Calcium in PDB 5nbm: Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody

The structure of Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody, PDB code: 5nbm 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)	47.74 / 3.40
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	190.581, 190.581, 220.616, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / 19.3

The binding sites of Calcium atom in the Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody (pdb code 5nbm). 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(Atp-State) Heterodimer Bound By A Nanobody, PDB code: 5nbm:
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(Atp-State) Heterodimer Bound By A Nanobody


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(Atp-State) Heterodimer Bound By A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:86.3 occ:1.00 O1G A:ATP502 2.1 68.0 1.0 O2B A:ATP502 2.3 90.7 1.0 OD2 A:ASP159 3.4 0.6 1.0 PG A:ATP502 3.5 74.8 1.0 PB A:ATP502 3.7 85.7 1.0 OD1 A:ASP159 3.7 1.0 1.0 CG A:ASP159 3.9 0.8 1.0 O2A A:ATP502 4.0 58.7 1.0 O3B A:ATP502 4.0 71.7 1.0 O2G A:ATP502 4.4 55.2 1.0 O3G A:ATP502 4.5 70.5 1.0 OG A:SER452 4.6 0.3 1.0 O3A A:ATP502 4.6 75.6 1.0 O1B A:ATP502 4.7 90.3 1.0 PA A:ATP502 4.9 76.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody


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(Atp-State) Heterodimer Bound By A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:85.2 occ:1.00 O2G B:ATP502 2.3 92.2 1.0 O1B B:ATP502 2.5 96.2 1.0 OD2 B:ASP159 3.4 0.3 1.0 PG B:ATP502 3.5 71.4 1.0 OD1 B:ASP159 3.7 0.8 1.0 O3G B:ATP502 3.7 67.6 1.0 PB B:ATP502 3.8 86.1 1.0 CG B:ASP159 3.9 0.7 1.0 O1A B:ATP502 4.0 72.3 1.0 O3B B:ATP502 4.1 60.8 1.0 OG B:SER452 4.7 0.7 1.0 O3A B:ATP502 4.7 77.3 1.0 O1G B:ATP502 4.8 50.0 1.0 O2B B:ATP502 5.0 93.4 1.0 PA B:ATP502 5.0 78.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody


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(Atp-State) Heterodimer Bound By A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:87.9 occ:1.00 O2B C:ATP502 2.5 0.5 1.0 O3G C:ATP502 2.7 0.3 1.0 OE1 C:GLN137 3.5 0.7 1.0 O2G C:ATP502 3.6 0.1 1.0 PG C:ATP502 3.7 99.1 1.0 PB C:ATP502 3.8 93.9 1.0 OD2 C:ASP11 4.0 91.9 1.0 OD2 C:ASP154 4.2 0.9 1.0 O3B C:ATP502 4.2 94.5 1.0 O3A C:ATP502 4.2 95.3 1.0 OD1 C:ASP11 4.3 0.2 1.0 OD1 C:ASP154 4.3 0.3 1.0 O1A C:ATP502 4.4 0.5 1.0 NZ C:LYS18 4.4 0.3 1.0 CD C:GLN137 4.4 0.2 1.0 CG2 C:VAL339 4.4 95.6 1.0 CA C:GLY13 4.5 0.4 1.0 CG C:ASP11 4.6 97.7 1.0 CG C:ASP154 4.7 0.7 1.0 PA C:ATP502 4.8 87.5 1.0 CB C:VAL339 4.9 76.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody


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(Atp-State) Heterodimer Bound By A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:85.3 occ:1.00 O1G D:ATP502 2.4 0.6 1.0 O2B D:ATP502 2.5 0.8 1.0 OE1 D:GLN137 3.3 1.0 1.0 PB D:ATP502 3.8 0.8 1.0 PG D:ATP502 3.9 0.7 1.0 OD2 D:ASP11 4.0 86.4 1.0 OD2 D:ASP154 4.1 0.2 1.0 O2A D:ATP502 4.1 79.0 1.0 OD1 D:ASP11 4.2 99.2 1.0 CD D:GLN137 4.2 0.8 1.0 O3A D:ATP502 4.3 0.2 1.0 CG2 D:VAL339 4.3 0.2 1.0 NZ D:LYS18 4.3 0.3 1.0 O3B D:ATP502 4.3 0.8 1.0 OD1 D:ASP154 4.4 0.2 1.0 CA D:GLY13 4.5 0.3 1.0 CG D:ASP11 4.6 98.9 1.0 CG D:ASP154 4.7 0.3 1.0 PA D:ATP502 4.7 89.2 1.0 O2G D:ATP502 4.8 0.7 1.0 CB D:VAL339 4.8 84.2 1.0 O3G D:ATP502 4.8 98.6 1.0 NE2 D:GLN137 4.8 0.4 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