Calcium in PDB 8gt1: Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Adp-Pi State) in Complex with Fragmin F1 Domain

The structure of Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Adp-Pi State) in Complex with Fragmin F1 Domain, PDB code: 8gt1 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)	30.23 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.135, 90.925, 114.73, 90, 90, 90
R / Rfree (%)	18.4 / 20.2

The structure of Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Adp-Pi 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 (Adp-Pi State) in Complex with Fragmin F1 Domain (pdb code 8gt1). 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 (Adp-Pi State) in Complex with Fragmin F1 Domain, PDB code: 8gt1:
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 (Adp-Pi 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 (Adp-Pi State) in Complex with Fragmin F1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:14.7 occ:1.00 O B:PRO122 2.3 16.9 1.0 O B:HOH463 2.3 19.6 1.0 OD2 B:ASP115 2.4 16.9 1.0 O B:HOH490 2.5 16.1 1.0 O B:GLY120 2.5 15.5 1.0 OE1 A:GLU167 2.6 17.8 1.0 OD1 B:ASP115 2.6 14.2 1.0 CG B:ASP115 2.8 13.7 1.0 C B:GLY120 3.4 13.7 1.0 C B:PRO122 3.5 12.1 1.0 CD A:GLU167 3.7 16.9 1.0 CA B:GLY120 4.0 13.7 1.0 O A:HOH651 4.0 16.3 1.0 N B:PRO122 4.1 14.1 1.0 OE2 A:GLU167 4.2 14.8 1.0 O B:HOH534 4.2 39.4 1.0 C B:LEU121 4.2 14.0 1.0 O A:HOH874 4.3 24.8 1.0 CA B:PRO122 4.3 13.3 1.0 CB B:ASP115 4.3 10.7 1.0 N B:LEU121 4.4 14.3 1.0 N B:VAL123 4.5 10.2 1.0 O B:HOH366 4.5 22.0 1.0 O B:LEU121 4.5 15.6 1.0 O A:HOH547 4.5 21.2 1.0 O B:HOH511 4.6 44.7 1.0 CA B:VAL123 4.7 12.0 1.0 O B:HOH336 4.7 17.3 1.0 NE2 B:GLN124 4.7 12.6 1.0 CD B:PRO122 4.7 13.1 1.0 CA B:LEU121 4.8 14.9 1.0 CB B:PRO122 4.8 15.2 1.0 CG A:GLU167 4.9 14.8 1.0 CB A:GLU167 4.9 12.2 1.0 CG B:GLN124 5.0 9.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Cardiac Alpha Actin A108G Mutant (Adp-Pi 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 (Adp-Pi State) in Complex with Fragmin F1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:11.2 occ:1.00 OD1 B:ASP70 2.3 10.2 1.0 O B:GLY69 2.3 12.3 1.0 O B:HOH424 2.4 12.7 1.0 O B:HOH444 2.4 14.4 1.0 O B:VAL152 2.4 10.4 1.0 OE2 B:GLU103 2.4 10.9 1.0 OE1 B:GLU103 2.5 11.4 1.0 CD B:GLU103 2.8 9.0 1.0 C B:GLY69 3.4 10.6 1.0 CG B:ASP70 3.5 10.9 1.0 C B:VAL152 3.5 10.9 1.0 N B:VAL152 3.9 10.6 1.0 CA B:ASP70 4.0 9.3 1.0 N B:ASP70 4.1 10.5 1.0 CA B:VAL152 4.2 11.1 1.0 O B:HOH349 4.3 9.9 1.0 CG2 B:VAL152 4.3 13.7 1.0 CA B:GLY69 4.3 9.8 1.0 C B:GLY151 4.3 12.8 1.0 CG B:GLU103 4.3 11.4 1.0 CB B:ASP70 4.4 11.5 1.0 O B:HOH394 4.4 19.0 1.0 OD2 B:ASP70 4.4 10.5 1.0 OG1 B:THR100 4.6 11.2 1.0 N B:GLU153 4.6 11.2 1.0 CA B:GLY151 4.6 15.0 1.0 O B:HOH454 4.6 16.7 1.0 C B:GLU153 4.7 10.9 1.0 O B:HOH370 4.7 25.4 1.0 N B:THR154 4.8 11.6 1.0 O B:HOH342 4.8 11.0 1.0 OG1 B:THR99 4.8 10.9 1.0 CA B:GLU153 4.9 15.0 1.0 N B:THR100 4.9 10.5 1.0 CB B:VAL152 4.9 10.6 1.0 CA B:THR99 4.9 11.2 1.0 O B:GLY151 5.0 18.4 1.0 O B:GLU153 5.0 12.3 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