Calcium in PDB 6qt2: Radiation Damage Study on A 16MER Dna Segment, Structure at 6.2 Mgy Dose

The structure of Radiation Damage Study on A 16MER Dna Segment, Structure at 6.2 Mgy Dose, PDB code: 6qt2 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)	31.34 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	36.864, 36.864, 162.063, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 28.2

The binding sites of Calcium atom in the Radiation Damage Study on A 16MER Dna Segment, Structure at 6.2 Mgy Dose (pdb code 6qt2). 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 6.2 Mgy Dose, PDB code: 6qt2:
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 6.2 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 6.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:35.5 occ:0.33 OP1 A:DC17 2.2 40.1 1.0 O A:HOH224 2.2 38.2 1.0 P A:DC17 3.6 43.4 1.0 C5' A:DC17 4.2 45.5 1.0 OP2 A:DC17 4.3 46.4 1.0 O5' A:DC17 4.4 44.0 1.0 C4' A:DC17 4.6 42.9 1.0 O3' A:DG16 4.7 40.7 1.0

Calcium binding site 2 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 6.2 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 6.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:39.9 occ:0.33 OP1 A:DA7 2.3 38.6 1.0 O A:HOH223 2.3 38.4 1.0 P A:DA7 3.6 37.4 1.0 C5' A:DA7 4.1 36.6 1.0 O5' A:DA7 4.2 41.7 1.0 OP2 A:DA7 4.4 37.4 1.0 C5' A:DG6 4.5 40.3 1.0 C4' A:DG6 4.7 38.3 1.0 O3' A:DG6 4.8 38.3 1.0 C3' A:DG6 5.0 39.4 1.0

Calcium binding site 3 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 6.2 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 6.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:41.2 occ:0.33 OP2 A:DA7 2.3 37.4 1.0 O A:HOH229 2.7 38.9 1.0 P A:DA7 3.5 37.4 1.0 O5' A:DA7 3.8 41.7 1.0 O A:HOH220 4.1 53.6 1.0 OP1 A:DA7 4.1 38.6 1.0 O3' A:DG6 4.8 38.3 1.0 C5' A:DA7 5.0 36.6 1.0

Calcium binding site 4 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 6.2 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 6.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:44.2 occ:1.00 OP1 A:DG16 2.4 36.7 1.0 O A:HOH228 2.5 27.3 0.5 O A:HOH235 2.7 43.6 1.0 O A:HOH228 3.2 39.2 0.5 P A:DG16 3.7 42.2 1.0 O A:HOH219 4.0 54.1 1.0 C5' A:DG16 4.2 39.1 1.0 O5' A:DG16 4.2 41.0 1.0 OP2 A:DG16 4.5 41.5 1.0 O3' A:DA15 4.8 40.6 1.0

Calcium binding site 5 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 6.2 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 6.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:66.9 occ:1.00 O A:HOH233 2.4 67.6 1.0 O A:HOH237 2.5 57.9 1.0 O A:HOH236 2.5 46.5 1.0 O A:HOH232 2.6 49.1 1.0 N3 A:DA7 4.5 42.1 1.0 O4' A:DA8 4.6 50.4 1.0 C4' A:DA8 4.7 54.1 1.0 C5' A:DA8 4.8 53.7 1.0 C2 A:DA7 4.9 40.0 1.0

Calcium binding site 6 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 6.2 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 6.2 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:55.2 occ:1.00 OP2 A:DA8 2.3 47.7 1.0 O A:HOH222 2.4 56.9 1.0 P A:DA8 3.6 49.2 1.0 O5' A:DA8 4.0 50.0 1.0 OP1 A:DA8 4.4 55.0 1.0 O A:HOH229 4.4 38.9 1.0 O3' A:DA7 4.7 44.2 1.0 C3' A:DA7 4.8 41.8 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