Calcium in PDB 6svs: Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples

The structure of Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples, PDB code: 6svs was solved by A.Ruszkowska, M.Ruszkowski, J.P.Hulewicz, Z.Dauter, J.A.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.70 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.716, 78.114, 84.018, 90.00, 104.20, 90.00
R / Rfree (%)	16.7 / 21.3

The binding sites of Calcium atom in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples (pdb code 6svs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples, PDB code: 6svs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:81.6 occ:1.00 OP2 A:G2 2.4 63.7 1.0 O1A A:GTP106 2.4 97.4 1.0 CA A:CA105 3.7 0.9 1.0 P A:G2 3.8 54.8 1.0 PA A:GTP106 3.8 73.5 1.0 O1G A:GTP106 3.9 74.6 1.0 N7 A:G2 3.9 59.0 1.0 C8 A:G2 4.1 58.7 1.0 O5' A:G2 4.2 40.2 1.0 O2A A:GTP106 4.4 88.5 1.0 C5' A:GTP106 4.6 59.1 1.0 N7 A:A3 4.6 54.2 1.0 O5' A:GTP106 4.6 39.4 1.0 C3' A:GTP106 4.7 52.3 1.0 N6 A:A3 4.7 70.0 1.0 O3' A:GTP106 4.8 36.2 1.0 OP1 A:G2 4.8 73.2 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:46.7 occ:1.00 OP1 A:U57 2.4 72.0 1.0 OP2 A:A62 2.4 58.8 1.0 OP1 A:U59 2.4 81.7 1.0 OP2 A:U60 2.4 93.3 1.0 P A:U57 3.6 54.5 1.0 P A:A62 3.7 55.2 1.0 P A:U60 3.7 72.5 1.0 P A:U59 3.8 64.4 1.0 O5' A:U57 3.9 50.2 1.0 O5' A:A62 3.9 58.7 1.0 C5' A:U57 4.3 48.0 1.0 OP1 A:U60 4.3 70.8 1.0 O3' A:U56 4.3 48.2 1.0 C3' A:C58 4.4 52.5 1.0 C5' A:A62 4.5 44.1 1.0 OP2 A:U59 4.6 79.9 1.0 O3' A:U59 4.6 88.9 1.0 O3' A:C58 4.7 45.7 1.0 O3' A:A61 4.7 58.0 1.0 OP1 A:A62 4.7 64.3 1.0 O5' A:U59 4.7 72.5 1.0 C3' A:A61 4.7 49.2 1.0 OP2 A:U57 4.8 75.8 1.0 O5' A:U60 4.8 57.7 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:65.6 occ:1.00 OP2 A:A64 2.4 60.9 1.0 OP1 A:A63 2.4 69.1 1.0 P A:A63 3.7 61.5 1.0 N6 A:A65 3.8 0.0 1.0 P A:A64 3.9 75.1 1.0 N7 A:A65 4.1 0.1 1.0 OP2 A:A63 4.3 60.6 1.0 O5' A:A63 4.5 67.4 1.0 O5' A:A64 4.6 80.7 1.0 OP1 A:A64 4.7 75.7 1.0 C6 A:A65 4.7 0.6 1.0 O3' A:A63 4.7 72.7 1.0 C5 A:A65 4.8 93.7 1.0 N6 A:A66 4.9 85.2 1.0 O3' A:A62 4.9 42.5 1.0 C3' A:A63 4.9 57.8 1.0 C5' A:A63 5.0 59.5 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:0.9 occ:1.00 OP1 A:G52 2.4 87.7 1.0 O2A A:GTP106 2.4 88.5 1.0 PA A:GTP106 3.2 73.5 1.0 O1A A:GTP106 3.2 97.4 1.0 CA A:CA102 3.7 81.6 1.0 P A:G52 3.8 64.7 1.0 O1B A:GTP106 4.1 79.5 1.0 O1G A:GTP106 4.3 74.6 1.0 O3' A:G51 4.3 74.3 1.0 O3A A:GTP106 4.4 78.6 1.0 OP2 A:G2 4.5 63.7 1.0 O5' A:GTP106 4.5 39.4 1.0 C5' A:GTP106 4.6 59.1 1.0 O5' A:G52 4.7 71.3 1.0 OP1 A:C53 4.7 0.8 1.0 C5' A:G52 4.8 76.9 1.0 OP2 A:G52 4.9 49.3 1.0 PB A:GTP106 5.0 0.5 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:80.2 occ:1.00 OP2 B:G2 2.4 81.6 1.0 O1A B:GTP106 2.4 0.4 1.0 CA B:CA105 3.5 87.0 0.7 PA B:GTP106 3.6 0.9 1.0 P B:G2 3.8 77.5 1.0 O2A B:GTP106 3.8 0.5 1.0 O5' B:GTP106 4.1 81.7 1.0 O2G B:GTP106 4.3 0.1 1.0 O3' B:GTP106 4.4 78.6 1.0 N7 B:G2 4.5 65.9 1.0 O5' B:G2 4.5 67.7 1.0 C3' B:GTP106 4.5 82.0 1.0 C5' B:GTP106 4.8 78.4 1.0 C8 B:G2 4.8 67.3 1.0 OP1 B:G2 4.9 83.4 1.0 N7 B:A3 5.0 68.9 1.0 O3A B:GTP106 5.0 0.7 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:41.8 occ:1.00 OP2 B:A62 2.4 76.2 1.0 OP2 B:U60 2.4 90.8 1.0 OP1 B:U57 2.4 69.8 1.0 OP1 B:U59 2.4 62.0 1.0 P B:U60 3.6 77.7 1.0 P B:A62 3.6 68.7 1.0 P B:U57 3.6 55.4 1.0 P B:U59 3.9 60.2 1.0 OP1 B:U60 4.0 57.1 1.0 OP1 B:A62 4.1 69.6 1.0 OP2 B:U57 4.1 70.7 1.0 O5' B:U57 4.4 51.9 1.0 O5' B:A62 4.5 66.9 1.0 C5' B:A62 4.5 54.4 1.0 O5' B:U60 4.5 81.8 1.0 C5' B:U59 4.5 72.1 1.0 O5' B:U59 4.5 65.9 1.0 C3' B:C58 4.6 59.2 1.0 O3' B:U59 4.6 84.7 1.0 OP2 B:U59 4.7 69.5 1.0 O3' B:U56 4.7 52.0 1.0 O3' B:A61 4.7 70.9 1.0 C3' B:A61 4.7 70.9 1.0 O3' B:C58 4.8 55.5 1.0 C5' B:U57 4.8 58.0 1.0 C5 B:U60 4.9 91.5 1.0 C3' B:U59 4.9 77.3 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:79.1 occ:1.00 OP1 B:A63 2.4 80.2 1.0 OP2 B:A64 2.4 65.1 1.0 P B:A63 3.6 67.7 1.0 N6 B:A65 3.7 0.3 1.0 P B:A64 3.9 79.6 1.0 OP2 B:A63 4.0 56.0 1.0 O5' B:A63 4.3 69.2 1.0 N7 B:A65 4.4 97.2 1.0 O5' B:A64 4.5 81.5 1.0 O3' B:A63 4.7 91.2 1.0 C6 B:A65 4.8 90.0 1.0 C3' B:A63 4.8 79.5 1.0 OP1 B:A64 4.9 80.8 1.0 C5' B:A63 4.9 67.1 1.0 O3' B:A62 4.9 70.8 1.0 N6 B:A66 4.9 87.7 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca105 b:87.0 occ:0.70 O2A B:GTP106 2.4 0.5 1.0 OP1 B:G52 2.4 0.8 1.0 PA B:GTP106 3.2 0.9 1.0 O1A B:GTP106 3.4 0.4 1.0 CA B:CA102 3.5 80.2 1.0 P B:G52 3.8 0.1 1.0 O3A B:GTP106 4.2 0.7 1.0 O3' B:G51 4.3 89.4 1.0 OP2 B:G2 4.6 81.6 1.0 O5' B:GTP106 4.6 81.7 1.0 OP2 B:G52 4.7 97.8 1.0 O2' B:U50 4.7 86.6 1.0 O5' B:G52 4.8 98.4 1.0 C5' B:GTP106 4.9 78.4 1.0

A.Ruszkowska, M.Ruszkowski, J.P.Hulewicz, Z.Dauter, J.A.Brown. Molecular Structure of A U:A-U-Rich Rna Triple Helix with 11 Consecutive Base Triples To Be Published.