Calcium in PDB 4pki: Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin

The structure of Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin, PDB code: 4pki was solved by J.N.Rao, R.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.393, 81.211, 170.708, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.1

The binding sites of Calcium atom in the Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin (pdb code 4pki). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin, PDB code: 4pki:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:37.0 occ:1.00 O2B A:ATP401 2.3 35.0 1.0 O A:HOH510 2.3 36.1 1.0 O3G A:ATP401 2.4 34.5 1.0 O A:HOH512 2.6 43.6 1.0 O A:HOH511 2.6 37.2 1.0 O A:HOH541 2.7 39.8 1.0 O A:HOH532 2.8 39.7 1.0 HZ1 A:LYS18 3.4 40.5 1.0 PG A:ATP401 3.5 34.2 1.0 PB A:ATP401 3.6 34.1 1.0 HA3 A:GLY13 3.7 38.9 1.0 O1G A:ATP401 3.8 32.7 1.0 O3B A:ATP401 3.9 34.8 1.0 HA2 A:GLY13 4.0 38.9 1.0 O A:HOH517 4.1 40.0 1.0 OE1 A:GLN137 4.2 33.2 1.0 NZ A:LYS18 4.3 33.8 1.0 HG2 A:GLN137 4.3 40.5 1.0 O3A A:ATP401 4.3 34.0 1.0 HG21 A:VAL339 4.3 33.1 1.0 CA A:GLY13 4.4 32.5 1.0 HA3 A:GLY156 4.4 38.5 1.0 CD A:GLN137 4.4 35.7 1.0 O1A A:ATP401 4.4 33.2 1.0 O A:HOH533 4.5 41.4 1.0 HZ2 A:LYS18 4.5 40.5 1.0 OD2 A:ASP154 4.6 32.8 1.0 HZ3 A:LYS18 4.6 40.5 1.0 O A:HOH609 4.7 29.1 1.0 H A:SER14 4.8 44.3 1.0 O1B A:ATP401 4.8 32.6 1.0 OD1 A:ASP11 4.8 32.3 1.0 OD1 A:ASP154 4.8 42.3 1.0 OD2 A:ASP11 4.8 29.1 1.0 PA A:ATP401 4.8 34.3 1.0 O2G A:ATP401 4.8 33.0 1.0 CG A:GLN137 4.9 33.7 1.0 NE2 A:GLN137 4.9 36.0 1.0 HB3 A:GLN137 5.0 36.9 1.0

Calcium binding site 2 out of 3 in the Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:41.1 occ:1.00 OD2 G:ASP136 2.3 36.3 1.0 O G:ALA143 2.4 34.0 1.0 OE1 A:GLU167 2.4 39.6 1.0 O G:HOH1525 2.4 52.7 1.0 O G:GLY141 2.4 32.7 1.0 O G:HOH1528 2.6 43.1 1.0 OD1 G:ASP136 2.8 32.6 1.0 CG G:ASP136 2.9 32.8 1.0 C G:GLY141 3.3 32.7 1.0 CD A:GLU167 3.5 34.7 1.0 C G:ALA143 3.5 34.3 1.0 HA2 G:GLY141 3.6 35.2 1.0 HE21 G:GLN145 3.8 34.8 1.0 H G:ALA143 3.9 36.3 1.0 N G:ALA143 3.9 30.2 1.0 CA G:GLY141 4.0 29.4 1.0 OE2 A:GLU167 4.0 33.6 1.0 HG3 G:GLN145 4.0 40.4 1.0 HA G:VAL144 4.1 43.6 1.0 HB3 G:ALA143 4.2 36.6 1.0 N G:ARG142 4.2 40.8 1.0 HB3 A:GLU167 4.2 30.1 1.0 HA3 G:GLY141 4.3 35.2 1.0 CA G:ALA143 4.3 33.6 1.0 C G:ARG142 4.3 42.5 1.0 CB G:ASP136 4.3 29.9 1.0 O A:HOH535 4.4 39.0 1.0 NE2 G:GLN145 4.5 29.0 1.0 HA G:ARG142 4.5 53.0 1.0 HB3 G:ASP136 4.6 35.8 1.0 N G:VAL144 4.6 39.0 1.0 CA G:ARG142 4.6 44.2 1.0 O G:HOH1541 4.6 46.5 1.0 CG A:GLU167 4.7 30.1 1.0 HB2 G:ASP136 4.7 35.8 1.0 CB G:ALA143 4.7 30.5 1.0 CA G:VAL144 4.8 36.3 1.0 H G:ARG142 4.8 48.9 1.0 CB A:GLU167 4.9 25.1 1.0 H G:GLN145 4.9 45.1 1.0 CG G:GLN145 4.9 33.6 1.0 O G:ARG142 4.9 43.1 1.0 HB2 A:GLU167 5.0 30.1 1.0 HE22 G:GLN145 5.0 34.8 1.0

Calcium binding site 3 out of 3 in the Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Atp-Actin with the C-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1401 b:40.2 occ:1.00 OD1 G:ASP93 2.3 43.1 1.0 O G:VAL172 2.3 40.2 1.0 O G:HOH1574 2.3 43.2 1.0 OE2 G:GLU124 2.4 48.0 1.0 O G:GLY92 2.4 44.2 1.0 OE1 G:GLU124 2.6 43.9 1.0 O G:HOH1521 2.7 39.6 1.0 CD G:GLU124 2.8 44.1 1.0 HA G:ASP93 3.2 38.2 1.0 C G:GLY92 3.4 41.3 1.0 CG G:ASP93 3.5 41.5 1.0 C G:VAL172 3.5 41.7 1.0 HG23 G:VAL172 3.7 46.6 1.0 HA G:CYS120 3.8 41.6 1.0 H G:VAL172 3.9 48.5 1.0 CA G:ASP93 3.9 31.9 1.0 N G:VAL172 4.0 40.4 1.0 HA3 G:GLY171 4.0 48.8 1.0 H G:SER121 4.0 41.5 1.0 N G:ASP93 4.1 33.4 1.0 HG22 G:VAL172 4.1 46.6 1.0 O G:HOH1536 4.2 28.8 1.0 HA3 G:GLY92 4.2 47.4 1.0 O G:HOH1577 4.3 52.4 1.0 CG G:GLU124 4.3 39.8 1.0 CA G:VAL172 4.3 41.1 1.0 CG2 G:VAL172 4.3 38.9 1.0 CB G:ASP93 4.3 36.2 1.0 HA G:ALA173 4.4 47.0 1.0 C G:GLY171 4.4 42.7 1.0 OD2 G:ASP93 4.4 45.7 1.0 CA G:GLY92 4.4 39.5 1.0 HB2 G:CYS120 4.4 36.5 1.0 N G:ALA173 4.5 40.7 1.0 OG G:SER121 4.6 35.2 1.0 HG3 G:GLU124 4.6 47.8 1.0 C G:ALA173 4.7 37.3 1.0 HG2 G:GLU124 4.7 47.8 1.0 CA G:GLY171 4.7 40.7 1.0 CA G:CYS120 4.7 34.7 1.0 CA G:ALA173 4.7 39.2 1.0 HA2 G:GLY92 4.8 47.4 1.0 N G:SER174 4.8 38.7 1.0 N G:SER121 4.8 34.6 1.0 HA G:SER174 4.8 44.1 1.0 HB3 G:ASP93 4.8 43.5 1.0 HG G:SER121 4.9 42.2 1.0 H G:SER174 4.9 46.5 1.0 O G:HOH1542 4.9 45.9 1.0 O G:ALA173 4.9 36.3 1.0 H G:ASP93 4.9 40.1 1.0 CB G:VAL172 5.0 42.2 1.0

J.N.Rao, Y.Madasu, R.Dominguez. Actin Cytoskeleton. Mechanism of Actin Filament Pointed-End Capping By Tropomodulin. Science V. 345 463 2014.
ISSN: ESSN 1095-9203
PubMed: 25061212
DOI: 10.1126/SCIENCE.1256159