Calcium in PDB 6qt1: Radiation Damage Study on A 16MER Dna Segment, Structure at 0.48 Mgy Dose

The structure of Radiation Damage Study on A 16MER Dna Segment, Structure at 0.48 Mgy Dose, PDB code: 6qt1 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)	31.29 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	36.823, 36.823, 161.926, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 25.6

The binding sites of Calcium atom in the Radiation Damage Study on A 16MER Dna Segment, Structure at 0.48 Mgy Dose (pdb code 6qt1). 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 0.48 Mgy Dose, PDB code: 6qt1:
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 0.48 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 0.48 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:33.8 occ:0.33 OP1 A:DC17 2.2 39.7 1.0 O A:HOH223 2.2 34.7 1.0 P A:DC17 3.6 40.6 1.0 C5' A:DC17 4.2 43.4 1.0 O5' A:DC17 4.4 40.5 1.0 OP2 A:DC17 4.4 44.8 1.0 C4' A:DC17 4.6 42.4 1.0 O3' A:DG16 4.7 38.7 1.0

Calcium binding site 2 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 0.48 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 0.48 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:37.1 occ:0.33 OP1 A:DA7 2.3 38.4 1.0 O A:HOH226 2.3 36.8 1.0 P A:DA7 3.7 37.1 1.0 C5' A:DA7 4.1 38.4 1.0 O5' A:DA7 4.2 39.4 1.0 C5' A:DG6 4.4 37.2 1.0 OP2 A:DA7 4.4 36.0 1.0 C4' A:DG6 4.7 38.2 1.0 O3' A:DG6 4.9 37.4 1.0 O A:HOH215 5.0 43.5 1.0

Calcium binding site 3 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 0.48 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 0.48 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:40.5 occ:0.33 OP2 A:DA7 2.3 36.0 1.0 O A:HOH229 2.8 39.8 1.0 P A:DA7 3.5 37.1 1.0 O5' A:DA7 3.8 39.4 1.0 O A:HOH216 4.1 47.9 1.0 OP1 A:DA7 4.2 38.4 1.0 O3' A:DG6 4.8 37.4 1.0 C5' A:DA7 5.0 38.4 1.0

Calcium binding site 4 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 0.48 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 0.48 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:42.0 occ:1.00 OP1 A:DG16 2.4 32.6 1.0 O A:HOH228 2.5 27.0 0.5 O A:HOH234 2.6 42.5 1.0 O A:HOH228 3.3 31.9 0.5 P A:DG16 3.7 37.4 1.0 O A:HOH217 3.9 51.4 1.0 C5' A:DG16 4.1 35.3 1.0 O5' A:DG16 4.2 35.6 1.0 OP2 A:DG16 4.5 38.8 1.0 O3' A:DA15 4.8 37.4 1.0

Calcium binding site 5 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 0.48 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 0.48 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:63.1 occ:1.00 O A:HOH235 2.5 56.5 1.0 O A:HOH232 2.5 45.6 1.0 O A:HOH238 2.6 47.2 1.0 O A:HOH237 2.6 52.7 1.0 N3 A:DA7 4.6 41.5 1.0 O4' A:DA8 4.6 47.4 1.0 C4' A:DA8 4.7 50.5 1.0 C5' A:DA8 4.8 53.6 1.0

Calcium binding site 6 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 0.48 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 0.48 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:54.0 occ:1.00 OP2 A:DA8 2.2 50.5 1.0 O A:HOH225 2.5 54.5 1.0 P A:DA8 3.6 48.1 1.0 O5' A:DA8 4.0 49.0 1.0 OP1 A:DA8 4.4 49.9 1.0 O A:HOH229 4.5 39.8 1.0 O3' A:DA7 4.7 43.6 1.0 C3' A:DA7 4.8 41.9 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