Calcium in PDB 8olw: Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B

Protein crystallography data

The structure of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B, PDB code: 8olw was solved by I.Silvestri, M.Marcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.68 / 4.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.147, 94.133, 222.878, 90, 90, 90
R / Rfree (%) 22 / 25.8

Other elements in 8olw:

The structure of Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B also contains other interesting chemical elements:

Potassium (K) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B (pdb code 8olw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B, PDB code: 8olw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 8olw

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Calcium binding site 1 out of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B


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 Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:238.1
occ:1.00
 CA A:CA402 2.0 238.8 1.0
OP1 A:G1 2.2 241.8 1.0
OP2 A:C377 2.3 162.1 1.0
O5' A:G1 2.3 275.4 1.0
P A:G1 2.4 262.6 1.0
OP2 A:G359 2.6 209.5 1.0
O3' A:U0 2.6 215.0 1.0
O A:HOH507 2.7 139.5 1.0
OP1 A:C377 3.0 177.2 1.0
P A:C377 3.1 168.3 1.0
OP1 A:G359 3.4 228.6 1.0
P A:G359 3.4 207.8 1.0
C5' A:G1 3.5 279.6 1.0
O2' A:U0 3.9 203.4 1.0
OP2 A:G1 3.9 298.0 1.0
C3' A:U0 4.0 207.3 1.0
OP1 A:C358 4.1 192.4 1.0
O3' A:A376 4.2 172.8 1.0
O5' A:C377 4.4 172.6 1.0
C2' A:U0 4.4 209.8 1.0
O5' A:G359 4.5 195.1 1.0
O5' A:C358 4.6 209.6 1.0
OP1 A:U375 4.6 170.3 1.0
O3' A:C358 4.7 199.2 1.0
C4' A:G1 4.7 277.6 1.0
K A:K418 4.8 179.8 1.0
C3' A:A376 4.9 178.1 1.0
P A:C358 4.9 193.9 1.0
C4' A:U0 5.0 208.2 1.0

Calcium binding site 2 out of 9 in 8olw

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Calcium binding site 2 out of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B


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 Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:238.8
occ:1.00
 CA A:CA401 2.0 238.1 1.0
OP1 A:C358 2.1 192.4 1.0
OP2 A:G359 2.2 209.5 1.0
OP1 A:C377 2.3 177.2 1.0
O A:HOH507 2.5 139.5 1.0
O5' A:G1 2.8 275.4 1.0
O5' A:C358 3.1 209.6 1.0
P A:C358 3.1 193.9 1.0
P A:C377 3.3 168.3 1.0
OP2 A:C377 3.3 162.1 1.0
P A:G359 3.6 207.8 1.0
OP1 A:G1 3.7 241.8 1.0
C5' A:G1 3.7 279.6 1.0
P A:G1 3.8 262.6 1.0
C5' A:C358 3.8 215.9 1.0
OP2 A:C358 4.0 189.8 1.0
K A:K418 4.1 179.8 1.0
OP1 A:G359 4.3 228.6 1.0
O3' A:U0 4.3 215.0 1.0
O3' A:A376 4.3 172.8 1.0
O3' A:C357 4.3 193.0 1.0
O5' A:C377 4.5 172.6 1.0
O3' A:C358 4.5 199.2 1.0
C4' A:G1 4.5 277.6 1.0
O5' A:G359 4.6 195.1 1.0
C4' A:C358 4.8 215.6 1.0
C3' A:C358 4.9 202.9 1.0

Calcium binding site 3 out of 9 in 8olw

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Calcium binding site 3 out of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B


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 Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:186.7
occ:1.00
 OP2 A:G374 2.5 169.4 1.0
OP1 A:C360 2.7 170.0 1.0
OP2 A:C360 3.5 167.1 1.0
P A:C360 3.6 170.7 1.0
P A:G374 4.0 179.2 1.0
N7 A:G374 4.2 195.9 1.0
C5' A:G374 4.2 183.3 1.0
C8 A:G374 4.3 188.6 1.0
O5' A:C360 4.5 185.2 1.0
O5' A:G373 4.5 210.7 1.0
OP2 A:G373 4.6 215.5 1.0
C3' A:G373 4.6 209.2 1.0
O5' A:G374 4.6 180.3 1.0
O3' A:G373 4.8 197.5 1.0
OP2 A:C361 5.0 217.6 1.0
O3' A:G359 5.0 175.5 1.0

Calcium binding site 4 out of 9 in 8olw

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Calcium binding site 4 out of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B


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 Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:184.6
occ:1.00
 O A:HOH501 1.9 162.8 1.0
O4 A:U45 3.2 185.1 1.0
O6 A:G46 3.5 155.9 1.0
OP2 A:U59 3.6 138.0 1.0
C4 A:U45 4.0 193.9 1.0
C5 A:U45 4.3 204.2 1.0
C6 A:G46 4.5 154.0 1.0
O4 A:U47 4.5 129.2 1.0
N7 A:G46 4.7 176.7 1.0
P A:U59 4.7 142.8 1.0
OP1 A:U59 4.8 140.6 1.0
C5 A:G46 5.0 166.3 1.0

Calcium binding site 5 out of 9 in 8olw

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Calcium binding site 5 out of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B


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 Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:201.7
occ:1.00
 OP1 A:G239 2.0 186.0 1.0
P A:G239 3.3 196.4 1.0
OP1 A:C119 3.4 200.4 1.0
OP2 A:A120 3.7 224.1 1.0
OP2 A:G239 3.9 208.4 1.0
OP1 A:A174 3.9 180.5 1.0
C5' A:C119 4.0 200.0 1.0
O3' A:U238 4.2 189.9 1.0
P A:A120 4.4 224.6 1.0
P A:C119 4.5 186.1 1.0
O5' A:G239 4.5 193.4 1.0
O5' A:C119 4.5 188.3 1.0
OP1 A:A120 4.5 248.2 1.0
O3' A:C119 4.5 209.8 1.0
OP1 A:U238 4.7 268.0 1.0
C5' A:G239 4.8 193.8 1.0

Calcium binding site 6 out of 9 in 8olw

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Calcium binding site 6 out of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B


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 Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:265.5
occ:1.00
 O A:HOH505 1.9 172.3 1.0
O A:HOH506 2.2 208.5 1.0
O A:HOH504 2.6 221.0 1.0
OP2 A:A154 2.6 240.3 1.0
O6 A:G156 3.3 226.5 1.0
O4 A:U221 3.5 267.1 1.0
P A:A154 3.7 254.8 1.0
OP1 A:A154 3.9 253.8 1.0
N7 A:G155 4.0 238.0 1.0
O6 A:G155 4.0 233.1 1.0
N4 A:C157 4.2 224.4 1.0
C6 A:G156 4.4 230.8 1.0
C4 A:U221 4.4 269.4 1.0
N3 A:U221 4.5 263.2 1.0
N7 A:G156 4.5 251.3 1.0
C6 A:G155 4.6 230.2 1.0
C5 A:G155 4.6 235.6 1.0
O3' A:G153 4.6 268.9 1.0
O6 A:G220 4.8 269.9 1.0
C5 A:G156 4.9 237.1 1.0
O2' A:G153 5.0 281.4 1.0
C8 A:G155 5.0 245.3 1.0
O5' A:A154 5.0 264.5 1.0
OP2 A:G155 5.0 269.3 1.0

Calcium binding site 7 out of 9 in 8olw

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Calcium binding site 7 out of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B


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 Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:189.8
occ:1.00
 O4 A:U65 3.0 250.1 1.0
N7 A:G64 3.8 195.1 1.0
C4 A:U65 4.0 242.5 1.0
OP2 A:A63 4.2 177.1 1.0
O6 A:G64 4.3 217.2 1.0
C5 A:U65 4.5 249.2 1.0
C5 A:G64 4.7 191.7 1.0
N7 A:A63 4.7 187.5 1.0
OP2 A:G64 4.7 209.0 1.0
C8 A:G64 4.7 197.1 1.0
C6 A:G64 4.9 191.9 1.0

Calcium binding site 8 out of 9 in 8olw

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Calcium binding site 8 out of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B


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 Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:195.5
occ:1.00
 O A:HOH509 2.3 174.7 1.0
OP2 A:A283 2.4 199.6 1.0
O6 A:G284 3.5 165.5 1.0
P A:A283 3.8 198.0 1.0
N7 A:G284 3.9 180.1 1.0
N7 A:A283 4.1 210.1 1.0
C6 A:G284 4.3 166.1 1.0
O5' A:A283 4.4 198.7 1.0
OP1 A:A283 4.4 192.4 1.0
C8 A:A283 4.4 210.4 1.0
C5 A:G284 4.5 171.8 1.0
OP2 A:A282 4.9 191.7 1.0
O5' A:A282 4.9 196.6 1.0
C3' A:A282 5.0 187.1 1.0
O3' A:A282 5.0 189.8 1.0

Calcium binding site 9 out of 9 in 8olw

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Calcium binding site 9 out of 9 in the Structure of Oceanobacillus Iheyensis Group II Intron Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B


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 Before the First Step of Splicing in the Presence of K+, CA2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:209.9
occ:1.00
 OP1 A:A49 3.3 152.2 1.0
C5' A:A49 4.3 162.3 1.0
P A:A49 4.7 151.5 1.0
O5' A:A49 5.0 158.1 1.0

Reference:

I.Silvestri, J.Manigrasso, A.Andreani, N.Brindani, C.Mas, J.B.Reiser, P.Vidossich, G.Martino, A.Mccarthy, M.De Vivo, M.Marcia. Targeting the Conserved Active Site of Splicing Machines with Specific and Selective Small Molecule Modulators Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-48697-0
Page generated: Fri Jul 19 11:00:58 2024

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