Calcium in PDB 8gt3: Crystal Structure of Human Cardiac Alpha Actin P109A Mutant (Adp-Pi State) in Complex with Fragmin F1 Domain

The structure of Crystal Structure of Human Cardiac Alpha Actin P109A Mutant (Adp-Pi State) in Complex with Fragmin F1 Domain, PDB code: 8gt3 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)	45.55 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.171, 91.108, 115.142, 90, 90, 90
R / Rfree (%)	16.5 / 19.6

The structure of Crystal Structure of Human Cardiac Alpha Actin P109A 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 P109A Mutant (Adp-Pi State) in Complex with Fragmin F1 Domain (pdb code 8gt3). 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 P109A Mutant (Adp-Pi State) in Complex with Fragmin F1 Domain, PDB code: 8gt3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human Cardiac Alpha Actin P109A 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 P109A Mutant (Adp-Pi State) in Complex with Fragmin F1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:16.8 occ:1.00 O B:PRO122 2.3 16.4 1.0 O B:HOH461 2.3 24.9 1.0 OD2 B:ASP115 2.3 17.1 1.0 O B:HOH465 2.5 21.9 1.0 O B:GLY120 2.6 18.4 1.0 OD1 B:ASP115 2.6 17.7 1.0 OE1 A:GLU167 2.7 22.3 1.0 CG B:ASP115 2.8 14.2 1.0 C B:GLY120 3.5 17.9 1.0 C B:PRO122 3.5 14.0 1.0 CD A:GLU167 3.7 21.4 1.0 CA B:GLY120 4.0 15.9 1.0 O A:HOH629 4.1 19.1 1.0 N B:PRO122 4.1 15.4 1.0 OE2 A:GLU167 4.2 14.7 1.0 C B:LEU121 4.2 13.9 1.0 CA B:PRO122 4.3 13.6 1.0 CB B:ASP115 4.3 10.9 1.0 N B:LEU121 4.4 15.2 1.0 O A:HOH846 4.4 29.4 1.0 N B:VAL123 4.5 11.7 1.0 O B:LEU121 4.5 15.8 1.0 O B:HOH332 4.5 24.5 1.0 O A:HOH544 4.6 24.4 1.0 CD B:PRO122 4.7 12.6 1.0 O B:HOH482 4.7 42.7 1.0 O B:HOH339 4.7 20.3 1.0 CA B:VAL123 4.7 13.9 1.0 NE2 B:GLN124 4.8 13.2 1.0 CA B:LEU121 4.8 15.1 1.0 CB B:PRO122 4.8 13.0 1.0 O B:HOH462 4.9 36.7 1.0 CG A:GLU167 4.9 13.4 1.0 CB A:GLU167 4.9 13.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Cardiac Alpha Actin P109A 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 P109A Mutant (Adp-Pi State) in Complex with Fragmin F1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:11.8 occ:1.00 OD1 B:ASP70 2.3 11.2 1.0 O B:VAL152 2.4 10.8 1.0 O B:GLY69 2.4 12.7 1.0 O B:HOH386 2.4 14.4 1.0 OE2 B:GLU103 2.4 13.3 1.0 O B:HOH440 2.4 13.6 1.0 OE1 B:GLU103 2.5 11.2 1.0 CD B:GLU103 2.8 10.2 1.0 C B:GLY69 3.4 11.7 1.0 CG B:ASP70 3.5 12.4 1.0 C B:VAL152 3.5 13.3 1.0 N B:VAL152 3.8 11.3 1.0 CA B:ASP70 4.0 9.5 1.0 N B:ASP70 4.1 11.2 1.0 O B:HOH343 4.2 11.0 1.0 CA B:VAL152 4.2 11.3 1.0 CG2 B:VAL152 4.3 13.2 1.0 CA B:GLY69 4.3 9.5 1.0 CG B:GLU103 4.3 11.6 1.0 CB B:ASP70 4.3 11.2 1.0 C B:GLY151 4.3 15.0 1.0 OD2 B:ASP70 4.4 12.9 1.0 O B:HOH372 4.4 19.7 1.0 N B:GLU153 4.6 12.7 1.0 C B:GLU153 4.6 11.4 1.0 OG1 B:THR100 4.6 12.7 1.0 O B:HOH431 4.6 17.4 1.0 CA B:GLY151 4.6 14.0 1.0 O B:HOH446 4.7 21.4 0.5 N B:THR154 4.7 13.2 1.0 OG1 B:THR99 4.8 11.6 1.0 O B:HOH345 4.8 11.8 1.0 CA B:GLU153 4.9 12.5 1.0 N B:THR100 4.9 11.7 1.0 CB B:VAL152 4.9 10.7 1.0 CA B:THR99 4.9 11.5 1.0 O B:GLU153 5.0 11.8 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