Calcium in PDB 5nbn: Crystal Structure of the ARP4-N-Actin-ARP8-INO80HSA Module of INO80

All present enzymatic activity of Crystal Structure of the ARP4-N-Actin-ARP8-INO80HSA Module of INO80:
3.6.4.12;

The structure of Crystal Structure of the ARP4-N-Actin-ARP8-INO80HSA Module of INO80, PDB code: 5nbn was solved by K.R.Knoll, S.Eustermann, K.P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.40 / 4.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	172.294, 263.909, 241.402, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.2

The binding sites of Calcium atom in the Crystal Structure of the ARP4-N-Actin-ARP8-INO80HSA Module of INO80 (pdb code 5nbn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the ARP4-N-Actin-ARP8-INO80HSA Module of INO80, PDB code: 5nbn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the ARP4-N-Actin-ARP8-INO80HSA Module of INO80


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 the ARP4-N-Actin-ARP8-INO80HSA Module of INO80 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:0.5 occ:1.00 O2B A:ATP502 2.6 0.4 1.0 PB A:ATP502 2.9 0.6 1.0 O3B A:ATP502 2.9 0.1 1.0 O1B A:ATP502 3.2 0.5 1.0 OD2 A:ASP159 3.5 0.8 1.0 PG A:ATP502 4.1 0.7 1.0 OG A:SER452 4.2 96.3 1.0 O1G A:ATP502 4.2 98.6 1.0 O2G A:ATP502 4.3 0.6 1.0 CG A:ASP159 4.4 0.5 1.0 O3A A:ATP502 4.5 89.1 1.0 CG2 A:THR142 4.5 0.4 1.0 CB A:THR142 4.6 0.5 1.0 OD1 A:ASP159 4.6 0.8 1.0 OG1 A:THR142 4.7 0.4 1.0 OD1 A:ASP20 5.0 0.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the ARP4-N-Actin-ARP8-INO80HSA Module of INO80


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 the ARP4-N-Actin-ARP8-INO80HSA Module of INO80 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:0.1 occ:1.00 O3B B:ATP502 2.6 0.8 1.0 O1G B:ATP502 2.9 0.7 1.0 O3A B:ATP502 3.3 0.4 1.0 PB B:ATP502 3.4 0.4 1.0 O2A B:ATP502 3.4 0.0 1.0 PG B:ATP502 3.4 0.2 1.0 O1B B:ATP502 3.4 0.3 1.0 PA B:ATP502 3.7 92.9 1.0 O1A B:ATP502 3.9 0.2 1.0 O2G B:ATP502 4.0 0.3 1.0 OD2 B:ASP159 4.3 0.9 1.0 O B:GLN449 4.3 88.5 1.0 OG B:SER452 4.4 0.6 1.0 OD1 B:ASP159 4.6 0.5 1.0 O3G B:ATP502 4.7 0.5 1.0 O2B B:ATP502 4.8 94.0 1.0 OD2 B:ASP20 4.8 0.5 1.0 CA B:GLY22 4.8 0.1 1.0 CG B:ASP159 4.9 0.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the ARP4-N-Actin-ARP8-INO80HSA Module of INO80


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 the ARP4-N-Actin-ARP8-INO80HSA Module of INO80 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:74.3 occ:1.00 O2B C:ATP502 2.4 0.8 1.0 O2G C:ATP502 2.6 0.3 1.0 OE1 C:GLN137 2.9 0.4 1.0 O1G C:ATP502 3.0 0.4 1.0 PG C:ATP502 3.2 0.1 1.0 PB C:ATP502 3.5 0.7 1.0 O3B C:ATP502 3.6 95.3 1.0 O3A C:ATP502 3.8 0.3 1.0 CD C:GLN137 3.9 0.7 1.0 OD2 C:ASP154 4.1 0.9 1.0 OD1 C:ASP154 4.2 0.2 1.0 OD1 C:ASP11 4.5 0.4 1.0 NE2 C:GLN137 4.5 71.5 1.0 CG C:ASP154 4.6 0.6 1.0 CA C:GLY13 4.6 0.5 1.0 CG2 C:VAL339 4.6 0.5 1.0 OD2 C:ASP11 4.6 0.2 1.0 O3G C:ATP502 4.7 92.9 1.0 NZ C:LYS18 4.7 0.3 1.0 O1B C:ATP502 4.9 60.5 1.0 CA C:GLY156 5.0 0.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the ARP4-N-Actin-ARP8-INO80HSA Module of INO80


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 the ARP4-N-Actin-ARP8-INO80HSA Module of INO80 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:62.2 occ:1.00 O1B D:ATP502 2.4 99.9 1.0 O3G D:ATP502 2.5 70.9 1.0 OE1 D:GLN137 3.0 0.1 1.0 PB D:ATP502 3.6 56.8 1.0 PG D:ATP502 3.7 82.0 1.0 O3A D:ATP502 3.8 77.0 1.0 CD D:GLN137 3.9 0.1 1.0 O3B D:ATP502 4.0 89.1 1.0 OD2 D:ASP11 4.1 73.5 1.0 NZ D:LYS18 4.2 80.3 1.0 O1G D:ATP502 4.2 79.4 1.0 OD2 D:ASP154 4.4 0.1 1.0 OD1 D:ASP11 4.4 0.8 1.0 NE2 D:GLN137 4.4 0.1 1.0 CG2 D:VAL339 4.5 0.2 1.0 OD1 D:ASP154 4.6 0.5 1.0 CG D:ASP11 4.7 88.6 1.0 CA D:GLY13 4.7 0.6 1.0 PA D:ATP502 4.9 76.8 1.0 O2A D:ATP502 4.9 92.7 1.0 O2B D:ATP502 4.9 56.1 1.0 CG D:ASP154 5.0 0.4 1.0 O2G D:ATP502 5.0 80.6 1.0

K.R.Knoll, S.Eustermann, V.Niebauer, E.Oberbeckmann, G.Stoehr, K.Schall, A.Tosi, M.Schwarz, A.Buchfellner, P.Korber, K.P.Hopfner. The Nuclear Actin-Containing ARP8 Module Is A Linker Dna Sensor Driving INO80 Chromatin Remodeling. Nat. Struct. Mol. Biol. V. 25 823 2018.
ISSN: ESSN 1545-9985
PubMed: 30177756
DOI: 10.1038/S41594-018-0115-8