Calcium in PDB 3ub5: Profilin:Actin with A Wide Open Nucleotide Cleft

The structure of Profilin:Actin with A Wide Open Nucleotide Cleft, PDB code: 3ub5 was solved by J.C.Porta, G.E.Borgstahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.24 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.000, 72.000, 186.800, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 29

The structure of Profilin:Actin with A Wide Open Nucleotide Cleft also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Profilin:Actin with A Wide Open Nucleotide Cleft (pdb code 3ub5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Profilin:Actin with A Wide Open Nucleotide Cleft, PDB code: 3ub5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Profilin:Actin with A Wide Open Nucleotide Cleft


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Profilin:Actin with A Wide Open Nucleotide Cleft within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca377 b:66.6 occ:1.00 N A:MET16 2.3 53.1 1.0 O2B A:ATP376 2.3 89.1 1.0 O1B A:ATP376 2.6 93.3 1.0 PB A:ATP376 2.7 91.3 1.0 N A:GLY15 3.1 42.6 1.0 C A:GLY15 3.2 49.0 1.0 O2A A:ATP376 3.3 0.1 1.0 CA A:MET16 3.3 51.1 1.0 CA A:GLY15 3.3 46.3 1.0 O A:MET16 3.5 47.0 1.0 CB A:MET16 3.6 53.5 1.0 CA A:GLY13 3.7 36.2 1.0 C A:MET16 3.8 50.0 1.0 C A:GLY13 3.9 40.6 1.0 O3B A:ATP376 3.9 88.6 1.0 N A:SER14 3.9 40.2 1.0 O3A A:ATP376 4.0 0.7 1.0 CG A:MET16 4.1 58.9 1.0 NZ A:LYS18 4.1 38.2 1.0 C A:SER14 4.2 45.4 1.0 PA A:ATP376 4.3 0.5 1.0 O A:GLY15 4.4 47.8 1.0 CE A:LYS18 4.5 33.9 1.0 O A:GLY13 4.5 42.0 1.0 N A:GLY13 4.6 33.8 1.0 CA A:SER14 4.6 44.3 1.0

Calcium binding site 2 out of 2 in the Profilin:Actin with A Wide Open Nucleotide Cleft


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Profilin:Actin with A Wide Open Nucleotide Cleft within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca378 b:52.5 occ:0.50 OE2 A:GLU205 2.3 48.0 1.0 OG1 A:THR201 2.3 56.9 1.0 O A:SER199 2.3 55.0 1.0 CD A:GLU205 3.1 51.6 1.0 OE1 A:GLU205 3.3 54.3 1.0 N A:THR201 3.5 58.8 1.0 C A:SER199 3.5 52.4 1.0 OG A:SER199 3.6 50.2 1.0 CB A:THR201 3.7 54.9 1.0 CA A:THR201 4.1 54.2 1.0 N A:THR202 4.1 50.7 1.0 C A:PHE200 4.2 52.9 1.0 CB A:SER199 4.2 47.1 1.0 CA A:PHE200 4.3 52.2 1.0 CG2 A:THR201 4.3 52.7 1.0 N A:PHE200 4.3 55.5 1.0 CG2 A:THR202 4.4 46.1 1.0 C A:THR201 4.5 53.9 1.0 CA A:SER199 4.5 48.6 1.0 CG A:GLU205 4.6 48.5 1.0 OG1 A:THR202 5.0 41.2 1.0

J.C.Porta, G.E.Borgstahl. Structural Basis For Profilin-Mediated Actin Nucleotide Exchange. J.Mol.Biol. V. 418 103 2012.
ISSN: ISSN 0022-2836
PubMed: 22366544
DOI: 10.1016/J.JMB.2012.02.012