Calcium in PDB 7whg: Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin

The structure of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin, PDB code: 7whg was solved by R.C.Robinson, C.Akil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.662, 72.057, 100.385, 90, 92.08, 90
R / Rfree (%)	17.5 / 23.2

The binding sites of Calcium atom in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin (pdb code 7whg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin, PDB code: 7whg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:40.7 occ:1.00 O2B A:ADP401 2.2 37.7 1.0 OD1 A:ASP154 3.5 52.0 1.0 PB A:ADP401 3.6 33.7 1.0 OE1 A:GLN137 3.7 45.4 1.0 OD1 A:ASP11 3.8 38.5 1.0 O2A A:ADP401 4.0 36.9 1.0 OD2 A:ASP11 4.1 39.3 1.0 OD2 A:ASP154 4.2 51.7 1.0 O1B A:ADP401 4.3 34.8 1.0 O3A A:ADP401 4.3 33.2 1.0 CG A:ASP154 4.3 50.0 1.0 CG A:ASP11 4.4 38.8 1.0 CD A:GLN137 4.5 42.3 1.0 CG2 A:VAL339 4.5 36.2 1.0 CA A:GLY13 4.7 36.9 1.0 O3B A:ADP401 4.7 34.4 1.0 PA A:ADP401 4.8 34.5 1.0 CB A:GLN137 4.9 39.5 1.0

Calcium binding site 2 out of 9 in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:93.2 occ:1.00 OD2 A:ASP56 2.9 70.0 1.0 O A:VAL30 3.2 42.2 1.0 CG A:ASP56 4.0 68.7 1.0 OE2 A:GLU93 4.1 56.8 1.0 C A:VAL30 4.3 38.3 1.0 CB A:PHE31 4.4 33.6 1.0 CA A:PHE31 4.6 36.4 1.0 OD1 A:ASP56 4.8 69.1 1.0 OE1 A:GLU93 4.8 56.9 1.0 CD A:GLU93 4.9 54.2 1.0 CB A:ASP56 4.9 66.0 1.0 N A:PHE31 5.0 37.2 1.0

Calcium binding site 3 out of 9 in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:55.8 occ:1.00 O2B B:ADP401 3.1 54.5 1.0 O3B B:ADP401 3.1 56.1 1.0 OE1 B:GLN137 3.3 75.5 1.0 PB B:ADP401 3.5 55.0 1.0 OD1 B:ASP11 3.8 56.4 1.0 O3A B:ADP401 3.8 53.5 1.0 OD2 B:ASP11 4.0 58.0 1.0 OD2 B:ASP154 4.1 82.7 1.0 O2A B:ADP401 4.2 48.9 1.0 CD B:GLN137 4.3 74.3 1.0 OD1 B:ASP154 4.3 82.5 1.0 CG B:ASP11 4.4 56.0 1.0 CA B:GLY13 4.5 54.2 1.0 PA B:ADP401 4.7 49.0 1.0 CG B:ASP154 4.7 81.2 1.0 CE B:LYS18 4.7 54.1 1.0 CG2 B:VAL339 4.8 54.2 1.0 NE2 B:GLN137 4.9 74.5 1.0 O1B B:ADP401 5.0 53.2 1.0

Calcium binding site 4 out of 9 in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:82.3 occ:1.00 O G:GLY22 2.4 101.1 1.0 OE1 G:GLU45 2.4 77.4 1.0 O G:ALA96 2.5 117.2 1.0 OE2 G:GLU45 2.7 77.3 1.0 OD1 G:ASP23 2.8 86.5 1.0 CD G:GLU45 2.9 77.4 1.0 CB G:TYR95 3.3 108.4 1.0 C G:GLY22 3.6 100.2 1.0 C G:ALA96 3.6 114.6 1.0 CG G:TYR95 3.8 111.6 1.0 N G:ALA96 4.0 109.5 1.0 CG G:ASP23 4.0 85.4 1.0 CB G:SER224 4.1 109.8 1.0 CD1 G:TYR95 4.2 113.4 1.0 CG G:GLU45 4.3 77.8 1.0 O G:LYS97 4.3 100.4 1.0 CA G:TYR95 4.3 107.4 1.0 CA G:ASP23 4.4 88.1 1.0 N G:ASP23 4.4 95.1 1.0 CA G:ALA96 4.4 112.3 1.0 C G:LYS97 4.5 100.5 1.0 N G:LYS97 4.5 110.7 1.0 OG G:SER42 4.6 97.6 1.0 C G:TYR95 4.6 107.8 1.0 CA G:GLY22 4.6 104.4 1.0 CD2 G:TYR95 4.6 114.0 1.0 CA G:LYS97 4.7 105.5 1.0 CB G:ASP23 4.8 86.4 1.0 CA G:CYS41 4.8 96.9 1.0 CB G:CYS41 4.8 97.6 1.0 N G:SER224 4.9 109.8 1.0 OD2 G:ASP23 4.9 83.5 1.0 N G:SER42 5.0 89.1 1.0

Calcium binding site 5 out of 9 in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca402 b:59.5 occ:1.00 O G:VAL103 2.2 65.2 1.0 O G:LEU220 2.3 71.2 1.0 OD1 G:ASP102 2.3 74.3 1.0 OD2 B:ASP25 2.4 59.8 1.0 OD1 B:ASP25 3.1 58.3 1.0 CG B:ASP25 3.1 59.6 1.0 C G:LEU220 3.4 71.6 1.0 C G:VAL103 3.5 64.5 1.0 CG G:ASP102 3.5 74.6 1.0 N G:LEU220 3.7 67.2 1.0 N G:VAL103 4.0 68.8 1.0 CA G:LEU220 4.1 69.0 1.0 OD2 G:ASP102 4.1 76.3 1.0 N G:SER104 4.3 61.0 1.0 CA G:VAL103 4.4 65.7 1.0 N G:LYS221 4.4 75.4 1.0 CA G:SER104 4.4 60.1 1.0 CB B:ASP25 4.6 59.8 1.0 C G:ASP102 4.6 72.7 1.0 OE1 G:GLN219 4.6 54.7 1.0 CB G:LEU220 4.6 67.5 1.0 CB G:ASP102 4.7 73.1 1.0 OG G:SER104 4.7 63.0 1.0 CA G:ASP102 4.7 71.8 1.0 CA G:LYS221 4.8 79.9 1.0 O B:ASP25 4.8 56.4 1.0 CB B:ALA26 4.8 51.9 1.0 C G:GLN219 4.8 66.3 1.0 CG2 G:VAL103 5.0 61.4 1.0

Calcium binding site 6 out of 9 in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca403 b:64.3 occ:1.00 OD1 G:ASP148 2.1 102.4 1.0 OE2 G:GLU170 2.4 64.0 1.0 O G:GLU147 2.4 61.2 1.0 OE1 G:GLU124 2.7 83.0 1.0 CG G:ASP148 3.3 102.7 1.0 CD G:GLU170 3.3 62.1 1.0 C G:GLU147 3.4 67.2 1.0 OE1 G:GLU170 3.7 64.1 1.0 CD G:GLU124 3.7 82.4 1.0 OD2 G:ASP148 4.0 107.2 1.0 CB G:GLU147 4.0 69.1 1.0 CA G:CA406 4.1 78.7 1.0 CG G:GLU124 4.2 84.9 1.0 N G:ASP148 4.2 74.6 1.0 CA G:GLU147 4.2 67.5 1.0 CA G:ASP148 4.3 82.1 1.0 CB G:ASP148 4.3 97.2 1.0 CB G:GLU124 4.5 86.9 1.0 O G:SER165 4.5 69.9 1.0 OE2 G:GLU124 4.6 79.4 1.0 CG G:GLU170 4.6 57.2 1.0 N G:GLU124 4.8 87.2 1.0 OE1 G:GLU147 4.8 79.8 1.0 CA G:SER166 4.9 63.5 1.0

Calcium binding site 7 out of 9 in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca404 b:35.4 occ:1.00 O G:GLY187 2.4 48.0 1.0 O G:ASP182 2.4 56.2 1.0 OD1 G:ASP182 2.6 60.5 1.0 O G:ARG185 2.6 45.3 1.0 OE1 G:GLN189 2.8 39.5 1.0 C G:ASP182 3.3 55.4 1.0 C G:GLY187 3.5 47.2 1.0 CG G:ASP182 3.7 59.7 1.0 CD G:GLN189 3.8 39.7 1.0 C G:ARG185 3.8 44.0 1.0 NE2 G:GLN189 4.0 40.2 1.0 CA G:ASP182 4.1 53.3 1.0 C G:ALA186 4.1 47.2 1.0 CA G:LEU188 4.1 48.6 1.0 N G:GLY187 4.2 46.9 1.0 N G:LEU188 4.3 46.9 1.0 N G:TYR183 4.3 57.1 1.0 O G:TYR183 4.3 60.4 1.0 CA G:ALA186 4.4 46.2 1.0 O G:ALA186 4.4 49.8 1.0 CA G:GLY187 4.5 47.7 1.0 OE1 B:GLU57 4.5 86.4 1.0 CA G:TYR183 4.5 58.5 1.0 CB G:ASP182 4.5 55.8 1.0 C G:TYR183 4.5 60.4 1.0 N G:ALA186 4.6 42.3 1.0 N G:ARG185 4.6 52.1 1.0 N G:GLN189 4.6 46.5 1.0 OD2 G:ASP182 4.6 61.7 1.0 CA G:ARG185 4.8 45.8 1.0 C G:LEU188 4.8 47.2 1.0

Calcium binding site 8 out of 9 in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca405 b:116.9 occ:1.00 OE1 B:GLU167 2.2 168.8 1.0 O G:GLY62 2.5 142.3 1.0 O G:ALA64 2.8 135.8 1.0 OD2 G:ASP57 3.1 133.3 1.0 C G:GLY62 3.1 141.5 1.0 CD B:GLU167 3.1 161.7 1.0 OD1 G:ASP57 3.3 132.0 1.0 OE2 B:GLU167 3.5 165.7 1.0 CG G:ASP57 3.6 132.4 1.0 N G:ALA64 3.7 141.0 1.0 N G:ALA63 3.7 143.3 1.0 C G:ALA64 3.9 135.3 1.0 C G:ALA63 3.9 143.8 1.0 CA G:ALA63 3.9 144.2 1.0 CA G:GLY62 3.9 141.1 1.0 CA G:ALA64 4.4 139.8 1.0 CG B:GLU167 4.5 149.3 1.0 O G:ALA63 4.6 147.0 1.0 CB B:GLU167 4.8 138.9 1.0 N G:LYS65 5.0 127.6 1.0

Calcium binding site 9 out of 9 in the Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Lokiarchaeota Gelsolin (2DGEL) Bound to Two Molecules of Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca406 b:78.7 occ:1.00 OD2 G:ASP148 2.1 107.2 1.0 OE2 G:GLU124 2.3 79.4 1.0 OE1 G:GLU124 2.4 83.0 1.0 CD G:GLU124 2.6 82.4 1.0 CG G:ASP148 2.9 102.7 1.0 NH1 G:ARG120 3.1 70.8 1.0 OD1 G:ASP148 3.3 102.4 1.0 CB G:GLU147 3.5 69.1 1.0 NH2 G:ARG120 3.8 69.2 1.0 CZ G:ARG120 3.9 70.1 1.0 OG G:SER122 4.0 81.6 1.0 OD2 G:ASP145 4.0 78.3 1.0 CG G:GLU124 4.1 84.9 1.0 CA G:CA403 4.1 64.3 1.0 CB G:ASP148 4.1 97.2 1.0 OE1 G:GLU147 4.2 79.8 1.0 C G:GLU147 4.4 67.2 1.0 CA G:GLU147 4.5 67.5 1.0 N G:ASP148 4.6 74.6 1.0 CB G:SER122 4.6 80.2 1.0 CG G:GLU147 4.6 74.3 1.0 O G:GLU147 4.6 61.2 1.0 CD G:GLU147 4.7 78.1 1.0 CA G:ASP148 5.0 82.1 1.0

C.Akil, L.T.Tran, M.Orhant-Prioux, Y.Baskaran, Y.Senju, S.Takeda, P.Chotchuang, D.Muengsaen, A.Schulte, E.Manser, L.Blanchoin, R.C.Robinson. Structural and Biochemical Evidence For the Emergence of A Calcium-Regulated Actin Cytoskeleton Prior to Eukaryogenesis Commun Biol V. 5 890 2022.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-022-03783-1