Calcium in PDB 8x9k: CTE_BRANCHING,Ca,Inactive

The structure of CTE_BRANCHING,Ca,Inactive also contains other interesting chemical elements:

Potassium

(K)

25 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the CTE_BRANCHING,Ca,Inactive (pdb code 8x9k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the CTE_BRANCHING,Ca,Inactive, PDB code: 8x9k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:32.1 occ:1.00 OP1 A:U218 2.3 53.3 1.0 OP2 A:U423 2.4 48.6 1.0 OP2 A:A422 2.4 45.6 1.0 P A:A422 3.7 39.9 1.0 P A:U218 3.7 46.3 1.0 P A:U423 3.8 41.9 1.0 O5' A:A422 4.0 49.3 1.0 OP1 A:A422 4.3 45.2 1.0 C4' A:A422 4.4 46.4 1.0 OP2 A:U218 4.4 55.6 1.0 O3' A:A422 4.6 48.8 1.0 O5' A:U218 4.6 55.8 1.0 OP1 A:U423 4.6 46.7 1.0 O3' A:G217 4.7 50.3 1.0 C5' A:U218 4.8 55.6 1.0 C5' A:A422 4.8 50.6 1.0 O5' A:U423 4.8 51.1 1.0 O3' A:C421 4.9 63.9 1.0 C3' A:A422 5.0 42.5 1.0

Calcium binding site 2 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:34.5 occ:1.00 OP1 A:A566 2.2 37.2 1.0 OP2 A:C569 2.2 49.4 1.0 OP1 A:G568 2.5 51.2 1.0 P A:A566 3.7 48.0 1.0 P A:C569 3.7 58.6 1.0 P A:G568 3.9 53.0 1.0 OP1 A:C569 4.4 59.1 1.0 OP2 A:G568 4.5 53.2 1.0 O5' A:C569 4.5 60.9 1.0 OP2 A:A566 4.5 51.8 1.0 O5' A:A566 4.5 57.2 1.0 O3' A:A565 4.5 31.8 1.0 O3' A:G568 4.6 51.7 1.0 C5' A:A566 4.6 49.1 1.0 O5' A:G568 4.7 51.2 1.0 C3' A:A567 4.7 38.6 1.0 C5' A:G568 4.8 49.3 1.0 C3' A:G568 4.8 47.2 1.0 O3' A:A567 4.9 41.8 1.0

Calcium binding site 3 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:35.4 occ:1.00 OP2 A:G523 2.4 48.5 1.0 OP2 A:G568 2.8 53.2 1.0 P A:G523 3.3 47.2 1.0 OP1 A:G523 3.4 34.4 1.0 O5' A:G523 4.0 47.3 1.0 OP1 A:A565 4.0 47.0 1.0 P A:G568 4.2 53.0 1.0 O3' A:A567 4.5 41.8 1.0 OP2 A:A566 4.7 51.8 1.0 O2' A:A567 4.7 45.2 1.0 O3' A:A522 4.7 48.3 1.0 N7 A:G568 4.8 53.4 1.0 O5' A:G568 5.0 51.2 1.0 C5' A:G523 5.0 41.0 1.0

Calcium binding site 4 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:43.0 occ:1.00 OP1 A:C620 2.3 55.6 1.0 OP1 A:C262 2.4 44.3 1.0 P A:C620 3.7 57.1 1.0 P A:C262 3.9 45.1 1.0 OP2 A:C263 4.0 47.4 1.0 OP1 A:G265 4.0 49.9 1.0 O5' A:C620 4.2 53.0 1.0 C5' A:C620 4.4 53.8 1.0 OP1 A:C263 4.4 48.2 1.0 OP2 A:C620 4.6 56.2 1.0 P A:C263 4.6 44.3 1.0 O5' A:C262 4.6 45.8 1.0 OP2 A:G265 4.7 44.0 1.0 O3' A:A261 4.7 55.4 1.0 C5' A:C262 4.7 43.5 1.0 OP2 A:C262 4.8 46.3 1.0 P A:G265 4.8 46.4 1.0 O3' A:C619 4.8 51.1 1.0 OP2 A:G621 4.8 55.3 1.0 O3' A:C262 5.0 41.1 1.0

Calcium binding site 5 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca905 b:84.0 occ:1.00 OP1 A:C81 2.4 47.3 1.0 OP2 A:G83 2.5 59.5 1.0 OP2 A:C81 3.1 52.4 1.0 P A:C81 3.1 32.9 1.0 OP2 A:G61 3.4 65.7 1.0 P A:G83 3.5 54.5 1.0 O3' A:U219 3.5 61.2 1.0 OP1 A:G83 3.6 52.9 1.0 OP2 A:G220 3.7 88.2 1.0 O3' A:G80 3.8 47.3 1.0 P A:G220 4.2 91.4 1.0 O2' A:U219 4.2 68.5 1.0 O5' A:G83 4.3 59.0 1.0 OP1 A:G61 4.4 68.1 1.0 P A:G61 4.4 80.3 1.0 O5' A:C81 4.5 44.2 1.0 C3' A:U219 4.6 61.6 1.0 OP1 A:G220 4.7 91.2 1.0 O3' A:U82 4.8 45.1 1.0 C3' A:G80 4.9 45.9 1.0 C4' A:U219 4.9 59.7 1.0 OP2 A:G84 5.0 47.1 1.0

Calcium binding site 6 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:67.6 occ:1.00 OP1 A:A225 2.4 42.4 1.0 OP2 A:C226 3.0 47.2 1.0 P A:A225 3.9 43.6 1.0 P A:C226 4.1 41.5 1.0 OP1 A:C226 4.3 43.7 1.0 O4' A:A628 4.3 46.0 1.0 O2' A:C85 4.5 47.2 1.0 C5' A:A225 4.6 43.4 1.0 O3' A:G224 4.6 45.2 1.0 O5' A:A225 4.7 47.1 1.0 O3' A:A225 4.7 41.0 1.0 OP2 A:A225 4.7 49.6 1.0

Calcium binding site 7 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca907 b:32.4 occ:1.00 OP2 A:A367 2.3 52.9 1.0 OP1 A:G366 2.3 50.3 1.0 OP2 A:G417 2.5 46.1 1.0 P A:A367 3.5 43.4 1.0 O5' A:A367 3.7 47.6 1.0 P A:G366 3.8 46.6 1.0 OP2 A:C416 3.8 43.3 1.0 P A:G417 4.0 50.3 1.0 O5' A:C416 4.0 45.5 1.0 P A:C416 4.2 40.6 1.0 OP1 A:C416 4.3 47.5 1.0 OP2 A:G366 4.5 49.8 1.0 C3' A:G366 4.5 46.1 1.0 O5' A:G366 4.5 49.3 1.0 O3' A:G366 4.6 51.8 1.0 OP1 A:A367 4.6 37.8 1.0 C5' A:G366 4.6 46.4 1.0 OP1 A:G417 4.6 54.9 1.0 O3' A:A365 4.8 48.1 1.0 C3' A:C416 4.8 34.9 1.0 O5' A:G417 4.8 48.8 1.0 O3' A:C416 4.9 38.8 1.0 C5' A:C416 4.9 43.1 1.0

Calcium binding site 8 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca908 b:65.6 occ:1.00 OP1 A:U494 2.4 56.8 1.0 OP2 A:G495 2.4 57.2 1.0 P A:U494 3.8 58.3 1.0 O2' A:U729 3.8 59.1 1.0 P A:G495 3.9 60.8 1.0 C5' A:U494 4.3 60.3 1.0 O5' A:U494 4.4 53.4 1.0 OP1 A:G495 4.6 65.0 1.0 O3' A:U494 4.6 54.0 1.0 OP2 A:U494 4.6 60.9 1.0 O3' A:G493 4.8 66.9 1.0 C3' A:U494 4.9 53.3 1.0 O5' A:G495 4.9 60.1 1.0

Calcium binding site 9 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca909 b:51.9 occ:1.00 OP1 A:G425 2.4 41.1 1.0 OP2 A:C426 2.6 44.5 1.0 P A:G425 3.8 43.8 1.0 P A:C426 4.1 46.6 1.0 O5' A:G425 4.4 47.8 1.0 C5' A:G425 4.5 49.9 1.0 OP2 A:U427 4.5 36.9 1.0 OP2 A:G425 4.7 45.5 1.0 O3' A:A424 4.8 47.5 1.0 OP1 A:C426 4.8 46.0 1.0 O5' A:C426 4.9 43.5 1.0

Calcium binding site 10 out of 12 in the CTE_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_BRANCHING,Ca,Inactive within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca910 b:73.3 occ:1.00 OP2 A:G224 2.9 47.9 1.0 OP1 A:A695 2.9 69.7 1.0 O4 A:U82 3.7 65.5 1.0 C3' A:G694 4.2 51.5 1.0 P A:A695 4.3 78.1 1.0 OP2 A:C223 4.3 52.3 1.0 P A:G224 4.3 51.1 1.0 C8 A:G224 4.5 46.4 1.0 N7 A:G224 4.5 46.2 1.0 OP1 A:C223 4.6 48.9 1.0 O3' A:G694 4.6 57.5 1.0 P A:C223 4.7 47.2 1.0 O5' A:G224 4.8 52.6 1.0 C2' A:G694 4.8 47.3 1.0 O5' A:C223 4.8 43.6 1.0 C4 A:U82 4.8 62.3 1.0 O2' A:G694 4.9 53.0 1.0 OP2 A:A695 5.0 71.8 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