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

The structure of Complex of Atp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin, PDB code: 4pkg 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)	40.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.471, 75.866, 136.396, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.7

The binding sites of Calcium atom in the Complex of Atp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin (pdb code 4pkg). 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 N-Terminal Actin-Binding Domain of Tropomodulin, PDB code: 4pkg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Complex of Atp-Actin with the N-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 N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:19.1 occ:1.00 O A:HOH720 2.3 20.2 1.0 O1B A:ATP401 2.3 19.6 1.0 O A:HOH557 2.3 21.0 1.0 O A:HOH719 2.4 20.7 1.0 O3G A:ATP401 2.4 27.1 1.0 O A:HOH556 2.4 21.0 1.0 O A:HOH736 2.6 21.3 1.0 PG A:ATP401 3.5 67.0 1.0 HZ2 A:LYS18 3.5 25.0 1.0 PB A:ATP401 3.6 21.8 1.0 HA3 A:GLY13 3.8 27.6 1.0 O1G A:ATP401 3.9 25.2 1.0 O3B A:ATP401 3.9 24.5 1.0 HA2 A:GLY13 3.9 27.6 1.0 OE1 A:GLN137 4.1 21.8 1.0 O A:HOH561 4.2 24.8 1.0 O3A A:ATP401 4.3 18.9 1.0 CA A:GLY13 4.3 23.0 1.0 HG21 A:VAL339 4.3 28.2 1.0 O1A A:ATP401 4.4 20.7 1.0 NZ A:LYS18 4.4 20.9 1.0 HA3 A:GLY156 4.4 29.4 1.0 CD A:GLN137 4.5 21.3 1.0 O A:HOH579 4.5 25.9 1.0 HZ3 A:LYS18 4.5 25.0 1.0 OD1 A:ASP11 4.6 22.3 1.0 HG2 A:GLN137 4.7 24.9 1.0 OD2 A:ASP154 4.7 26.6 1.0 O2G A:ATP401 4.7 24.9 1.0 OD2 A:ASP11 4.7 21.2 1.0 HB3 A:GLN137 4.8 23.9 1.0 PA A:ATP401 4.8 22.2 1.0 H A:SER14 4.8 30.3 1.0 O2B A:ATP401 4.8 20.0 1.0 O A:HOH604 4.8 30.8 1.0 HZ1 A:LYS18 4.9 25.0 1.0 NE2 A:GLN137 4.9 19.7 1.0 OD1 A:ASP154 4.9 35.4 1.0 HE22 A:GLN137 4.9 23.6 1.0

Calcium binding site 2 out of 3 in the Complex of Atp-Actin with the N-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 N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:40.9 occ:1.00 OD2 G:ASP136 2.3 29.1 1.0 O G:ALA143 2.3 31.8 1.0 O G:HOH1422 2.5 46.5 1.0 O G:GLY141 2.6 32.7 1.0 O A:HOH699 2.6 43.6 1.0 OD1 G:ASP136 2.8 27.2 1.0 OE1 A:GLU167 2.9 29.4 1.0 CG G:ASP136 2.9 32.0 1.0 C G:GLY141 3.4 34.7 1.0 C G:ALA143 3.4 37.5 1.0 O G:HOH1423 3.4 51.7 1.0 HA2 G:GLY141 3.6 34.0 1.0 H G:ALA143 3.6 34.3 1.0 N G:ALA143 3.7 28.6 1.0 CD A:GLU167 3.8 49.2 1.0 O A:HOH631 3.9 47.6 1.0 HE21 G:GLN145 4.0 30.1 1.0 CA G:GLY141 4.0 28.3 1.0 HG3 G:GLN145 4.0 28.4 1.0 CA G:ALA143 4.1 25.0 1.0 HA G:VAL144 4.1 30.1 1.0 C G:ARG142 4.1 29.9 0.6 C G:ARG142 4.2 30.2 0.5 N G:ARG142 4.2 29.6 0.6 N G:ARG142 4.2 29.0 0.5 HB3 G:ALA143 4.2 34.8 1.0 HA3 G:GLY141 4.3 34.0 1.0 OE2 A:GLU167 4.3 29.5 1.0 HB3 A:GLU167 4.4 27.5 1.0 CB G:ASP136 4.4 25.0 1.0 O G:HOH1420 4.5 54.6 1.0 N G:VAL144 4.5 26.4 1.0 HA G:ARG142 4.5 35.0 0.5 CA G:ARG142 4.6 29.1 0.5 CA G:ARG142 4.6 28.1 0.6 O A:HOH621 4.6 45.5 1.0 HA G:ARG142 4.6 33.8 0.6 NE2 G:GLN145 4.6 25.0 1.0 HB2 G:ASP136 4.7 29.9 1.0 O G:ARG142 4.7 35.8 0.6 O G:HOH1405 4.7 48.6 1.0 HB3 G:ASP136 4.7 29.9 1.0 CB G:ALA143 4.8 29.0 1.0 CA G:VAL144 4.8 25.1 1.0 O G:ARG142 4.9 36.0 0.5 H G:ARG142 4.9 35.5 0.6 H G:ARG142 4.9 34.8 0.5 O G:HOH1334 4.9 45.0 1.0 H G:GLN145 4.9 28.4 1.0 HA G:ALA143 5.0 30.1 1.0 CG G:GLN145 5.0 23.7 1.0 CG A:GLU167 5.0 30.8 1.0 CB A:GLU167 5.0 22.9 1.0

Calcium binding site 3 out of 3 in the Complex of Atp-Actin with the N-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 N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1201 b:27.5 occ:1.00 O G:GLY92 2.2 28.8 1.0 O G:HOH1348 2.3 31.7 1.0 OD1 G:ASP93 2.3 34.3 1.0 O G:HOH1360 2.4 24.8 1.0 O G:VAL172 2.4 36.5 1.0 OE2 G:GLU124 2.4 25.6 1.0 OE1 G:GLU124 2.5 22.9 1.0 CD G:GLU124 2.8 23.1 1.0 HA G:ASP93 3.2 29.1 1.0 C G:GLY92 3.3 26.2 1.0 HG23 G:VAL172 3.4 33.3 0.6 CG G:ASP93 3.5 30.0 1.0 C G:VAL172 3.6 38.2 1.0 HA G:CYS120 3.8 26.6 1.0 HA3 G:GLY171 3.9 42.1 1.0 H G:VAL172 3.9 41.3 0.4 H G:VAL172 3.9 41.3 0.6 H G:SER121 4.0 27.3 1.0 CA G:ASP93 4.0 24.3 1.0 HG22 G:VAL172 4.0 33.3 0.6 N G:VAL172 4.0 34.5 1.0 N G:ASP93 4.1 24.8 1.0 CG2 G:VAL172 4.2 27.7 0.6 HA3 G:GLY92 4.2 35.3 1.0 O G:HOH1351 4.3 26.2 1.0 CG G:GLU124 4.3 22.1 1.0 CA G:VAL172 4.4 40.6 0.6 HA G:ALA173 4.4 46.5 1.0 CB G:ASP93 4.4 29.2 1.0 CA G:VAL172 4.4 40.0 0.4 CA G:GLY92 4.4 29.4 1.0 O G:HOH1313 4.4 33.4 1.0 C G:GLY171 4.4 36.7 1.0 OD2 G:ASP93 4.5 31.6 1.0 HB G:VAL172 4.5 54.8 0.4 OG G:SER121 4.6 27.0 1.0 HB2 G:CYS120 4.6 26.2 1.0 N G:ALA173 4.6 36.8 1.0 C G:ALA173 4.6 31.1 1.0 CA G:GLY171 4.7 35.0 1.0 O G:HOH1371 4.7 43.1 1.0 HG3 G:GLU124 4.7 26.5 1.0 HG2 G:GLU124 4.7 26.5 1.0 N G:SER174 4.7 29.9 1.0 N G:SER121 4.7 22.8 1.0 CA G:CYS120 4.7 22.2 1.0 HA2 G:GLY92 4.7 35.3 1.0 H G:SER174 4.8 35.9 1.0 CA G:ALA173 4.8 38.8 1.0 HA G:SER174 4.8 38.9 1.0 O G:HOH1419 4.8 52.2 1.0 HB3 G:ASP93 4.8 35.0 1.0 O G:HOH1353 4.9 28.1 1.0 CB G:VAL172 4.9 41.9 0.6 HG21 G:VAL172 4.9 33.3 0.6 H G:ASP93 4.9 29.8 1.0 HG G:SER121 4.9 32.4 1.0 O G:ALA173 5.0 32.7 1.0 CB G:VAL172 5.0 45.6 0.4

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