Calcium in PDB 4e8t: Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset), PDB code: 4e8t was solved by M.Marcia, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.61 / 3.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.458, 95.765, 225.688, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.5

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) also contains other interesting chemical elements:

Potassium

(K)

14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Calcium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) (pdb code 4e8t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 25 binding sites of Calcium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset), PDB code: 4e8t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:92.8 occ:1.00 OP2 A:C377 2.2 72.8 1.0 OP1 A:U375 2.4 78.6 1.0 O3' B:U6 2.5 0.0 1.0 P A:U375 3.1 79.6 1.0 OP1 B:U7 3.2 0.6 1.0 O2' B:U6 3.2 89.2 1.0 OP2 A:U375 3.2 80.0 1.0 P B:U7 3.4 0.9 1.0 P A:C377 3.5 78.7 1.0 C3' B:U6 3.6 98.9 1.0 C4' B:U6 3.8 93.2 1.0 O3' A:G374 3.8 82.7 1.0 OP1 A:G359 3.8 75.1 1.0 O5' A:C377 3.9 77.9 1.0 C2' B:U6 4.0 90.9 1.0 O5' B:U7 4.0 0.9 1.0 CA A:CA402 4.3 85.0 1.0 C5' A:C377 4.3 80.7 1.0 OP1 A:C377 4.4 82.9 1.0 O5' A:U375 4.6 61.8 1.0 OP2 A:G359 4.6 87.0 1.0 P A:G359 4.7 82.1 1.0 C5' B:U6 4.7 90.1 1.0 O3' A:A376 4.7 74.7 1.0 C3' A:A376 4.7 74.4 1.0 OP2 B:U7 4.7 0.9 1.0 C5' A:A376 4.8 59.5 1.0 O4' B:U6 4.8 90.9 1.0 C4' A:A376 4.9 67.0 1.0 C3' A:G374 5.0 76.9 1.0

Calcium binding site 2 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:85.0 occ:1.00 OP1 B:U7 2.0 0.6 1.0 OP1 A:C377 2.1 82.9 1.0 OP2 A:G359 2.2 87.0 1.0 OP1 A:C358 2.2 85.6 1.0 O B:HOH101 2.8 60.5 1.0 O B:HOH102 2.9 0.6 1.0 P A:C377 3.1 78.7 1.0 P B:U7 3.2 0.9 1.0 OP2 A:C377 3.3 72.8 1.0 P A:C358 3.4 87.3 1.0 O5' A:C358 3.5 84.8 1.0 O5' B:U7 3.5 0.9 1.0 P A:G359 3.5 82.1 1.0 C5' A:C358 3.9 81.9 1.0 K A:K433 3.9 79.1 1.0 O5' A:C377 4.0 77.9 1.0 OP1 A:G359 4.1 75.1 1.0 OP2 B:U7 4.2 0.9 1.0 CA A:CA401 4.3 92.8 1.0 C5' B:U7 4.3 0.4 1.0 O A:HOH936 4.3 57.1 1.0 O3' B:U6 4.3 0.0 1.0 O3' A:A376 4.4 74.7 1.0 OP2 A:C358 4.4 83.2 1.0 O5' A:G359 4.4 82.5 1.0 O3' A:C357 4.6 89.5 1.0 O3' A:C358 4.6 84.7 1.0

Calcium binding site 3 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:0.8 occ:1.00 OP2 A:G374 2.3 81.8 1.0 OP1 A:C360 2.3 91.4 1.0 P A:C360 3.6 86.4 1.0 P A:G374 3.7 89.0 1.0 O A:HOH924 3.9 60.1 1.0 OP2 A:C360 4.0 86.3 1.0 C5' A:G374 4.2 73.9 1.0 O5' A:C360 4.4 90.6 1.0 O5' A:G374 4.5 77.2 1.0 C5' A:C360 4.6 92.5 1.0 OP2 A:G373 4.6 0.6 1.0 O3' A:G373 4.6 85.7 1.0 OP1 A:G374 4.7 86.1 1.0 O3' A:G359 4.7 80.3 1.0 C3' A:G373 4.7 79.9 1.0 O5' A:G373 4.8 84.1 1.0

Calcium binding site 4 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:0.1 occ:1.00 O6 A:G325 2.5 0.4 1.0 O A:HOH905 3.5 78.7 1.0 C6 A:G325 3.5 0.9 1.0 N7 A:G324 3.7 0.1 1.0 O6 A:G324 3.8 0.5 1.0 C5 A:G325 4.3 0.1 1.0 C5 A:G324 4.4 0.6 1.0 N7 A:G325 4.5 0.8 1.0 C6 A:G324 4.5 0.5 1.0 N1 A:G325 4.5 0.8 1.0 C8 A:G324 4.7 0.8 1.0 OP2 A:G324 4.8 1.0 1.0 OP2 A:C323 4.9 0.3 1.0

Calcium binding site 5 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:0.1 occ:1.00 O A:HOH912 2.4 65.2 1.0 O6 A:G46 3.4 93.8 1.0 OP2 A:U59 3.9 63.5 1.0 N7 A:G46 4.0 93.7 1.0 O4 A:U45 4.1 80.6 1.0 C6 A:G46 4.3 87.7 1.0 O4 A:U47 4.3 66.0 1.0 C5 A:U45 4.5 84.2 1.0 C4 A:U45 4.5 79.4 1.0 C5 A:G46 4.5 89.9 1.0 O2' A:G58 4.9 72.3 1.0 P A:U59 5.0 76.9 1.0

Calcium binding site 6 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:85.8 occ:1.00 OP1 A:G107 2.2 75.6 1.0 OP1 A:G108 2.7 65.7 1.0 C5' A:G107 3.5 70.1 1.0 P A:G107 3.5 75.2 1.0 O5' A:G107 3.9 66.3 1.0 C5 A:C261 4.0 86.9 1.0 P A:G108 4.1 79.9 1.0 O3' A:A106 4.4 87.4 1.0 C6 A:C261 4.4 81.7 1.0 N7 A:A105 4.5 95.8 1.0 OP2 A:G108 4.6 72.3 1.0 OP2 A:G107 4.7 73.9 1.0 C4' A:G107 4.7 72.1 1.0 O3' A:G107 4.8 75.4 1.0 C8 A:A105 4.9 0.1 1.0 C3' A:G107 5.0 73.1 1.0 C3' A:G108 5.0 70.9 1.0

Calcium binding site 7 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:0.1 occ:1.00 OP2 A:C372 3.0 0.5 1.0 O6 A:G373 3.4 77.5 1.0 N7 A:G373 4.1 76.4 1.0 C6 A:G373 4.3 68.5 1.0 O6 A:G374 4.3 68.5 1.0 P A:C372 4.3 91.3 1.0 OP1 A:A371 4.4 85.4 1.0 C5 A:G373 4.6 70.9 1.0 O5' A:A371 4.6 95.1 1.0 OP2 A:A371 4.6 85.0 1.0 O5' A:C372 4.7 82.2 1.0 N7 A:G374 4.8 63.8 1.0 P A:A371 4.8 89.4 1.0 C5 A:C372 5.0 69.1 1.0

Calcium binding site 8 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:92.2 occ:1.00 OP1 A:G239 2.3 75.9 1.0 OP1 A:C119 2.4 99.6 1.0 P A:G239 3.4 77.2 1.0 O3' A:U238 3.8 79.8 1.0 OP1 A:A174 3.9 70.7 1.0 P A:C119 3.9 78.8 1.0 OP2 A:G239 4.4 83.0 1.0 C5' A:C119 4.4 62.4 1.0 O5' A:G239 4.5 70.5 1.0 O5' A:C119 4.6 71.2 1.0 O3' A:G118 4.6 78.4 1.0 C5' A:G239 4.7 72.2 1.0 OP2 A:A120 4.8 80.4 1.0 OP1 A:U238 4.9 87.8 1.0 OP2 A:C119 4.9 77.5 1.0

Calcium binding site 9 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:0.8 occ:1.00 OP2 A:A186 2.4 0.4 1.0 P A:A186 3.8 99.1 1.0 O5' A:C185 4.4 85.3 1.0 O5' A:A186 4.5 88.7 1.0 OP1 A:A186 4.6 94.8 1.0 C3' A:C185 4.8 90.7 1.0 O3' A:C185 4.8 96.2 1.0 N7 A:A187 4.9 91.3 1.0 N7 A:A186 4.9 0.7 1.0 C8 A:A186 5.0 99.2 1.0

Calcium binding site 10 out of 25 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, CA2+ and An Oligonucleotide Fragment Substrate (Low Energy Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca410 b:0.2 occ:1.00 OP1 A:A105 4.3 76.1 1.0 O6 A:G75 4.9 0.8 1.0

M.Marcia, A.M.Pyle. Visualizing Group II Intron Catalysis Through the Stages of Splicing. Cell(Cambridge,Mass.) V. 151 497 2012.
ISSN: ISSN 0092-8674
PubMed: 23101623
DOI: 10.1016/J.CELL.2012.09.033