Calcium in PDB 6qt5: Radiation Damage Study on A 16MER Dna Segment, Structure at 63.7 Mgy Dose

The structure of Radiation Damage Study on A 16MER Dna Segment, Structure at 63.7 Mgy Dose, PDB code: 6qt5 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)	31.40 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	36.931, 36.931, 162.485, 90.00, 90.00, 120.00
R / Rfree (%)	24.8 / 34.5

The binding sites of Calcium atom in the Radiation Damage Study on A 16MER Dna Segment, Structure at 63.7 Mgy Dose (pdb code 6qt5). 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 63.7 Mgy Dose, PDB code: 6qt5:
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 63.7 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 63.7 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:42.1 occ:0.33 OP1 A:DC17 2.1 40.6 1.0 O A:HOH224 2.2 45.6 1.0 P A:DC17 3.5 53.9 1.0 C5' A:DC17 4.1 57.0 1.0 OP2 A:DC17 4.2 49.6 1.0 O5' A:DC17 4.3 51.6 1.0 O3' A:DG16 4.6 49.7 1.0 C4' A:DC17 4.7 54.5 1.0

Calcium binding site 2 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 63.7 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 63.7 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:48.8 occ:0.33 O A:HOH222 2.3 51.4 1.0 OP1 A:DA7 2.3 49.0 1.0 P A:DA7 3.7 42.2 1.0 O5' A:DA7 4.3 47.8 1.0 C5' A:DA7 4.3 42.8 1.0 OP2 A:DA7 4.5 42.5 1.0 C5' A:DG6 4.6 50.8 1.0 C4' A:DG6 4.7 47.1 1.0 O3' A:DG6 4.7 43.7 1.0 C3' A:DG6 5.0 48.5 1.0

Calcium binding site 3 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 63.7 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 63.7 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:49.8 occ:0.33 OP2 A:DA7 2.4 42.5 1.0 O A:HOH229 2.7 42.0 1.0 P A:DA7 3.5 42.2 1.0 O5' A:DA7 3.8 47.8 1.0 OP1 A:DA7 4.0 49.0 1.0 O A:HOH221 4.2 68.3 1.0 O3' A:DG6 4.8 43.7 1.0

Calcium binding site 4 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 63.7 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 63.7 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:62.0 occ:1.00 O A:HOH231 2.3 38.1 0.5 OP1 A:DG16 2.4 52.6 1.0 O A:HOH234 2.6 55.9 1.0 O A:HOH231 3.2 46.6 0.5 P A:DG16 3.7 54.0 1.0 O A:HOH212 4.0 68.7 1.0 C5' A:DG16 4.2 50.4 1.0 O5' A:DG16 4.2 53.9 1.0 OP2 A:DG16 4.5 55.3 1.0 O3' A:DA15 4.8 51.9 1.0

Calcium binding site 5 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 63.7 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 63.7 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:85.8 occ:1.00 O A:HOH238 2.1 74.3 1.0 O A:HOH237 2.5 57.8 1.0 N3 A:DA7 4.5 43.2 1.0 O4' A:DA8 4.6 54.2 1.0 C5' A:DA8 4.6 64.7 1.0 C4' A:DA8 4.7 58.1 1.0 C2 A:DA7 4.9 41.7 1.0

Calcium binding site 6 out of 6 in the Radiation Damage Study on A 16MER Dna Segment, Structure at 63.7 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 63.7 Mgy Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:70.2 occ:1.00 O A:HOH221 1.8 68.3 1.0 O A:HOH220 2.4 65.8 1.0 OP2 A:DA8 2.5 57.1 1.0 P A:DA8 3.8 59.2 1.0 O5' A:DA8 4.3 58.7 1.0 OP1 A:DA8 4.5 60.6 1.0 O A:HOH229 4.6 42.0 1.0 O3' A:DA7 5.0 52.3 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