4.3 10.8 1.0 CG B:GLU103 4.3 12.4 1.0 C B:GLY151 4.4 16.8 1.0 O B:HOH389 4.4 20.6 1.0 OD2 B:ASP70 4.4 13.5 1.0 OG1 B:THR100 4.6 13.4 1.0 CA B:GLY151 4.6 12.4 1.0 O B:HOH405 4.6 18.8 1.0 N B:GLU153 4.6 13.6 1.0 C B:GLU153 4.7 14.1 1.0 OG1 B:THR99 4.7 13.4 1.0 N B:THR154 4.8 11.8 1.0 O B:HOH332 4.8 13.2 1.0 O B:HOH457 4.9 19.6 0.4 N B:THR100 4.9 11.7 1.0 O B:HOH457 4.9 24.3 0.6 CA B:THR99 4.9 14.2 1.0 CB B:VAL152 4.9 13.4 1.0 CA B:GLU153 4.9 14.4 1.0 O B:GLU153 5.0 13.6 1.0

T.Mitani, S.Takeda, T.Oda, A.Narita, Y.Maeda, H.Honda, I.Fujiwara. Microscopic and Structural Observations of Actin Filament Capping and Severing By Cytochalasin D Proc.Natl.Acad.Sci.Usa 2025.
ISSN: ESSN 1091-6490