Calcium in PDB 5ubo: Mical-Oxidized Actin Complex with Gelsolin Segment 1

The structure of Mical-Oxidized Actin Complex with Gelsolin Segment 1, PDB code: 5ubo was solved by E.E.Grintsevich, M.R.Sawaya, E.Reisler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	89.59 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.200, 69.250, 179.180, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.1

The binding sites of Calcium atom in the Mical-Oxidized Actin Complex with Gelsolin Segment 1 (pdb code 5ubo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Mical-Oxidized Actin Complex with Gelsolin Segment 1, PDB code: 5ubo:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Mical-Oxidized Actin Complex with Gelsolin Segment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mical-Oxidized Actin Complex with Gelsolin Segment 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:54.6 occ:1.00 O A:HOH528 2.3 48.2 1.0 O1B A:ATP402 2.3 52.6 1.0 O A:HOH539 2.3 51.6 1.0 O A:HOH547 2.4 51.4 1.0 O1G A:ATP402 2.4 58.1 1.0 O A:HOH559 2.5 57.1 1.0 O A:HOH517 2.7 51.4 1.0 PG A:ATP402 3.4 55.0 1.0 PB A:ATP402 3.5 54.0 1.0 O3B A:ATP402 3.7 54.6 1.0 O3G A:ATP402 3.8 52.0 1.0 O3A A:ATP402 4.2 53.6 1.0 OE1 A:GLN137 4.2 57.8 1.0 CA A:GLY13 4.2 51.8 1.0 O A:HOH521 4.2 62.9 1.0 O1A A:ATP402 4.4 53.9 1.0 O A:HOH520 4.5 56.5 1.0 CD A:GLN137 4.5 60.7 1.0 O A:HOH511 4.6 66.0 1.0 NZ A:LYS18 4.6 61.3 1.0 OD2 A:ASP154 4.7 66.6 1.0 OD1 A:ASP11 4.7 45.0 1.0 O2B A:ATP402 4.8 48.6 1.0 O2G A:ATP402 4.8 56.1 1.0 PA A:ATP402 4.8 54.2 1.0 OD2 A:ASP11 4.9 50.0 1.0 OD1 A:ASP154 4.9 70.6 1.0 NE2 A:GLN137 4.9 46.7 1.0

Calcium binding site 2 out of 3 in the Mical-Oxidized Actin Complex with Gelsolin Segment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mical-Oxidized Actin Complex with Gelsolin Segment 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:60.0 occ:1.00 O S:ALA92 2.2 51.2 1.0 OD2 S:ASP85 2.3 58.1 1.0 O A:HOH554 2.4 60.8 1.0 O S:HOH339 2.5 53.0 1.0 OE1 A:GLU167 2.5 52.8 1.0 O S:GLY90 2.5 52.7 1.0 OD1 S:ASP85 2.6 50.3 1.0 CG S:ASP85 2.8 47.8 1.0 C S:GLY90 3.3 55.0 1.0 C S:ALA92 3.4 50.5 1.0 CD A:GLU167 3.6 61.7 1.0 N S:ALA92 3.8 47.7 1.0 CA S:GLY90 3.9 50.4 1.0 OE2 A:GLU167 4.0 53.2 1.0 CA S:ALA92 4.1 47.7 1.0 C S:ARG91 4.3 55.9 1.0 CB S:ASP85 4.3 46.2 1.0 N S:ARG91 4.3 50.1 1.0 N S:VAL93 4.4 46.1 1.0 O A:HOH526 4.5 67.4 1.0 O A:HOH540 4.6 63.2 1.0 CB S:ALA92 4.6 47.3 1.0 NE2 S:GLN94 4.7 49.6 1.0 CA S:ARG91 4.7 50.0 1.0 CA S:VAL93 4.7 46.0 1.0 CG A:GLU167 4.8 48.7 1.0 O S:ARG91 4.8 58.7 1.0 CB A:GLU167 5.0 43.5 1.0

Calcium binding site 3 out of 3 in the Mical-Oxidized Actin Complex with Gelsolin Segment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mical-Oxidized Actin Complex with Gelsolin Segment 1 within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca201 b:60.8 occ:1.00 O S:HOH319 2.3 57.4 1.0 OD1 S:ASP42 2.3 65.6 1.0 O S:HOH342 2.3 69.0 1.0 O S:VAL121 2.3 58.1 1.0 O S:GLY41 2.4 55.5 1.0 OE2 S:GLU73 2.5 56.5 1.0 OE1 S:GLU73 2.5 68.7 1.0 CD S:GLU73 2.9 66.8 1.0 C S:GLY41 3.5 55.4 1.0 CG S:ASP42 3.5 65.0 1.0 C S:VAL121 3.5 62.0 1.0 N S:VAL121 4.0 62.4 1.0 CA S:ASP42 4.0 52.0 1.0 N S:ASP42 4.2 52.9 1.0 CG1 S:VAL121 4.3 62.1 1.0 O S:HOH306 4.3 53.4 1.0 O S:HOH333 4.3 60.2 1.0 CA S:VAL121 4.3 61.9 1.0 CB S:ASP42 4.3 54.0 1.0 CG S:GLU73 4.4 51.0 1.0 OD2 S:ASP42 4.4 68.0 1.0 C S:GLY120 4.4 65.5 1.0 OG S:SER70 4.5 55.8 1.0 CA S:GLY41 4.5 50.1 1.0 N S:ALA122 4.5 61.0 1.0 C S:ALA122 4.5 64.2 1.0 CA S:ALA122 4.6 60.6 1.0 CA S:GLY120 4.7 63.0 1.0 N S:SER123 4.7 59.4 1.0 N S:SER70 4.8 47.3 1.0 O S:HOH313 4.8 53.2 1.0 O S:ALA122 4.8 65.5 1.0 CA S:CYS69 4.9 51.7 1.0 CB S:VAL121 5.0 65.3 1.0

E.E.Grintsevich, P.Ge, M.R.Sawaya, H.G.Yesilyurt, J.R.Terman, Z.H.Zhou, E.Reisler. Catastrophic Disassembly of Actin Filaments Via Mical-Mediated Oxidation. Nat Commun V. 8 2183 2017.
ISSN: ESSN 2041-1723
PubMed: 29259197
DOI: 10.1038/S41467-017-02357-8