Calcium in PDB 6qt3: Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose

The structure of Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose, PDB code: 6qt3 was solved by V.Bugris, V.Harmat, G.Ferenc, S.Brockhauser, I.Carmichael, E.F.Garman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.36 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	36.888, 36.888, 162.203, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 29.1

The binding sites of Calcium atom in the Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose (pdb code 6qt3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose, PDB code: 6qt3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:37.6 occ:0.33 OP1 A:DC17 2.1 40.3 1.0 O A:HOH225 2.3 40.9 1.0 P A:DC17 3.6 46.5 1.0 C5' A:DC17 4.1 52.2 1.0 OP2 A:DC17 4.3 49.8 1.0 O5' A:DC17 4.3 47.6 1.0 C4' A:DC17 4.6 49.8 1.0 O3' A:DG16 4.6 43.9 1.0

Calcium binding site 2 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:40.2 occ:0.33 OP1 A:DA7 2.3 40.2 1.0 O A:HOH223 2.4 42.6 1.0 P A:DA7 3.6 37.8 1.0 C5' A:DA7 4.2 38.4 1.0 O5' A:DA7 4.2 43.4 1.0 OP2 A:DA7 4.4 37.9 1.0 C5' A:DG6 4.5 44.1 1.0 C4' A:DG6 4.7 40.8 1.0 O3' A:DG6 4.8 40.4 1.0 C3' A:DG6 5.0 41.4 1.0

Calcium binding site 3 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:43.0 occ:0.33 OP2 A:DA7 2.3 37.9 1.0 O A:HOH228 2.7 40.1 1.0 P A:DA7 3.5 37.8 1.0 O5' A:DA7 3.9 43.4 1.0 O A:HOH219 4.1 62.6 1.0 OP1 A:DA7 4.1 40.2 1.0 O3' A:DG6 4.8 40.4 1.0 O A:HOH222 5.0 58.7 1.0

Calcium binding site 4 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:48.9 occ:1.00 OP1 A:DG16 2.3 40.1 1.0 O A:HOH230 2.5 31.2 0.5 O A:HOH235 2.7 47.3 1.0 O A:HOH230 3.2 41.4 0.5 P A:DG16 3.7 46.3 1.0 O A:HOH220 3.8 59.9 1.0 O5' A:DG16 4.2 45.0 1.0 C5' A:DG16 4.2 42.3 1.0 OP2 A:DG16 4.5 42.8 1.0 O3' A:DA15 4.8 46.1 1.0

Calcium binding site 5 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:72.1 occ:1.00 O A:HOH234 2.3 70.8 1.0 O A:HOH238 2.4 56.6 1.0 O A:HOH232 2.5 52.4 1.0 O A:HOH236 2.6 48.3 1.0 N3 A:DA7 4.5 45.1 1.0 O4' A:DA8 4.6 51.3 1.0 C4' A:DA8 4.8 55.4 1.0 C2 A:DA7 4.9 43.0 1.0 C5' A:DA8 4.9 58.7 1.0

Calcium binding site 6 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Radiation Damage Study on A 16MER Dna Segment, Structure at 12.0 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:59.9 occ:1.00 OP2 A:DA8 2.3 56.1 1.0 O A:HOH222 2.4 58.7 1.0 P A:DA8 3.6 50.4 1.0 O5' A:DA8 4.1 53.4 1.0 OP1 A:DA8 4.4 55.5 1.0 O A:HOH228 4.5 40.1 1.0 O3' A:DA7 4.8 46.5 1.0 C3' A:DA7 4.9 43.0 1.0

V.Bugris, V.Harmat, G.Ferenc, S.Brockhauser, I.Carmichael, E.F.Garman. Radiation-Damage Investigation of A Dna 16-Mer. J.Synchrotron Radiat. V. 26 998 2019.
ISSN: ESSN 1600-5775
PubMed: 31274421
DOI: 10.1107/S160057751900763X