Calcium in PDB 2a40: Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I

All present enzymatic activity of Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I:
3.1.21.1;

The structure of Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I, PDB code: 2a40 was solved by D.Chereau, F.Kerff, R.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.51 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	118.719, 41.598, 153.048, 90.00, 108.79, 90.00
R / Rfree (%)	16.6 / 21.5

The structure of Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I (pdb code 2a40). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I, PDB code: 2a40:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1381 b:20.1 occ:1.00 O A:HOH1387 2.3 20.8 1.0 O1B A:ATP1379 2.3 19.7 1.0 O A:HOH1385 2.4 16.4 1.0 O A:HOH1384 2.4 17.6 1.0 O2G A:ATP1379 2.4 19.3 1.0 O A:HOH1391 2.4 17.8 1.0 O A:HOH1395 2.6 20.0 1.0 PG A:ATP1379 3.5 20.8 1.0 PB A:ATP1379 3.6 19.9 1.0 O3B A:ATP1379 3.9 21.4 1.0 O3G A:ATP1379 3.9 23.1 1.0 O A:HOH1402 4.2 20.1 1.0 O3A A:ATP1379 4.2 21.1 1.0 OE1 A:GLN137 4.3 26.7 1.0 CA A:GLY13 4.3 23.4 1.0 O1A A:ATP1379 4.4 18.4 1.0 NZ A:LYS18 4.4 26.5 1.0 CD A:GLN137 4.5 27.4 1.0 OD2 A:ASP154 4.6 28.4 1.0 O A:HOH1412 4.7 22.5 1.0 OD1 A:ASP11 4.7 27.4 1.0 PA A:ATP1379 4.7 20.2 1.0 OD2 A:ASP11 4.8 24.9 1.0 O2B A:ATP1379 4.8 19.1 1.0 O A:HOH1428 4.8 25.1 1.0 O1G A:ATP1379 4.8 23.2 1.0 OD1 A:ASP154 4.8 31.3 1.0 CG A:GLN137 5.0 24.2 1.0

Calcium binding site 2 out of 4 in the Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1273 b:24.4 occ:1.00 O B:THR207 2.4 27.8 1.0 O B:HOH1491 2.4 23.5 1.0 OD2 B:ASP201 2.4 25.5 1.0 O B:THR203 2.4 24.8 1.0 O B:THR205 2.5 26.4 1.0 O B:HOH1388 2.5 21.6 1.0 OG1 B:THR203 2.5 25.6 1.0 OD1 B:ASP201 2.6 23.5 1.0 CG B:ASP201 2.8 22.9 1.0 C B:THR203 3.4 26.8 1.0 C B:THR207 3.6 27.6 1.0 CB B:THR203 3.7 25.1 1.0 C B:THR205 3.7 26.8 1.0 CA B:THR203 3.9 24.6 1.0 N B:THR203 4.1 27.3 1.0 N B:THR205 4.2 25.2 1.0 N B:THR207 4.3 25.0 1.0 CB B:ASP201 4.3 23.4 1.0 N B:ALA204 4.4 23.8 1.0 C B:SER206 4.4 27.3 1.0 C B:ALA204 4.4 25.4 1.0 N B:ASN208 4.5 23.8 1.0 N B:SER206 4.6 25.5 1.0 CA B:THR207 4.6 26.7 1.0 CA B:ASN208 4.6 22.8 1.0 CA B:THR205 4.6 25.3 1.0 OG1 B:THR207 4.6 29.8 1.0 CA B:SER206 4.6 28.7 1.0 CA B:ALA204 4.7 24.7 1.0 OH B:TYR253 4.8 24.2 1.0 OG1 B:THR205 4.8 28.1 1.0 CE2 B:TYR253 4.8 21.8 1.0 CG2 B:THR203 4.9 26.2 1.0 O B:ALA204 4.9 26.7 1.0 O B:SER206 4.9 27.6 1.0

Calcium binding site 3 out of 4 in the Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1382 b:23.7 occ:1.00 O1B D:ATP1380 2.3 24.2 1.0 O D:HOH1383 2.3 22.2 1.0 O D:HOH1389 2.4 21.8 1.0 O2G D:ATP1380 2.4 24.9 1.0 O D:HOH1385 2.4 21.5 1.0 O D:HOH1394 2.5 22.0 1.0 O D:HOH1387 2.6 22.2 1.0 PG D:ATP1380 3.5 24.3 1.0 PB D:ATP1380 3.6 23.0 1.0 O3G D:ATP1380 3.9 22.4 1.0 O3B D:ATP1380 3.9 25.4 1.0 O D:HOH1403 4.3 20.6 1.0 OE1 D:GLN137 4.3 29.6 1.0 O3A D:ATP1380 4.3 22.1 1.0 CA D:GLY13 4.3 28.6 1.0 O1A D:ATP1380 4.4 23.8 1.0 NZ D:LYS18 4.4 28.5 1.0 CD D:GLN137 4.5 30.0 1.0 OD2 D:ASP154 4.6 35.0 1.0 OD1 D:ASP11 4.7 28.9 1.0 O D:HOH1400 4.7 23.7 1.0 OD2 D:ASP11 4.7 28.7 1.0 O D:HOH1442 4.7 23.9 1.0 PA D:ATP1380 4.8 22.7 1.0 O2B D:ATP1380 4.8 21.6 1.0 OD1 D:ASP154 4.8 38.5 1.0 O1G D:ATP1380 4.8 23.6 1.0 NE2 D:GLN137 4.9 29.8 1.0

Calcium binding site 4 out of 4 in the Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Complex of the WH2 Domain of Wave with Actin-Dnase I within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1272 b:23.1 occ:1.00 OD2 E:ASP201 2.4 22.3 1.0 O E:HOH1276 2.4 21.0 1.0 O E:THR207 2.4 23.9 1.0 O E:THR203 2.4 23.2 1.0 O E:THR205 2.5 25.5 1.0 OD1 E:ASP201 2.5 26.4 1.0 O E:HOH1278 2.5 20.9 1.0 OG1 E:THR203 2.6 26.3 1.0 CG E:ASP201 2.8 22.9 1.0 C E:THR203 3.4 24.1 1.0 C E:THR207 3.6 25.6 1.0 C E:THR205 3.7 27.4 1.0 CB E:THR203 3.8 24.3 1.0 CA E:THR203 3.9 24.3 1.0 N E:THR203 4.1 24.1 1.0 N E:THR207 4.2 26.5 1.0 N E:THR205 4.3 26.1 1.0 CB E:ASP201 4.3 19.9 1.0 N E:ALA204 4.4 24.3 1.0 C E:ALA204 4.4 25.8 1.0 C E:SER206 4.4 27.5 1.0 N E:ASN208 4.5 23.4 1.0 CA E:ASN208 4.5 23.0 1.0 CA E:THR207 4.6 23.1 1.0 N E:SER206 4.6 25.0 1.0 CA E:THR205 4.6 27.2 1.0 OG1 E:THR207 4.6 26.3 1.0 CA E:SER206 4.6 27.4 1.0 CA E:ALA204 4.7 24.8 1.0 OG1 E:THR205 4.8 28.3 1.0 O E:ALA204 4.9 25.0 1.0 CE2 E:TYR253 4.9 22.2 1.0 OH E:TYR253 4.9 23.5 1.0 CG2 E:THR203 4.9 24.8 1.0

D.Chereau, F.Kerff, P.Graceffa, Z.Grabarek, K.Langsetmo, R.Dominguez. Actin-Bound Structures of Wiskott-Aldrich Syndrome Protein (Wasp)-Homology Domain 2 and the Implications For Filament Assembly Proc.Natl.Acad.Sci.Usa V. 102 16644 2005.
ISSN: ISSN 0027-8424
PubMed: 16275905
DOI: 10.1073/PNAS.0507021102