Calcium in PDB 1pjg: Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg

The structure of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg, PDB code: 1pjg was solved by M.L.Kopka, L.Lavelle, G.W.Han, H.-L.Ng, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.701, 41.073, 46.116, 90.00, 90.00, 90.00
R / Rfree (%)	13.2 / 16.3

The binding sites of Calcium atom in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg (pdb code 1pjg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg, PDB code: 1pjg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca32 b:22.8 occ:0.50 CA A:CA32 0.0 22.8 0.5 O A:HOH140 2.0 17.4 1.0 O A:HOH139 2.1 20.6 1.0 O A:HOH141 2.1 21.3 0.5 O A:HOH143 2.2 24.4 1.0 O A:HOH138 2.2 24.3 0.5 CA A:CA32 2.3 19.2 0.5 OP2 A:G5 2.3 18.2 1.0 O A:HOH142 2.5 25.3 0.5 O A:HOH84 3.3 29.7 1.0 H3' A:A4 3.6 13.5 1.0 P A:G5 3.7 14.3 1.0 O A:HOH142 3.9 24.7 0.5 O A:HOH138 3.9 13.6 0.5 N7 A:G5 4.0 10.0 1.0 O5' A:G5 4.1 12.6 1.0 O A:HOH141 4.2 32.0 0.5 OP2 A:A6 4.3 15.9 1.0 H8 A:G5 4.3 12.6 1.0 N7 A:A6 4.4 10.2 1.0 H2' A:A4 4.4 12.5 1.0 C8 A:G5 4.4 10.5 1.0 O A:HOH78 4.4 24.6 1.0 C3' A:A4 4.5 11.2 1.0 H3' A:G5 4.5 13.4 1.0 H62 A:A6 4.5 11.0 1.0 O A:HOH71 4.6 29.1 1.0 O3' A:A4 4.6 14.5 1.0 OP1 A:G5 4.7 17.9 1.0 C5 A:G5 4.9 8.7 1.0 H8 A:A6 4.9 12.6 1.0 C2' A:A4 5.0 10.4 1.0

Calcium binding site 2 out of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca32 b:19.2 occ:0.50 CA A:CA32 0.0 19.2 0.5 O A:HOH142 1.9 24.7 0.5 CA A:CA32 2.3 22.8 0.5 O A:HOH140 2.3 17.4 1.0 O A:HOH139 2.3 20.6 1.0 O A:HOH142 2.3 25.3 0.5 O A:HOH143 2.4 24.4 1.0 O A:HOH138 2.5 13.6 0.5 O A:HOH141 2.6 32.0 0.5 H62 A:A6 3.7 11.0 1.0 O A:HOH141 3.8 21.3 0.5 O A:HOH138 4.1 24.3 0.5 OP2 A:G5 4.2 18.2 1.0 O A:HOH84 4.3 29.7 1.0 N7 A:A4 4.3 9.1 1.0 O A:HOH65 4.3 23.9 1.0 O B:HOH30 4.3 19.6 1.0 O B:HOH26 4.5 12.6 1.0 H3' A:A4 4.5 13.5 1.0 N6 A:A6 4.6 9.1 1.0 C8 A:A4 4.6 8.9 1.0 H8 A:A4 4.6 10.7 1.0 O A:HOH78 4.6 24.6 1.0 OP2 A:A4 4.7 21.4 1.0 N7 A:G5 4.8 10.0 1.0 H61 A:A6 4.9 11.0 1.0 H62 A:A7 4.9 11.9 1.0 O6 A:G5 4.9 8.9 1.0 C5 A:A4 4.9 7.7 1.0

Calcium binding site 3 out of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca33 b:11.9 occ:1.00 OP2 A:A9 2.0 8.6 1.0 O A:HOH147 2.0 12.3 1.0 O A:HOH144 2.0 13.7 1.0 O A:HOH146 2.1 10.3 1.0 O A:HOH145 2.1 10.0 1.0 O A:HOH148 2.1 10.8 1.0 P A:A9 3.5 7.4 1.0 H3' A:A8 3.5 10.3 1.0 O A:HOH66 4.0 19.6 1.0 O5' A:A9 4.1 7.5 1.0 H8 A:A9 4.2 9.8 1.0 O A:HOH44 4.2 9.6 1.0 N7 A:A9 4.2 8.0 1.0 OP2 A:G10 4.3 7.4 1.0 C3' A:A8 4.3 8.6 1.0 O3' A:A8 4.4 7.6 1.0 OP1 A:A9 4.4 8.2 1.0 C8 A:A9 4.5 8.2 1.0 H3' A:A9 4.6 9.1 1.0 O A:HOH60 4.7 27.6 1.0 O A:HOH41 4.8 13.8 1.0 N7 A:G10 4.8 7.2 1.0 H5' A:A8 4.8 15.0 1.0 H2' A:A8 4.8 11.5 1.0 H5'' A:A8 5.0 15.0 1.0

Calcium binding site 4 out of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca31 b:8.7 occ:1.00 OP2 B:DT18 2.2 8.3 1.0 O B:HOH136 2.3 11.8 1.0 O B:HOH137 2.3 10.3 1.0 O B:HOH134 2.3 10.5 1.0 O B:HOH135 2.3 13.1 1.0 P B:DT18 3.5 7.5 1.0 H3' B:DT17 3.8 8.2 1.0 H72 B:DT18 4.0 14.3 1.0 OP1 B:DT18 4.1 9.1 1.0 H73 B:DT18 4.2 14.3 1.0 O3' B:DT17 4.2 7.2 1.0 O5' B:DT17 4.3 7.4 1.0 H5'' B:DT17 4.4 9.4 1.0 O B:HOH38 4.4 26.0 1.0 OP2 B:DT17 4.4 9.1 1.0 OP1 B:DT17 4.5 9.8 1.0 C3' B:DT17 4.5 6.9 1.0 C7 B:DT18 4.6 9.5 1.0 P B:DT17 4.6 8.6 1.0 O5' B:DT18 4.7 7.1 1.0 C5' B:DT17 4.8 7.8 1.0 H71 B:DT18 5.0 14.3 1.0

Calcium binding site 5 out of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca34 b:12.6 occ:1.00 O B:HOH150 2.0 26.2 1.0 OP1 B:DT18 2.2 9.1 1.0 O B:HOH149 2.4 22.7 1.0 O B:HOH151 2.5 20.0 1.0 O B:HOH152 2.5 12.9 1.0 H5'' B:DT18 3.4 8.4 1.0 P B:DT18 3.7 7.5 1.0 O B:HOH50 4.0 19.3 1.0 C5' B:DT18 4.2 7.0 1.0 H5' B:DT18 4.3 8.4 1.0 O5' B:DT18 4.3 7.1 1.0 O B:HOH136 4.4 11.8 1.0 O3' B:DT17 4.5 7.2 1.0 OP2 B:DT18 4.6 8.3 1.0 O B:HOH91 4.8 37.1 1.0

M.L.Kopka, L.Lavelle, G.W.Han, H.L.Ng, R.E.Dickerson. An Unusual Sugar Conformation in the Structure of An Rna/Dna Decamer of the Polypurine Tract May Affect Recognition By Rnase H. J.Mol.Biol. V. 334 653 2003.
ISSN: ISSN 0022-2836
PubMed: 14636594
DOI: 10.1016/J.JMB.2003.09.057