Calcium in PDB 3a5n: Crystal Structure of A Dictyostelium P109A CA2+-Actin in Complex with Human Gelsolin Segment 1

The structure of Crystal Structure of A Dictyostelium P109A CA2+-Actin in Complex with Human Gelsolin Segment 1, PDB code: 3a5n 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)	6.00 / 2.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.533, 68.679, 181.717, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 20.4

The binding sites of Calcium atom in the Crystal Structure of A Dictyostelium P109A CA2+-Actin in Complex with Human Gelsolin Segment 1 (pdb code 3a5n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Dictyostelium P109A CA2+-Actin in Complex with Human Gelsolin Segment 1, PDB code: 3a5n:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Dictyostelium P109A CA2+-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 P109A CA2+-Actin in Complex with Human Gelsolin Segment 1 within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca128 b:17.0 occ:1.00 OD2 S:ASP44 2.1 15.4 1.0 O S:GLY43 2.2 18.0 1.0 O S:HOH1031 2.3 16.7 1.0 O S:VAL123 2.3 19.1 1.0 OE2 S:GLU75 2.3 16.7 1.0 O S:HOH1117 2.3 24.5 1.0 OE1 S:GLU75 2.6 20.1 1.0 CD S:GLU75 2.8 13.8 1.0 C S:GLY43 3.3 17.7 1.0 CG S:ASP44 3.4 18.2 1.0 C S:VAL123 3.5 19.6 1.0 CA S:ASP44 3.9 16.7 1.0 N S:VAL123 4.0 21.4 1.0 N S:ASP44 4.0 16.9 1.0 O S:HOH1101 4.2 13.5 1.0 CA S:VAL123 4.3 19.2 1.0 CB S:ASP44 4.3 14.9 1.0 OD1 S:ASP44 4.3 16.8 1.0 CG S:GLU75 4.3 14.6 1.0 CG1 S:VAL123 4.3 15.8 1.0 O S:HOH1073 4.4 21.0 1.0 CA S:GLY43 4.4 17.0 1.0 OG S:SER72 4.5 16.2 1.0 C S:GLY122 4.5 21.9 1.0 N S:ALA124 4.5 21.0 1.0 C S:ALA124 4.6 20.6 1.0 CA S:CYS71 4.7 16.4 1.0 CA S:GLY122 4.7 21.9 1.0 N S:SER72 4.7 13.9 1.0 CA S:ALA124 4.7 20.5 1.0 O S:HOH1081 4.8 40.3 1.0 N S:SER125 4.8 20.1 1.0 O S:HOH1102 4.9 20.2 1.0 O S:ALA124 4.9 21.1 1.0 CB S:VAL123 5.0 20.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Dictyostelium P109A CA2+-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 P109A CA2+-Actin in Complex with Human Gelsolin Segment 1 within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca129 b:25.4 occ:1.00 OD2 S:ASP87 2.3 16.8 1.0 O S:ALA94 2.4 18.8 1.0 OE1 C:GLU167 2.5 17.5 1.0 O S:GLY92 2.6 17.8 1.0 O S:HOH1223 2.6 38.5 1.0 O S:HOH1082 2.8 28.5 1.0 O S:HOH1004 2.8 22.0 1.0 OD1 S:ASP87 2.8 18.4 1.0 CG S:ASP87 2.9 17.5 1.0 C S:GLY92 3.3 19.2 1.0 C S:ALA94 3.6 18.5 1.0 CD C:GLU167 3.6 20.6 1.0 CA S:GLY92 3.8 19.5 1.0 N S:ALA94 4.0 20.0 1.0 OE2 C:GLU167 4.1 25.5 1.0 O C:HOH1307 4.2 59.2 1.0 N S:ARG93 4.3 19.0 1.0 CA S:ALA94 4.3 19.7 1.0 O S:HOH1265 4.4 41.5 1.0 CB S:ASP87 4.4 19.2 1.0 C S:ARG93 4.4 20.2 1.0 O C:HOH1139 4.5 27.6 1.0 NE2 S:GLN96 4.6 11.7 1.0 N S:VAL95 4.6 18.2 1.0 CA S:ARG93 4.7 21.0 1.0 CG C:GLU167 4.8 18.8 1.0 CB S:ALA94 4.9 17.3 1.0 O S:HOH1224 4.9 33.1 1.0 CA S:VAL95 4.9 17.9 1.0 CB C:GLU167 5.0 17.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A Dictyostelium P109A CA2+-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 3 of Crystal Structure of A Dictyostelium P109A CA2+-Actin in Complex with Human Gelsolin Segment 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca377 b:21.0 occ:1.00 O1B C:ATP376 2.2 20.3 1.0 O C:HOH1001 2.3 18.7 1.0 O C:HOH1065 2.3 18.6 1.0 O C:HOH1050 2.4 17.5 1.0 O C:HOH1008 2.4 17.7 1.0 O2G C:ATP376 2.5 26.2 1.0 O C:HOH1108 2.7 17.3 1.0 PB C:ATP376 3.5 19.8 1.0 PG C:ATP376 3.6 20.4 1.0 O3B C:ATP376 4.0 23.5 1.0 O3G C:ATP376 4.0 22.3 1.0 CA C:GLY13 4.1 20.6 1.0 O C:HOH1134 4.1 29.8 1.0 NZ C:LYS18 4.2 26.3 1.0 O C:HOH1165 4.2 34.3 1.0 O3A C:ATP376 4.3 22.9 1.0 O1A C:ATP376 4.3 20.3 1.0 OE1 C:GLN137 4.4 23.6 1.0 O C:HOH1164 4.5 29.0 1.0 CD C:GLN137 4.6 20.5 1.0 OD1 C:ASP154 4.6 30.6 1.0 OD2 C:ASP11 4.7 17.9 1.0 O C:HOH1203 4.7 43.3 1.0 O2B C:ATP376 4.7 16.7 1.0 PA C:ATP376 4.8 20.8 1.0 O C:ASN12 4.8 18.0 1.0 NE2 C:GLN137 4.8 20.5 1.0 OD1 C:ASP11 4.9 16.6 1.0 OD2 C:ASP154 4.9 35.9 1.0 N C:GLY13 4.9 18.9 1.0 O1G C:ATP376 4.9 23.9 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