Calcium in PDB 8aas: Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna

The structure of Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna, PDB code: 8aas was solved by C.Madru, P.Legrand, L.Sauguet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.26 / 3.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.234, 75.234, 215.487, 90, 90, 120
R / Rfree (%)	26.4 / 29.3

The structure of Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna (pdb code 8aas). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna, PDB code: 8aas:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna


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 Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:174.3 occ:1.00 O A:SER334 3.4 174.5 1.0 OD2 A:ASP269 3.6 193.0 1.0 OD1 A:ASP269 4.1 191.3 1.0 CG A:ASP269 4.2 190.3 1.0 C A:SER334 4.6 174.4 1.0 CA A:CA403 4.6 180.6 1.0 CB A:SER335 4.6 172.8 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna


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 Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:180.6 occ:1.00 O A:PHE266 3.1 176.4 1.0 OD2 A:ASP269 3.5 193.0 1.0 N A:ASP268 3.9 179.9 1.0 N A:ASP269 4.0 182.0 1.0 C A:PHE266 4.0 176.4 1.0 CG A:ASP269 4.1 190.3 1.0 OD1 A:ASP268 4.2 188.7 1.0 CB A:ASP268 4.3 183.3 1.0 CB A:ASP269 4.5 184.6 1.0 CA A:ASP268 4.5 181.2 1.0 C A:GLY267 4.6 179.2 1.0 CA A:GLY267 4.6 178.2 1.0 CA A:CA402 4.6 174.3 1.0 CG A:ASP268 4.7 188.4 1.0 N A:GLY267 4.7 177.1 1.0 C A:ASP268 4.7 182.0 1.0 CA A:ASP269 4.9 182.4 1.0 OD1 A:ASP269 5.0 191.3 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna


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 Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:169.6 occ:1.00 OD1 A:ASP197 2.9 185.2 1.0 O A:ALA195 3.7 178.2 1.0 N A:ASP197 4.0 175.4 1.0 C A:GLY196 4.1 176.1 1.0 CG A:ASP197 4.1 183.6 1.0 CA A:ASP197 4.1 175.3 1.0 O A:GLY196 4.2 176.3 1.0 CB A:GLU194 4.5 181.1 1.0 C A:ALA195 4.6 178.0 1.0 CB A:ASP197 4.7 177.8 1.0 CA A:GLY196 4.7 176.9 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna


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 Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:121.6 occ:1.00 OD2 B:ASP81 3.4 143.7 1.0 OD1 B:ASP81 3.8 142.2 1.0 OE1 A:GLU304 3.8 172.4 1.0 CG B:ASP81 4.0 142.4 1.0 OE2 A:GLU304 4.1 174.7 1.0 CD A:GLU304 4.4 172.5 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna


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 the Pyrococcus Abyssi Rpa Trimerization Core Bound to Poly-DT20 Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:151.7 occ:1.00 O C:ALA83 3.5 137.7 1.0 OG C:SER55 3.5 121.1 1.0 N C:GLU56 3.7 120.7 1.0 N C:SER57 4.0 120.8 1.0 OG C:SER57 4.0 128.9 1.0 N C:ASP58 4.1 123.3 1.0 CB C:GLU56 4.2 121.6 1.0 O C:GLU84 4.3 135.2 1.0 C C:ALA83 4.3 137.8 1.0 NZ B:LYS90 4.4 129.7 1.0 OD2 C:ASP58 4.4 138.5 1.0 CA C:GLU56 4.4 120.3 1.0 CA C:SER55 4.5 120.6 1.0 CD1 C:ILE86 4.5 131.2 1.0 CB C:SER55 4.5 120.1 1.0 CB C:ASP58 4.6 127.4 1.0 C C:SER55 4.6 121.2 1.0 CB C:ALA83 4.6 139.2 1.0 C C:GLU84 4.6 134.8 1.0 CG C:ASP58 4.8 135.4 1.0 C C:GLU56 4.8 120.1 1.0 O C:ASP58 4.8 123.8 1.0 CA C:ASP58 4.9 124.2 1.0 CA C:GLU84 4.9 135.8 1.0 N C:GLU84 4.9 136.4 1.0 CA C:SER57 4.9 122.3 1.0

C.Madru, M.Martinez-Carranza, S.Laurent, A.C.Alberti, M.Chevreuil, B.Raynal, A.Haouz, R.A.Le Meur, M.Delarue, G.Henneke, D.Flament, M.Krupovic, P.Legrand, L.Sauguet. Dna-Binding Mechanism and Evolution of Replication Protein A. Nat Commun V. 14 2326 2023.
ISSN: ESSN 2041-1723
PubMed: 37087464
DOI: 10.1038/S41467-023-38048-W