Calcium in PDB 1ryr: Replication of A Cis-Syn Thymine Dimer at Atomic Resolution

All present enzymatic activity of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution:
2.7.7.7;

The structure of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution, PDB code: 1ryr was solved by H.Ling, F.Boudsocq, B.Plosky, R.Woodgate, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.34 / 2.28
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.519, 101.556, 52.246, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 28.1

The binding sites of Calcium atom in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution (pdb code 1ryr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution, PDB code: 1ryr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:41.2 occ:1.00 O A:HOH1959 1.9 63.5 1.0 OD1 A:ASP7 2.2 39.1 1.0 OD2 A:ASP105 2.3 38.7 1.0 O A:PHE8 2.3 36.1 1.0 O2B A:ATP1814 2.4 81.1 1.0 O A:HOH1821 2.6 47.3 1.0 PB A:ATP1814 3.1 78.5 1.0 CG A:ASP7 3.3 41.3 1.0 C A:PHE8 3.4 37.8 1.0 CG A:ASP105 3.5 40.9 1.0 O3B A:ATP1814 3.5 79.4 1.0 O1G A:ATP1814 3.6 81.4 1.0 PG A:ATP1814 3.7 77.6 1.0 OD2 A:ASP7 3.8 41.6 1.0 O1B A:ATP1814 3.8 79.8 1.0 O2G A:ATP1814 3.9 77.7 1.0 CA A:CA404 3.9 58.9 1.0 O A:HOH1865 3.9 51.0 1.0 N A:PHE8 4.1 39.8 1.0 NZ A:LYS159 4.1 45.9 1.0 O A:HOH1816 4.2 57.9 1.0 O3A A:ATP1814 4.3 79.0 1.0 OD1 A:ASP105 4.3 43.0 1.0 C A:ASP7 4.3 41.0 1.0 CB A:ASP105 4.3 37.3 1.0 CA A:PHE8 4.3 38.6 1.0 N A:ASP9 4.3 37.4 1.0 N A:TYR10 4.4 33.9 1.0 CA A:ASP9 4.4 37.3 1.0 C A:ASP9 4.5 34.9 1.0 O A:HOH1910 4.6 50.8 1.0 CB A:ASP7 4.6 41.2 1.0 O A:ASP7 4.6 42.2 1.0 O A:ASP105 4.7 35.4 1.0 N A:PHE11 4.7 34.9 1.0 CA A:ASP7 4.8 41.0 1.0 O A:HOH1969 4.8 79.8 1.0 O A:HOH1920 4.9 68.8 1.0 CB A:PHE11 4.9 33.6 1.0 CB A:PHE8 4.9 37.1 1.0

Calcium binding site 2 out of 2 in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:58.9 occ:1.00 O A:HOH1816 2.2 57.9 1.0 O A:HOH1932 2.4 75.5 1.0 OD1 A:ASP105 2.7 43.0 1.0 O3A A:ATP1814 2.7 79.0 1.0 O A:HOH1963 2.8 78.5 1.0 OD2 A:ASP105 2.9 38.7 1.0 O1A A:ATP1814 2.9 78.1 1.0 CG A:ASP105 3.1 40.9 1.0 PB A:ATP1814 3.2 78.5 1.0 O2B A:ATP1814 3.3 81.1 1.0 PA A:ATP1814 3.4 77.9 1.0 O A:HOH1920 3.5 68.8 1.0 O5' A:ATP1814 3.6 78.2 1.0 O3B A:ATP1814 3.9 79.4 1.0 CA A:CA402 3.9 41.2 1.0 O A:HOH1959 4.3 63.5 1.0 CG A:GLU106 4.4 46.9 1.0 C5' A:ATP1814 4.4 77.4 1.0 OE2 A:GLU106 4.5 50.9 1.0 C4' A:ATP1814 4.5 76.6 1.0 CD A:GLU106 4.6 49.4 1.0 CB A:ASP105 4.6 37.3 1.0 O1B A:ATP1814 4.7 79.8 1.0 OG A:SER103 4.7 38.4 1.0 O2A A:ATP1814 4.7 78.7 1.0 O3' B:DC1813 4.7 70.2 1.0 OD1 A:ASP7 4.8 39.1 1.0 PG A:ATP1814 4.9 77.6 1.0

H.Ling, F.Boudsocq, B.Plosky, R.Woodgate, W.Yang. Replication of A Cis-Syn Thymine Dimer at Atomic Resolution Nature V. 424 1083 2003.
ISSN: ISSN 0028-0836
PubMed: 12904819
DOI: 10.1038/NATURE01919