Calcium in PDB 5ypu: Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide

The structure of Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide, PDB code: 5ypu was solved by C.P.M.Scipion, J.Wongsantichon, F.J.Ferrer, T.Y.Yuen, R.C.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.82 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	174.861, 40.832, 109.000, 90.00, 101.76, 90.00
R / Rfree (%)	19.3 / 24

The binding sites of Calcium atom in the Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide (pdb code 5ypu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide, PDB code: 5ypu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide


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 An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:18.6 occ:1.00 O1B A:ATP401 2.3 15.5 1.0 O A:HOH541 2.3 15.8 1.0 O A:HOH576 2.4 14.5 1.0 O2G A:ATP401 2.4 17.6 1.0 O A:HOH708 2.5 19.6 1.0 O A:HOH565 2.5 19.9 1.0 O A:HOH615 2.6 18.0 1.0 PG A:ATP401 3.5 17.0 1.0 PB A:ATP401 3.6 15.6 1.0 O3B A:ATP401 3.9 16.3 1.0 O3G A:ATP401 3.9 17.1 1.0 O A:HOH586 4.1 21.1 1.0 OE1 A:GLN137 4.1 16.6 1.0 CA A:GLY13 4.3 18.1 1.0 O3A A:ATP401 4.3 16.7 1.0 NZ A:LYS18 4.4 20.8 1.0 O1A A:ATP401 4.4 15.7 1.0 CD A:GLN137 4.5 19.4 1.0 OD2 A:ASP154 4.5 20.4 1.0 O A:HOH604 4.5 15.6 1.0 O A:HOH621 4.6 23.3 1.0 OD1 A:ASP11 4.7 18.6 1.0 OD2 A:ASP11 4.7 19.9 1.0 O1G A:ATP401 4.8 17.2 1.0 PA A:ATP401 4.8 16.8 1.0 O2B A:ATP401 4.9 14.8 1.0 OD1 A:ASP154 4.9 21.7 1.0 NE2 A:GLN137 4.9 19.2 1.0 CG A:GLN137 4.9 18.1 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide


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 An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:26.9 occ:1.00 O A:HOH569 2.0 39.8 1.0 OD2 A:ASP288 2.2 27.8 1.0 O A:HOH674 2.3 33.4 1.0 OD2 A:ASP286 2.4 30.0 1.0 OD1 A:ASP286 2.5 33.8 1.0 O A:HOH678 2.5 26.4 1.0 CG A:ASP286 2.8 31.2 1.0 CG A:ASP288 3.3 28.0 1.0 CB A:ASP288 3.8 26.6 1.0 O A:HOH666 4.1 40.4 1.0 CB A:ASP286 4.3 30.0 1.0 OD1 A:ASP288 4.4 29.9 1.0 O A:HOH515 4.5 38.8 1.0 N A:ASP288 4.6 24.7 1.0 O A:HOH650 4.6 45.1 1.0 CG2 A:ILE287 4.9 27.5 1.0 CA A:ASP288 4.9 25.3 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide


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 An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:40.0 occ:1.00 O B:GLU82 2.3 37.1 1.0 O B:HOH213 2.6 38.1 1.0 O B:HOH208 2.7 50.1 1.0 C B:GLU82 3.5 34.8 1.0 CA B:GLU82 4.2 34.7 1.0 N B:LYS83 4.5 33.3 1.0 O B:LEU84 4.6 27.4 1.0 CB B:GLU82 4.6 36.7 1.0 CA B:LYS83 4.6 33.0 1.0 O A:HOH659 4.7 31.5 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:18.4 occ:1.00 O1B C:ATP401 2.2 15.6 1.0 O C:HOH539 2.3 18.7 1.0 O2G C:ATP401 2.4 19.0 1.0 O C:HOH622 2.4 15.5 1.0 O C:HOH559 2.5 18.8 1.0 O C:HOH552 2.5 15.3 1.0 O C:HOH586 2.6 18.8 1.0 PG C:ATP401 3.5 17.8 1.0 PB C:ATP401 3.5 15.5 1.0 O3B C:ATP401 3.9 17.3 1.0 O3G C:ATP401 4.0 17.2 1.0 O C:HOH604 4.1 19.2 1.0 OE1 C:GLN137 4.2 17.4 1.0 O3A C:ATP401 4.2 17.2 1.0 CA C:GLY13 4.2 17.5 1.0 O1A C:ATP401 4.2 18.3 1.0 NZ C:LYS18 4.4 24.6 1.0 O C:HOH589 4.4 21.7 1.0 CD C:GLN137 4.4 18.4 1.0 O C:HOH550 4.6 32.3 1.0 OD2 C:ASP154 4.6 24.8 1.0 OD1 C:ASP11 4.6 18.3 1.0 PA C:ATP401 4.7 17.1 1.0 OD2 C:ASP11 4.7 16.9 1.0 O1G C:ATP401 4.8 17.7 1.0 O2B C:ATP401 4.8 14.2 1.0 NE2 C:GLN137 4.9 17.4 1.0 CG C:GLN137 4.9 17.7 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:28.9 occ:1.00 OD2 C:ASP288 2.3 25.1 1.0 O C:HOH674 2.3 41.5 1.0 O C:HOH675 2.4 34.9 1.0 OD2 C:ASP286 2.4 31.6 1.0 OD1 C:ASP286 2.5 27.4 1.0 CG C:ASP286 2.8 29.2 1.0 CG C:ASP288 3.4 27.6 1.0 CB C:ASP288 3.9 26.8 1.0 O C:HOH504 4.0 34.6 1.0 CB C:ASP286 4.3 30.6 1.0 O C:HOH747 4.4 34.3 1.0 OD1 C:ASP288 4.5 27.8 1.0 N C:ASP288 4.6 24.8 1.0 CG2 C:ILE287 4.9 34.9 1.0 CA C:ASP288 5.0 25.9 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca404 b:35.4 occ:1.00 O A:HOH748 2.4 44.1 1.0 OD2 C:ASP363 2.4 32.6 1.0 O C:HOH571 2.5 26.3 1.0 OD1 C:ASP363 2.5 27.0 1.0 O A:HOH581 2.6 39.5 1.0 CG C:ASP363 2.8 27.8 1.0 O A:HOH696 4.2 34.1 1.0 CB C:ASP363 4.3 26.9 1.0 O C:HOH771 4.5 40.8 1.0 OH A:TYR279 4.5 27.6 1.0 O C:HOH726 4.8 43.6 1.0 O A:HOH713 4.8 31.9 1.0 O A:HOH791 4.9 33.7 1.0 O C:HOH717 5.0 35.2 1.0 O C:ASP363 5.0 25.0 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of An Actin Monomer in Complex with the Nucleator Cordon-Bleu MET72NLE WH2-Motif Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:38.8 occ:1.00 O D:GLU82 2.4 31.5 1.0 O D:HOH210 2.6 41.4 1.0 O D:HOH212 2.6 39.1 1.0 O D:HOH209 2.8 40.8 1.0 C D:GLU82 3.5 32.0 1.0 CA D:GLU82 4.1 33.1 1.0 CB D:GLU82 4.4 35.4 1.0 N D:LYS83 4.6 30.3 1.0 O C:HOH606 4.6 34.2 1.0 O D:LEU84 4.8 26.4 1.0 CA D:LYS83 4.8 31.7 1.0

C.P.M.Scipion, U.Ghoshdastider, F.J.Ferrer, T.Y.Yuen, J.Wongsantichon, R.C.Robinson. Structural Evidence For the Roles of Divalent Cations in Actin Polymerization and Activation of Atp Hydrolysis Proc. Natl. Acad. Sci. V. 115 10345 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30254171
DOI: 10.1073/PNAS.1806394115