Calcium in PDB 2vyp: Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin

The structure of Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin, PDB code: 2vyp was solved by G.Hagelueken, S.C.Albrecht, H.Steinmetz, R.Jansen, D.W.Heinz, M.Kalesse, W.-D.Schubert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.41 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.653, 194.863, 53.038, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24.1

The binding sites of Calcium atom in the Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin (pdb code 2vyp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin, PDB code: 2vyp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1376 b:35.4 occ:1.00 O1G A:ATP1375 2.2 39.3 1.0 O A:HOH2002 2.3 32.8 1.0 O A:HOH2140 2.3 41.6 1.0 O1B A:ATP1375 2.3 39.1 1.0 O A:HOH2038 2.4 31.9 1.0 O A:HOH2003 2.5 35.6 1.0 O A:HOH2137 3.3 43.1 1.0 PG A:ATP1375 3.5 39.1 1.0 PB A:ATP1375 3.6 37.5 1.0 O3G A:ATP1375 3.9 36.0 1.0 O3B A:ATP1375 3.9 36.4 1.0 O A:HOH2139 4.1 40.5 1.0 OE1 A:GLN137 4.3 50.0 1.0 O3A A:ATP1375 4.3 35.4 1.0 O2A A:ATP1375 4.3 34.7 1.0 NZ A:LYS18 4.4 54.7 1.0 CA A:GLY13 4.4 49.5 1.0 CD A:GLN137 4.5 52.9 1.0 OD1 A:ASP11 4.6 47.4 1.0 OD2 A:ASP11 4.6 53.0 1.0 OD2 A:ASP154 4.6 56.6 1.0 PA A:ATP1375 4.7 34.9 1.0 O2G A:ATP1375 4.8 34.8 1.0 O2B A:ATP1375 4.8 40.3 1.0 CG2 A:VAL339 4.8 50.6 1.0 OD1 A:ASP154 4.9 67.5 1.0 NE2 A:GLN137 4.9 46.9 1.0

Calcium binding site 2 out of 4 in the Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1376 b:61.9 occ:1.00 O B:GLN354 2.4 46.7 1.0 OE1 B:GLU361 2.6 55.2 1.0 OE2 B:GLU361 2.8 52.3 1.0 O B:TRP356 2.9 45.2 1.0 CD B:GLU361 3.1 56.2 1.0 C B:GLN354 3.5 47.9 1.0 C B:TRP356 4.1 49.0 1.0 CA B:GLN354 4.3 47.9 0.4 CA B:GLN354 4.3 48.8 0.6 C B:MET355 4.4 50.6 1.0 NE2 B:GLN354 4.4 46.1 0.4 NZ B:LYS373 4.5 63.9 1.0 N B:MET355 4.5 50.7 1.0 N B:TRP356 4.5 49.0 1.0 CG B:GLU361 4.6 55.1 1.0 OE1 B:GLN354 4.6 53.4 0.6 CA B:MET355 4.6 50.8 1.0 O B:MET355 4.6 53.1 1.0 CB B:GLN354 4.8 47.6 0.4 O B:HOH2058 4.8 42.1 0.6 N B:THR358 4.9 47.5 1.0 CB B:GLN354 4.9 50.3 0.6 CG2 B:THR358 4.9 47.9 1.0 CA B:TRP356 4.9 50.2 1.0 CA B:ILE357 5.0 47.6 1.0 N B:ILE357 5.0 48.2 1.0 CE B:LYS373 5.0 65.7 1.0

Calcium binding site 3 out of 4 in the Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1378 b:54.8 occ:1.00 O B:HOH2002 2.1 43.4 1.0 O1B B:ATP1377 2.3 67.1 1.0 O B:HOH2021 2.4 47.5 1.0 O B:HOH2016 2.5 53.0 1.0 O1G B:ATP1377 2.5 69.3 1.0 O B:HOH2062 2.6 53.4 1.0 PB B:ATP1377 3.6 61.9 1.0 PG B:ATP1377 3.6 68.2 1.0 O3G B:ATP1377 3.9 56.8 1.0 O3B B:ATP1377 4.0 65.9 1.0 OE1 B:GLN137 4.2 47.0 1.0 O2A B:ATP1377 4.4 62.9 1.0 O B:HOH2022 4.4 49.0 1.0 CA B:GLY13 4.4 52.2 1.0 OD1 B:ASP11 4.4 58.0 1.0 NZ B:LYS18 4.5 55.0 1.0 CD B:GLN137 4.5 48.5 1.0 O2B B:ATP1377 4.6 65.8 1.0 OD2 B:ASP154 4.6 67.3 1.0 O3A B:ATP1377 4.6 61.2 1.0 CG2 B:VAL339 4.6 46.5 1.0 OD2 B:ASP11 4.6 53.6 1.0 O B:HOH2054 4.7 50.4 1.0 OD1 B:ASP154 4.7 68.8 1.0 PA B:ATP1377 4.8 57.2 1.0 O2G B:ATP1377 4.9 65.3 1.0 NE2 B:GLN137 4.9 40.9 1.0 O1A B:ATP1377 4.9 58.5 1.0 CG B:ASP11 5.0 54.8 1.0

Calcium binding site 4 out of 4 in the Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rabbit-Muscle G-Actin in Complex with Myxobacterial Rhizopodin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1379 b:96.0 occ:1.00 OD2 B:ASP288 2.4 59.5 1.0 OD2 B:ASP286 2.5 63.8 1.0 OD1 B:ASP286 2.7 54.9 1.0 CG B:ASP286 3.0 57.3 1.0 CG B:ASP288 3.5 57.2 1.0 CB B:ASP288 4.2 55.5 1.0 CB B:ASP286 4.5 56.3 1.0 OD1 B:ASP288 4.5 55.1 1.0

G.Hagelueken, S.C.Albrecht, H.Steinmetz, R.Jansen, D.W.Heinz, M.Kalesse, W.-D.Schubert. The Absolute Configuration of Rhizopodin and Its Inhibition of Actin Polymerization By Dimerization. Angew.Chem.Int.Ed.Engl. V. 48 595 2009.
ISSN: ISSN 1433-7851
PubMed: 19035596
DOI: 10.1002/ANIE.200802915