Calcium in PDB 8gsw: Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Amppnp State) in Complex with Fragmin F1 Domain

The structure of Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Amppnp State) in Complex with Fragmin F1 Domain, PDB code: 8gsw was solved by M.Iwasa, T.Oda, S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.88 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.979, 92.788, 116.71, 90, 90, 90
R / Rfree (%)	18.1 / 19.6

The structure of Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Amppnp State) in Complex with Fragmin F1 Domain also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Amppnp State) in Complex with Fragmin F1 Domain (pdb code 8gsw). 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 Human Cardiac Alpha Actin A108G Mutant (Amppnp State) in Complex with Fragmin F1 Domain, PDB code: 8gsw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Amppnp State) in Complex with Fragmin F1 Domain


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 Human Cardiac Alpha Actin A108G Mutant (Amppnp State) in Complex with Fragmin F1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:13.7 occ:1.00 O B:PRO122 2.3 15.2 1.0 O B:HOH477 2.3 21.4 1.0 OD2 B:ASP115 2.4 13.2 1.0 O B:HOH471 2.4 18.1 1.0 OE1 A:GLU167 2.4 16.9 1.0 O B:GLY120 2.5 14.7 1.0 OD1 B:ASP115 2.6 13.3 1.0 CG B:ASP115 2.8 12.8 1.0 C B:GLY120 3.4 14.7 1.0 C B:PRO122 3.5 13.1 1.0 CD A:GLU167 3.6 15.2 1.0 CA B:GLY120 4.0 13.4 1.0 OE2 A:GLU167 4.1 12.9 1.0 O A:HOH630 4.1 17.5 1.0 N B:PRO122 4.1 13.5 1.0 C B:LEU121 4.2 12.7 1.0 O A:HOH824 4.3 27.4 1.0 CB B:ASP115 4.4 10.5 1.0 CA B:PRO122 4.4 14.7 1.0 N B:LEU121 4.4 14.4 1.0 O B:HOH507 4.4 30.1 1.0 O A:HOH592 4.4 21.4 1.0 O B:LEU121 4.5 15.6 1.0 O B:HOH351 4.5 19.1 1.0 N B:VAL123 4.5 11.3 1.0 O B:HOH526 4.6 45.2 1.0 CA B:VAL123 4.7 11.1 1.0 CD B:PRO122 4.7 13.2 1.0 O B:HOH329 4.7 17.1 1.0 CA B:LEU121 4.8 15.1 1.0 CG A:GLU167 4.8 12.9 1.0 NE2 B:GLN124 4.8 11.5 1.0 CB A:GLU167 4.9 11.6 1.0 CB B:PRO122 4.9 12.9 1.0 O A:HOH919 4.9 33.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Amppnp State) in Complex with Fragmin F1 Domain


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 Human Cardiac Alpha Actin A108G Mutant (Amppnp State) in Complex with Fragmin F1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:11.8 occ:1.00 OD1 B:ASP70 2.3 13.5 1.0 O B:GLY69 2.4 12.7 1.0 O B:HOH414 2.4 13.4 1.0 O B:VAL152 2.4 12.7 1.0 O B:HOH450 2.4 14.1 1.0 OE2 B:GLU103 2.5 12.0 1.0 OE1 B:GLU103 2.5 12.6 1.0 CD B:GLU103 2.8 12.3 1.0 C B:GLY69 3.4 11.3 1.0 CG B:ASP70 3.5 13.3 1.0 C B:VAL152 3.6 14.5 1.0 N B:VAL152 3.9 13.8 1.0 CA B:ASP70 4.0 10.1 1.0 N B:ASP70 4.1 12.2 1.0 O B:HOH332 4.3 11.1 1.0 CA B:VAL152 4.3 12.2 1.0 CG2 B:VAL152 4.3 15.1 1.0 CA B:GLY69 4.3 12.5 1.0 CG B:GLU103 4.4 12.4 1.0 C B:GLY151 4.4 17.2 1.0 CB B:ASP70 4.4 11.9 1.0 O B:HOH384 4.4 18.4 1.0 OD2 B:ASP70 4.4 12.9 1.0 O B:HOH430 4.6 20.1 1.0 N B:GLU153 4.6 15.2 1.0 C B:GLU153 4.6 12.5 1.0 OG1 B:THR100 4.6 12.3 1.0 CA B:GLY151 4.7 16.2 1.0 N B:THR154 4.7 13.2 1.0 O B:HOH376 4.7 28.5 1.0 OG1 B:THR99 4.8 11.6 1.0 O B:HOH331 4.8 12.7 1.0 CA B:GLU153 4.8 14.5 1.0 N B:THR100 4.9 11.1 1.0 CA B:THR99 4.9 12.9 1.0 CB B:VAL152 5.0 13.6 1.0 O B:GLU153 5.0 13.3 1.0 O B:HOH532 5.0 39.4 1.0

M.Iwasa, S.Takeda, A.Narita, Y.Maeda, T.Oda. Mutagenic Analysis of Actin Reveals the Mechanism of HIS161 Flipping That Triggers Atp Hydrolysis Front Cell Dev Biol 2023.
ISSN: ESSN 2296-634X
DOI: 10.3389/FCELL.2023.1105460