Calcium in PDB 8x9o: Cte-U537INS-Branching,Ca,Inactive

The structure of Cte-U537INS-Branching,Ca,Inactive also contains other interesting chemical elements:

Potassium

(K)

19 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Cte-U537INS-Branching,Ca,Inactive (pdb code 8x9o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Cte-U537INS-Branching,Ca,Inactive, PDB code: 8x9o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:59.7 occ:1.00 OP1 A:U218 2.3 63.3 1.0 OP2 A:U423 2.3 67.8 1.0 OP2 A:A422 2.4 66.5 1.0 P A:A422 3.6 80.2 1.0 P A:U218 3.7 74.7 1.0 P A:U423 3.8 73.2 1.0 OP1 A:A422 4.1 59.5 1.0 O5' A:A422 4.2 77.3 1.0 O5' A:U218 4.4 73.0 1.0 OP2 A:U218 4.5 68.6 1.0 OP1 A:U423 4.5 74.7 1.0 C4' A:A422 4.6 64.8 1.0 O3' A:A422 4.6 66.2 1.0 O5' A:U423 4.7 61.3 1.0 O3' A:G217 4.8 72.8 1.0 C5' A:U218 4.9 66.9 1.0 O3' A:C421 4.9 79.5 1.0

Calcium binding site 2 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:66.4 occ:1.00 OP1 A:A567 2.2 78.0 1.0 OP2 A:C570 2.2 88.6 1.0 OP1 A:G569 2.6 94.6 1.0 P A:A567 3.6 90.8 1.0 P A:C570 3.7 92.5 1.0 P A:G569 4.0 100.6 1.0 OP2 A:A567 4.3 90.9 1.0 O3' A:A566 4.3 85.3 1.0 O5' A:C570 4.4 95.9 1.0 OP1 A:C570 4.5 95.3 1.0 O3' A:G569 4.6 92.1 1.0 O5' A:A567 4.7 78.6 1.0 OP2 A:G569 4.7 94.0 1.0 O5' A:G569 4.8 97.3 1.0 C3' A:G569 4.8 87.7 1.0 C5' A:A567 4.9 76.8 1.0 C3' A:A568 4.9 75.7 1.0 C5' A:G569 4.9 94.2 1.0

Calcium binding site 3 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:58.2 occ:1.00 OP2 A:G569 2.4 94.0 1.0 OP2 A:G523 2.5 92.2 1.0 P A:G523 3.4 98.1 1.0 OP1 A:G523 3.4 84.2 1.0 P A:G569 3.8 100.6 1.0 O5' A:G523 4.0 79.8 1.0 OP1 A:A566 4.0 88.5 1.0 O3' A:A568 4.4 76.9 1.0 OP2 A:A567 4.5 90.9 1.0 N7 A:G569 4.6 95.0 1.0 O5' A:G569 4.6 97.3 1.0 O2' A:A568 4.7 89.4 1.0 C5' A:G523 4.8 78.6 1.0 O3' A:A522 4.8 92.8 1.0 OP1 A:G569 4.8 94.6 1.0

Calcium binding site 4 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:60.1 occ:1.00 OP1 A:C621 2.3 76.3 1.0 OP1 A:C262 2.7 67.4 1.0 P A:C621 3.7 86.2 1.0 OP1 A:G265 4.0 73.8 1.0 O5' A:C621 4.1 67.5 1.0 P A:C262 4.1 83.7 1.0 C5' A:C621 4.3 63.3 1.0 OP2 A:C621 4.4 73.8 1.0 OP2 A:G265 4.4 63.2 1.0 OP2 A:G622 4.5 72.3 1.0 OP2 A:C263 4.5 65.4 1.0 P A:G265 4.7 80.2 1.0 O3' A:C620 4.9 69.5 1.0 O3' A:A261 4.9 71.5 1.0 O5' A:C262 4.9 67.5 1.0 OP1 A:C263 5.0 65.8 1.0 OP2 A:C262 5.0 75.1 1.0

Calcium binding site 5 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca905 b:79.6 occ:1.00 OP2 A:G83 2.4 82.4 1.0 OP2 A:G220 2.4 88.9 1.0 OP1 A:C81 2.4 71.7 1.0 O3' A:U219 2.7 71.8 1.0 OP2 A:G61 2.9 76.5 1.0 P A:G220 2.9 97.3 1.0 P A:G83 3.4 82.0 1.0 OP1 A:G83 3.5 72.9 1.0 P A:C81 3.5 77.8 1.0 OP1 A:G220 3.6 84.4 1.0 OP1 A:G61 3.7 79.6 1.0 P A:G61 3.8 88.8 1.0 OP2 A:C81 3.8 69.4 1.0 C3' A:U219 4.0 69.4 1.0 O2' A:U219 4.0 73.4 1.0 O3' A:G80 4.2 69.2 1.0 CA A:CA909 4.4 105.2 1.0 O5' A:G83 4.4 72.1 1.0 O5' A:G220 4.4 74.5 1.0 C2' A:U219 4.5 72.0 1.0 O3' A:U82 4.6 74.1 1.0 C4' A:U219 4.6 65.6 1.0 O5' A:G61 4.8 68.9 1.0 C5' A:G220 4.8 70.3 1.0 O5' A:C81 4.8 63.1 1.0 C5' A:G83 4.9 69.2 1.0 O3' A:A60 5.0 70.3 1.0

Calcium binding site 6 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:57.9 occ:1.00 OP1 A:A225 2.4 76.2 1.0 OP2 A:C226 2.9 73.8 1.0 P A:A225 3.9 82.1 1.0 P A:C226 4.0 78.0 1.0 OP1 A:C226 4.1 69.1 1.0 O4' A:A629 4.4 65.3 1.0 C5' A:A225 4.5 68.1 1.0 O5' A:A225 4.6 73.3 1.0 O3' A:G224 4.7 67.4 1.0 O3' A:A225 4.7 76.8 1.0 OP2 A:A225 4.8 72.8 1.0

Calcium binding site 7 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca907 b:62.8 occ:1.00 OP2 A:A367 2.3 77.1 1.0 OP1 A:G366 2.3 66.6 1.0 OP2 A:G417 2.4 64.5 1.0 P A:A367 3.6 83.6 1.0 P A:G366 3.8 72.2 1.0 O5' A:A367 3.8 80.3 1.0 P A:G417 3.9 71.5 1.0 OP2 A:C416 3.9 62.9 1.0 O5' A:C416 3.9 65.5 1.0 P A:C416 4.2 67.9 1.0 OP1 A:C416 4.2 62.8 1.0 OP2 A:G366 4.5 61.9 1.0 C3' A:G366 4.5 66.2 1.0 OP1 A:G417 4.6 67.5 1.0 O3' A:G366 4.6 65.8 1.0 C3' A:C416 4.7 62.0 1.0 O5' A:G366 4.7 74.0 1.0 OP1 A:A367 4.7 62.8 1.0 O5' A:G417 4.7 63.0 1.0 O3' A:A365 4.7 61.5 1.0 O3' A:C416 4.8 66.1 1.0 C5' A:C416 4.9 58.0 1.0 C5' A:G366 4.9 62.1 1.0 C5' A:A367 4.9 71.9 1.0

Calcium binding site 8 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca908 b:69.3 occ:1.00 OP1 A:U494 2.3 93.3 1.0 OP2 A:G495 2.4 96.3 1.0 P A:G495 3.4 99.8 1.0 OP1 A:G495 3.6 98.5 1.0 P A:U494 3.8 100.7 1.0 C5' A:U494 4.2 102.7 1.0 O5' A:U494 4.3 98.6 1.0 O5' A:G495 4.5 90.4 1.0 O3' A:U494 4.6 96.0 1.0 OP2 A:U494 4.6 97.5 1.0 O3' A:G493 4.8 93.8 1.0 C3' A:U494 4.9 94.5 1.0

Calcium binding site 9 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca909 b:105.2 occ:1.00 OP1 A:G83 2.3 72.9 1.0 OP1 A:A60 2.3 72.8 1.0 O2' A:A127 2.4 73.4 1.0 OP2 A:G220 2.5 88.9 1.0 P A:G220 3.5 97.3 1.0 C2' A:A127 3.6 71.5 1.0 P A:G83 3.6 82.0 1.0 OP2 A:G61 3.7 76.5 1.0 P A:A60 3.8 76.8 1.0 C1' A:A127 3.9 72.2 1.0 O5' A:G220 3.9 74.5 1.0 OP1 A:G220 4.0 84.4 1.0 O3' A:U82 4.1 74.1 1.0 O4' A:A127 4.1 73.6 1.0 C4' A:A127 4.2 72.7 1.0 C5' A:A60 4.2 62.6 1.0 O5' A:A60 4.3 64.5 1.0 CA A:CA905 4.4 79.6 1.0 OP2 A:G83 4.4 82.4 1.0 C3' A:A127 4.4 75.8 1.0 C5' A:G220 4.4 70.3 1.0 O3' A:A127 4.6 84.8 1.0 O3' A:U59 4.6 77.7 1.0 OP2 A:A60 4.8 72.6 1.0 O5' A:G83 4.8 72.1 1.0 C4' A:G220 4.8 73.2 1.0 O3' A:U219 4.9 71.8 1.0

Calcium binding site 10 out of 14 in the Cte-U537INS-Branching,Ca,Inactive


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cte-U537INS-Branching,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca910 b:55.2 occ:1.00 OP2 A:C426 2.4 73.6 1.0 OP1 A:G425 2.6 64.5 1.0 P A:C426 3.8 76.1 1.0 P A:G425 4.0 78.4 1.0 OP2 A:U427 4.1 69.0 1.0 O5' A:G425 4.4 67.9 1.0 OP1 A:C426 4.5 63.7 1.0 O5' A:C426 4.6 62.6 1.0 C5' A:G425 4.6 57.3 1.0 O3' A:G425 4.8 64.3 1.0 OP2 A:G425 4.9 64.2 1.0

X.Ling, Y.Yao, J.Ma. Structures of A Natural Circularly Permuted Group II Intron Reveal Mechanisms of Branching and Backsplicing. Nat.Struct.Mol.Biol. 2025.
ISSN: ESSN 1545-9985
PubMed: 40016344
DOI: 10.1038/S41594-025-01489-6