Calcium in PDB 7whf: Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin

The structure of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin, PDB code: 7whf 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)	19.79 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.261, 100.353, 171.804, 90, 90, 90
R / Rfree (%)	16.5 / 21.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin (pdb code 7whf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin, PDB code: 7whf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:19.4 occ:1.00 O A:HOH544 2.3 10.8 1.0 O2B A:ATP401 2.3 14.0 1.0 O A:HOH537 2.3 18.3 1.0 O A:HOH547 2.4 9.6 1.0 O3G A:ATP401 2.5 14.1 1.0 O A:HOH519 2.6 20.1 1.0 O A:HOH555 2.7 21.1 1.0 PB A:ATP401 3.6 19.6 1.0 PG A:ATP401 3.6 22.6 1.0 O3B A:ATP401 3.9 17.7 1.0 O1G A:ATP401 4.1 23.0 1.0 OE1 A:GLN137 4.2 15.6 1.0 O3A A:ATP401 4.2 15.7 1.0 NZ A:LYS18 4.2 18.9 1.0 O A:HOH566 4.3 14.8 1.0 O1A A:ATP401 4.4 15.2 1.0 CA A:GLY13 4.4 22.3 1.0 O A:HOH533 4.5 26.5 1.0 O A:HOH512 4.5 40.5 1.0 CD A:GLN137 4.6 17.8 1.0 OD2 A:ASP154 4.6 39.3 1.0 OD1 A:ASP11 4.6 20.9 1.0 OD1 A:ASP154 4.7 34.9 1.0 O A:HOH565 4.7 22.3 1.0 OD2 A:ASP11 4.7 15.8 1.0 PA A:ATP401 4.7 17.9 1.0 O1B A:ATP401 4.8 17.0 1.0 NE2 A:GLN137 4.9 18.0 1.0 O2G A:ATP401 5.0 22.3 1.0

Calcium binding site 2 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca301 b:21.8 occ:1.00 OD1 G:ASP104 2.2 20.1 1.0 OD2 G:ASP60 2.3 25.8 1.0 O G:GLY24 2.3 16.5 1.0 OD1 G:ASP25 2.3 17.4 1.0 O G:THR105 2.3 17.9 1.0 O G:HOH489 2.5 13.9 1.0 C G:GLY24 3.3 15.9 1.0 CG G:ASP60 3.4 25.8 1.0 C G:THR105 3.4 26.3 1.0 CG G:ASP104 3.4 22.8 1.0 CG G:ASP25 3.5 23.2 1.0 N G:THR105 3.7 25.4 1.0 O G:HOH408 3.9 19.0 1.0 CA G:ASP25 3.9 15.5 1.0 OD1 G:ASP60 4.0 24.6 1.0 N G:ASP25 4.0 17.4 1.0 CA G:THR105 4.0 25.1 1.0 OD2 G:ASP104 4.1 25.3 1.0 O G:HOH444 4.3 16.0 1.0 C G:ASP104 4.3 24.7 1.0 CA G:GLY24 4.3 16.3 1.0 CB G:ASP25 4.3 17.0 1.0 CB G:THR105 4.4 22.9 1.0 CA G:ASP104 4.4 20.6 1.0 OD2 G:ASP25 4.4 21.1 1.0 CB G:ASP60 4.4 24.0 1.0 N G:PRO106 4.4 25.4 1.0 CB G:ASP104 4.5 19.7 1.0 CA G:PRO106 4.6 23.7 1.0 O G:HOH432 4.6 19.8 1.0 N G:GLY107 4.7 21.6 1.0 O G:HOH438 4.7 17.4 1.0 C G:PRO106 4.7 22.6 1.0 CA G:ALA56 5.0 17.6 1.0

Calcium binding site 3 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca302 b:30.3 occ:1.00 OD1 G:ASP190 2.3 32.3 1.0 O G:PRO197 2.3 27.6 1.0 O G:HOH493 2.4 30.8 1.0 OE1 A:GLU241 2.4 42.4 1.0 O G:ARG195 2.5 28.4 1.0 O G:HOH427 2.5 29.9 1.0 CG G:ASP190 3.1 36.5 1.0 OD2 G:ASP190 3.3 38.1 1.0 CD A:GLU241 3.3 44.7 1.0 C G:ARG195 3.4 30.1 1.0 C G:PRO197 3.5 28.7 1.0 O A:HOH504 3.5 52.7 1.0 OE2 A:GLU241 3.8 49.3 1.0 CA G:ARG195 3.9 31.3 1.0 N G:PRO197 3.9 28.4 1.0 CA G:PRO197 4.2 28.0 1.0 CB G:ARG195 4.2 35.2 1.0 C G:THR196 4.3 29.6 1.0 CB A:GLU241 4.4 36.2 1.0 CB G:ASP190 4.5 24.4 1.0 CG A:GLU241 4.5 40.4 1.0 N G:THR196 4.5 32.5 1.0 CD G:PRO197 4.5 28.2 1.0 N G:MET198 4.6 28.3 1.0 O G:THR196 4.7 28.1 1.0 CB G:PRO197 4.7 28.0 1.0 CA G:THR196 4.8 27.6 1.0 CG2 G:VAL199 4.8 29.1 1.0 CA G:MET198 4.9 30.3 1.0

Calcium binding site 4 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca303 b:31.9 occ:1.00 O G:HOH450 2.2 39.9 1.0 OD1 G:ASP72 2.3 37.4 1.0 OE2 A:GLU167 2.4 47.8 1.0 O G:GLN76 2.4 39.4 1.0 O G:ILE78 2.4 40.6 1.0 O G:HOH491 2.5 58.1 1.0 O G:HOH413 2.6 37.4 1.0 CD A:GLU167 3.4 47.1 1.0 C G:GLN76 3.4 43.1 1.0 CG G:ASP72 3.4 35.8 1.0 O A:HOH631 3.5 57.9 1.0 C G:ILE78 3.6 40.0 1.0 OE1 A:GLU167 3.8 50.1 1.0 OD2 G:ASP72 3.8 37.2 1.0 CA G:GLN76 4.0 45.7 1.0 N G:ILE78 4.1 39.1 1.0 C G:ALA77 4.3 40.3 1.0 CA G:ILE78 4.4 37.1 1.0 N G:ALA77 4.5 44.4 1.0 CB G:GLN76 4.5 52.6 1.0 N G:ASP79 4.6 38.8 1.0 O G:ALA77 4.6 41.6 1.0 CA G:ALA77 4.7 43.4 1.0 CB G:ASP72 4.7 33.8 1.0 CG A:GLU167 4.8 42.4 1.0 CB G:ILE78 4.8 33.5 1.0 CA G:ASP79 4.9 38.0 1.0 OH A:TYR166 4.9 53.4 1.0

Calcium binding site 5 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca304 b:36.9 occ:1.00 O G:HOH417 2.2 40.2 1.0 OD2 G:ASP222 2.3 36.8 1.0 O G:HOH467 2.3 29.8 1.0 O G:TYR121 2.4 32.7 1.0 O G:LYS224 2.5 56.9 1.0 OD1 G:ASP120 2.6 40.7 1.0 OD1 G:ASP222 2.6 37.6 1.0 CG G:ASP222 2.8 37.6 1.0 C G:LYS224 3.3 56.4 1.0 CG G:ASP120 3.6 39.2 1.0 C G:TYR121 3.6 30.5 1.0 N G:TYR121 3.8 33.5 1.0 OD2 G:ASP120 3.9 37.5 1.0 N G:LYS225 4.2 61.8 1.0 CA G:LYS224 4.2 53.4 1.0 CA G:TYR121 4.2 30.4 1.0 OE1 G:GLU122 4.2 44.7 1.0 N G:LYS224 4.2 51.4 1.0 CA G:LYS225 4.3 63.6 1.0 OE1 G:GLN226 4.3 94.5 1.0 CB G:ASP222 4.3 36.1 1.0 CB G:LYS224 4.3 52.4 1.0 O G:HOH440 4.5 36.9 1.0 N G:GLN226 4.6 78.9 1.0 CD G:GLU122 4.6 40.0 1.0 N G:GLU122 4.7 28.4 1.0 OE2 G:GLU122 4.7 43.9 1.0 CB G:TYR121 4.7 27.3 1.0 C G:ASP120 4.8 36.4 1.0 CA G:GLU122 4.9 27.4 1.0 CB G:ASP120 4.9 36.6 1.0 C G:LYS225 4.9 70.2 1.0

Calcium binding site 6 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca305 b:33.1 occ:1.00 O G:ASP130 2.2 39.0 1.0 OD2 G:ASP138 2.3 42.9 1.0 O G:SER135 2.4 41.7 1.0 OD2 G:ASP139 2.5 42.9 1.0 OD1 G:ASP128 2.5 41.1 1.0 OD1 G:ASP133 2.5 43.8 1.0 OD2 G:ASP133 2.6 45.5 1.0 CG G:ASP133 2.9 45.0 1.0 OD2 G:ASP128 3.0 38.3 1.0 CG G:ASP128 3.1 38.2 1.0 C G:ASP130 3.4 39.1 1.0 CG G:ASP138 3.5 45.6 1.0 CG G:ASP139 3.5 40.4 1.0 C G:SER135 3.5 42.6 1.0 OD1 G:ASP138 3.9 49.1 1.0 CB G:ASP139 4.1 38.3 1.0 CA G:CA306 4.1 37.7 1.0 CA G:ASP130 4.2 39.0 1.0 CB G:ASP130 4.3 41.3 1.0 N G:ASP130 4.3 38.0 1.0 N G:ASP139 4.3 38.5 1.0 CA G:SER135 4.3 44.3 1.0 N G:SER135 4.3 45.9 1.0 N G:LEU131 4.3 39.9 1.0 CB G:SER135 4.4 47.6 1.0 OD1 G:ASP139 4.5 42.4 1.0 CB G:ASP133 4.5 47.1 1.0 CA G:LEU131 4.5 40.4 1.0 N G:SER136 4.5 40.9 1.0 CB G:ASP128 4.6 35.0 1.0 CA G:SER136 4.6 41.7 1.0 N G:ASP138 4.6 38.9 1.0 OG G:SER135 4.7 49.0 1.0 CB G:ASP138 4.7 43.2 1.0 CA G:ASP139 4.8 38.5 1.0 CG G:ASP130 4.8 46.8 1.0 C G:ASP138 4.9 41.2 1.0 CD2 G:LEU131 4.9 36.9 1.0 CA G:ASP138 5.0 41.0 1.0

Calcium binding site 7 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca306 b:37.7 occ:1.00 OD1 G:ASP138 2.3 49.1 1.0 O G:HOH496 2.4 42.2 1.0 OD2 G:ASP133 2.4 45.5 1.0 O G:HOH501 2.5 45.9 1.0 O G:HOH407 2.5 42.2 1.0 OD1 G:ASP139 2.6 42.4 1.0 OD2 G:ASP139 2.6 42.9 1.0 CG G:ASP139 3.0 40.4 1.0 CG G:ASP138 3.3 45.6 1.0 CG G:ASP133 3.5 45.0 1.0 OD2 G:ASP138 3.7 42.9 1.0 CA G:CA305 4.1 33.1 1.0 CB G:ASP133 4.3 47.1 1.0 OD1 G:ASP133 4.4 43.8 1.0 CB G:ASP139 4.5 38.3 1.0 CB G:ASP138 4.6 43.2 1.0 OD2 G:ASP130 4.6 48.1 1.0 CB G:ASP130 4.8 41.3 1.0 O G:ASP138 4.9 43.6 1.0 C G:ASP138 5.0 41.2 1.0

Calcium binding site 8 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca307 b:29.5 occ:1.00 O G:GLU155 2.2 36.0 1.0 O C:HOH432 2.3 29.5 1.0 OE1 G:GLN175 2.4 35.8 1.0 OE2 G:GLU178 2.4 38.5 1.0 OD2 G:ASP156 2.4 35.5 1.0 O C:HOH406 2.6 38.0 1.0 OE1 G:GLU178 2.8 38.2 1.0 CD G:GLU178 3.0 36.8 1.0 C G:GLU155 3.4 39.3 1.0 CD G:GLN175 3.6 38.9 1.0 CG G:ASP156 3.6 39.4 1.0 CA G:ASP156 3.9 36.3 1.0 N G:ASP156 4.1 34.9 1.0 NE2 G:GLN175 4.2 42.9 1.0 O G:HOH418 4.3 81.0 1.0 CB G:ASP156 4.3 38.2 1.0 CB G:GLU155 4.3 51.6 1.0 CA G:GLU155 4.4 45.6 1.0 O C:ASP138 4.5 42.9 1.0 CG G:GLU178 4.5 33.9 1.0 OD1 C:ASP139 4.6 44.9 1.0 OD1 G:ASP156 4.6 39.8 1.0 CB G:TYR127 4.7 35.2 1.0 CA G:SER174 4.7 40.8 1.0 N G:GLN175 4.7 36.5 1.0 CD1 G:LEU131 4.7 38.9 1.0 CG G:GLN175 4.8 41.2 1.0 O G:HOH490 4.8 37.5 1.0 O G:ASP128 4.9 34.6 1.0 CA G:TYR127 5.0 35.1 1.0 N G:ASP128 5.0 31.7 1.0

Calcium binding site 9 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca308 b:74.7 occ:1.00 OD1 G:ASP79 2.4 57.5 1.0 OD1 G:ASP81 2.5 41.8 1.0 O G:HOH480 2.9 45.7 1.0 O A:HOH627 3.1 58.8 1.0 CG G:ASP79 3.2 55.4 1.0 O G:HOH495 3.2 38.8 1.0 OD2 G:ASP79 3.3 59.5 1.0 O G:ILE80 3.3 26.5 1.0 OD2 A:ASP292 3.5 48.0 1.0 CG G:ASP81 3.7 39.2 1.0 C G:ILE80 4.2 27.6 1.0 OD2 G:ASP81 4.3 42.9 1.0 NZ G:LYS47 4.5 49.7 1.0 CG A:ASP292 4.6 44.1 1.0 CA G:ASP81 4.7 25.8 1.0 CB G:ASP79 4.7 46.5 1.0 N G:ILE80 4.7 28.0 1.0 N G:ASP81 4.7 23.0 1.0 CB G:ASP81 4.8 30.3 1.0

Calcium binding site 10 out of 18 in the Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Heimdallarchaeota Gelsolin (2DGEL) Bound to Rabbit Actin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:22.2 occ:1.00 O B:HOH584 2.2 19.2 1.0 O2B B:ATP401 2.3 16.1 1.0 O B:HOH519 2.3 18.1 1.0 O B:HOH524 2.4 30.3 1.0 O3G B:ATP401 2.4 25.4 1.0 O B:HOH518 2.6 23.0 1.0 O B:HOH531 2.7 32.0 1.0 PG B:ATP401 3.6 29.6 1.0 PB B:ATP401 3.6 22.4 1.0 O3B B:ATP401 4.0 24.5 1.0 O1G B:ATP401 4.0 26.7 1.0 O B:HOH553 4.1 23.1 1.0 O1A B:ATP401 4.3 22.4 1.0 CA B:GLY13 4.3 26.3 1.0 O3A B:ATP401 4.4 19.5 1.0 OE1 B:GLN137 4.4 24.8 1.0 NZ B:LYS18 4.5 22.7 1.0 CD B:GLN137 4.5 24.8 1.0 O B:HOH572 4.5 26.2 1.0 NE2 B:GLN137 4.7 24.6 1.0 OD1 B:ASP11 4.7 21.2 1.0 OD2 B:ASP11 4.7 23.7 1.0 O B:HOH580 4.8 29.9 1.0 OD1 B:ASP154 4.8 44.9 1.0 PA B:ATP401 4.8 23.7 1.0 OD2 B:ASP154 4.8 47.1 1.0 O2G B:ATP401 4.9 33.3 1.0 O1B B:ATP401 4.9 23.5 1.0 CG B:GLN137 5.0 20.1 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