Calcium in PDB 6qt6: Radiation Damage Study on A 16MER Dna Segment, Structure at 29.2 Mgy Dose

The structure of Radiation Damage Study on A 16MER Dna Segment, Structure at 29.2 Mgy Dose, PDB code: 6qt6 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)	31.43 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	36.965, 36.965, 162.571, 90.00, 90.00, 120.00
R / Rfree (%)	27 / 36.9

The binding sites of Calcium atom in the Radiation Damage Study on A 16MER Dna Segment, Structure at 29.2 Mgy Dose (pdb code 6qt6). 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 29.2 Mgy Dose, PDB code: 6qt6:
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 29.2 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 29.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:44.5 occ:0.33 OP1 A:DC17 2.0 41.1 1.0 O A:HOH221 2.1 44.8 1.0 P A:DC17 3.4 52.8 1.0 C5' A:DC17 4.0 56.5 1.0 OP2 A:DC17 4.1 43.6 1.0 O5' A:DC17 4.2 49.1 1.0 O3' A:DG16 4.5 54.4 1.0 C4' A:DC17 4.9 49.9 1.0

Calcium binding site 2 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 29.2 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 29.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:57.3 occ:0.33 OP1 A:DA7 2.2 49.9 1.0 O A:HOH216 2.2 54.9 1.0 P A:DA7 3.5 44.1 1.0 O5' A:DA7 4.1 44.0 1.0 C5' A:DA7 4.2 39.4 1.0 OP2 A:DA7 4.3 42.8 1.0 C5' A:DG6 4.6 53.8 1.0 O3' A:DG6 4.6 42.7 1.0 C4' A:DG6 4.7 50.7 1.0 C3' A:DG6 4.8 49.8 1.0 CA A:CA103 4.9 50.8 0.3

Calcium binding site 3 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 29.2 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 29.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:50.8 occ:0.33 OP2 A:DA7 2.3 42.8 1.0 O A:HOH230 2.9 38.0 1.0 P A:DA7 3.4 44.1 1.0 O5' A:DA7 3.8 44.0 1.0 OP1 A:DA7 4.0 49.9 1.0 O3' A:DG6 4.7 42.7 1.0 O A:HOH217 4.8 53.4 1.0 CA A:CA102 4.9 57.3 0.3

Calcium binding site 4 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 29.2 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 29.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:71.2 occ:1.00 O A:HOH232 2.0 19.4 0.5 O A:HOH210 2.1 87.3 1.0 O A:HOH228 2.2 22.5 0.5 OP1 A:DG16 2.4 54.6 1.0 O A:HOH233 3.2 53.9 1.0 O A:HOH228 3.2 25.9 0.5 O A:HOH232 3.3 29.2 0.5 O A:HOH215 3.6 72.0 1.0 P A:DG16 3.8 56.8 1.0 O5' A:DG16 4.2 52.0 1.0 C5' A:DG16 4.3 51.1 1.0 OP2 A:DG16 4.6 52.4 1.0 O3' A:DA15 4.9 52.4 1.0

Calcium binding site 5 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 29.2 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 29.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:85.3 occ:1.00 O A:HOH236 2.2 61.8 1.0 O A:HOH237 2.2 68.9 1.0 O A:HOH235 2.4 54.4 1.0 C5' A:DA8 4.4 62.6 1.0 O4' A:DA8 4.5 56.7 1.0 C4' A:DA8 4.6 60.1 1.0 N3 A:DA7 4.6 47.0 1.0

Calcium binding site 6 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 29.2 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 29.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:96.8 occ:1.00 O A:HOH214 2.1 36.4 1.0 O A:HOH217 2.5 53.4 1.0 OP2 A:DA8 3.3 51.5 1.0 O A:HOH224 3.6 59.0 1.0 O5' A:DA8 4.1 55.9 1.0 P A:DA8 4.3 58.9 1.0 C2' A:DA8 4.4 57.9 1.0 C3' A:DA8 4.7 63.1 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