Calcium in PDB 3a5m: Crystal Structure of A Dictyostelium P109I MG2+-Actin in Complex with Human Gelsolin Segment 1

The structure of Crystal Structure of A Dictyostelium P109I MG2+-Actin in Complex with Human Gelsolin Segment 1, PDB code: 3a5m was solved by K.Murakami, T.Yasunaga, T.Q.Noguchi, T.Q.Uyeda, T.Wakabayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.55 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.701, 69.173, 181.690, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.3

The structure of Crystal Structure of A Dictyostelium P109I MG2+-Actin in Complex with Human Gelsolin Segment 1 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of A Dictyostelium P109I MG2+-Actin in Complex with Human Gelsolin Segment 1 (pdb code 3a5m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Dictyostelium P109I MG2+-Actin in Complex with Human Gelsolin Segment 1, PDB code: 3a5m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Dictyostelium P109I MG2+-Actin in Complex with Human Gelsolin Segment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Dictyostelium P109I MG2+-Actin in Complex with Human Gelsolin Segment 1 within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca128 b:27.6 occ:1.00 O S:GLY43 2.2 18.9 1.0 O S:VAL123 2.3 25.0 1.0 O S:HOH1031 2.3 32.1 1.0 OD2 S:ASP44 2.4 21.7 1.0 OE2 S:GLU75 2.4 25.0 1.0 O S:HOH1117 2.7 42.4 1.0 OE1 S:GLU75 2.7 22.5 1.0 CD S:GLU75 3.0 19.6 1.0 C S:GLY43 3.3 17.4 1.0 C S:VAL123 3.5 25.6 1.0 CG S:ASP44 3.6 18.6 1.0 CA S:ASP44 4.0 16.5 1.0 N S:ASP44 4.1 16.9 1.0 N S:VAL123 4.1 27.4 1.0 O S:HOH1073 4.2 29.2 1.0 CA S:GLY43 4.3 17.0 1.0 O S:HOH1101 4.3 14.4 1.0 CA S:VAL123 4.3 25.6 1.0 CB S:ASP44 4.4 16.8 1.0 N S:ALA124 4.4 26.0 1.0 OD1 S:ASP44 4.5 18.8 1.0 CG S:GLU75 4.5 13.5 1.0 CG1 S:VAL123 4.5 24.8 1.0 CA S:ALA124 4.5 26.5 1.0 OG S:SER72 4.5 25.0 1.0 C S:ALA124 4.5 26.4 1.0 O S:HOH1081 4.5 36.8 1.0 C S:GLY122 4.6 26.9 1.0 N S:SER125 4.7 25.8 1.0 CA S:CYS71 4.8 18.4 1.0 O S:ALA124 4.9 27.4 1.0 CA S:GLY122 5.0 27.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Dictyostelium P109I MG2+-Actin in Complex with Human Gelsolin Segment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Dictyostelium P109I MG2+-Actin in Complex with Human Gelsolin Segment 1 within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca129 b:68.0 occ:1.00 OD2 S:ASP87 2.4 23.4 1.0 O S:ALA94 2.4 25.6 1.0 OE1 C:GLU167 2.7 28.0 1.0 O S:GLY92 3.0 20.4 1.0 O C:HOH1082 3.1 47.3 1.0 CG S:ASP87 3.2 21.4 1.0 OD1 S:ASP87 3.3 24.5 1.0 C S:ALA94 3.5 23.8 1.0 CD C:GLU167 3.6 22.5 1.0 C S:GLY92 3.7 20.4 1.0 O S:HOH1265 3.9 46.7 1.0 OE2 C:GLU167 4.0 23.2 1.0 N S:ALA94 4.0 23.8 1.0 O C:HOH1139 4.1 34.4 1.0 CA S:GLY92 4.2 19.4 1.0 O S:HOH1034 4.3 43.7 1.0 CA S:ALA94 4.4 24.0 1.0 O C:HOH1307 4.4 38.9 1.0 N S:VAL95 4.4 23.6 1.0 N S:ARG93 4.5 20.5 1.0 C S:ARG93 4.5 24.4 1.0 O S:HOH1004 4.6 51.3 1.0 CA S:VAL95 4.6 22.6 1.0 CB S:ASP87 4.6 16.5 1.0 NE2 S:GLN96 4.7 10.1 1.0 CA S:ARG93 4.9 23.5 1.0 CG C:GLU167 4.9 19.6 1.0 CG S:GLN96 5.0 15.2 1.0

K.Murakami, T.Yasunaga, T.Q.P.Noguchi, Y.Gomibuchi, K.X.Ngo, T.Q.P.Uyeda, T.Wakabayashi. Structural Basis For Actin Assembly, Activation of Atp Hydrolysis, and Delayed Phosphate Release Cell(Cambridge,Mass.) V. 143 275 2010.
ISSN: ISSN 0092-8674
PubMed: 20946985
DOI: 10.1016/J.CELL.2010.09.034