Calcium in PDB 1lcu: Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution

The structure of Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution, PDB code: 1lcu was solved by M.R.Bubb, L.Govindasamy, E.G.Yarmola, S.M.Vorobiev, S.C.Almo, T.Somasundaram, M.S.Chapman, M.Agbandje-Mckenna, R.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.456, 103.029, 126.958, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 26.6

The structure of Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Calcium atom in the Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution (pdb code 1lcu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution, PDB code: 1lcu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca412 b:15.6 occ:1.00 O2B A:ATP390 2.2 15.1 1.0 O1G A:ATP390 2.8 13.6 1.0 O3G A:ATP390 3.0 15.7 1.0 NE2 A:GLN147 3.3 27.5 1.0 PG A:ATP390 3.4 15.4 1.0 PB A:ATP390 3.4 12.4 1.0 OD2 A:ASP164 3.5 27.2 1.0 O3B A:ATP390 3.7 12.1 1.0 O A:HOH539 3.8 88.8 1.0 CD A:GLN147 3.9 25.2 1.0 O3A A:ATP390 4.2 10.5 1.0 OE1 A:GLN147 4.2 26.6 1.0 O1A A:ATP390 4.3 12.3 1.0 OD1 A:ASP21 4.4 12.8 1.0 PA A:ATP390 4.5 12.7 1.0 CG A:ASP164 4.6 25.6 1.0 O1B A:ATP390 4.7 13.9 1.0 OD2 A:ASP21 4.7 13.4 1.0 O2G A:ATP390 4.8 14.5 1.0 CA A:GLY23 4.8 17.3 1.0 CG A:GLN147 4.9 21.8 1.0 OD1 A:ASP164 5.0 25.9 1.0

Calcium binding site 2 out of 4 in the Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:9.8 occ:1.00 CB A:TYR179 3.1 45.4 1.0 O A:ALA180 3.4 34.6 1.0 OE1 B:GLN1364 3.6 72.0 1.0 CD2 A:TYR179 3.9 56.1 1.0 CG A:TYR179 3.9 53.6 1.0 O B:HOH24 4.0 47.9 1.0 CA A:TYR179 4.1 40.4 1.0 C A:TYR179 4.1 38.5 1.0 CD B:GLN1364 4.1 70.4 1.0 C A:ALA180 4.2 33.6 1.0 N A:ALA180 4.2 36.5 1.0 CG B:GLN1364 4.3 68.0 1.0 CD A:PRO182 4.4 32.4 1.0 CD2 A:LEU181 4.5 27.0 1.0 O A:TYR179 4.5 39.3 1.0 N A:LEU181 4.8 31.7 1.0 CA A:LEU181 4.9 29.8 1.0 CA A:ALA180 4.9 34.4 1.0 NE2 B:GLN1364 4.9 71.5 1.0

Calcium binding site 3 out of 4 in the Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:9.8 occ:1.00 N A:VAL40 3.1 25.5 1.0 O A:VAL40 3.6 25.6 1.0 CA A:ALA39 3.8 26.9 1.0 O A:ARG38 3.9 28.9 1.0 C A:ALA39 4.0 25.8 1.0 CA A:VAL40 4.0 25.1 1.0 C A:VAL40 4.1 24.9 1.0 CB A:VAL40 4.4 24.6 1.0 CB A:ALA39 4.6 27.2 1.0 C A:ARG38 4.8 29.3 1.0 N A:ALA39 4.8 28.0 1.0 CG2 A:VAL40 4.8 23.3 1.0

Calcium binding site 4 out of 4 in the Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1412 b:9.8 occ:1.00 O B:HOH21 2.1 0.8 1.0 O3G B:ATP1390 2.6 25.9 1.0 O2B B:ATP1390 2.6 27.7 1.0 O B:HOH11 2.7 0.4 1.0 O B:HOH5 2.8 53.8 1.0 NE2 B:GLN1147 3.5 21.2 1.0 OD2 B:ASP1164 3.5 28.3 1.0 PG B:ATP1390 3.7 23.7 1.0 PB B:ATP1390 3.8 24.3 1.0 O1G B:ATP1390 3.9 21.8 1.0 O3B B:ATP1390 4.1 22.7 1.0 O B:HOH31 4.2 77.8 1.0 CD B:GLN1147 4.3 18.5 1.0 OD1 B:ASP1021 4.5 13.9 1.0 CG2 B:VAL1349 4.5 21.1 1.0 O1A B:ATP1390 4.5 24.7 1.0 O3A B:ATP1390 4.5 23.8 1.0 CG B:ASP1164 4.5 27.9 1.0 PA B:ATP1390 4.6 24.6 1.0 OD2 B:ASP1021 4.7 11.6 1.0 OD1 B:ASP1164 4.9 28.1 1.0 CA B:GLY1023 4.9 16.3 1.0 CG B:GLN1147 4.9 17.2 1.0 O2G B:ATP1390 5.0 23.4 1.0 OE1 B:GLN1147 5.0 17.6 1.0

M.R.Bubb, L.Govindasamy, E.G.Yarmola, S.M.Vorobiev, S.C.Almo, T.Somasundaram, M.S.Chapman, M.Agbandje-Mckenna, R.Mckenna. Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure at 3.5-A Resolution. J.Biol.Chem. V. 277 20999 2002.
ISSN: ISSN 0021-9258
PubMed: 11932258
DOI: 10.1074/JBC.M201371200