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Magnesium in PDB 5t5a: Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom

Protein crystallography data

The structure of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom, PDB code: 5t5a was solved by D.M.J.Lilley, Y.Liu, T.J.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.16 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 39.304, 39.304, 228.413, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.7

Other elements in 5t5a:

The structure of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom (pdb code 5t5a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom, PDB code: 5t5a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5t5a

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Magnesium binding site 1 out of 9 in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:29.3
occ:1.00
 O A:HOH317 2.2 25.7 1.0
O A:HOH266 2.2 23.2 1.0
O A:HOH316 2.2 40.1 1.0
O A:HOH329 2.2 28.0 1.0
O A:HOH254 2.2 29.4 1.0
O2 A:DC54 2.3 25.4 1.0
C2 A:DC54 3.3 25.2 1.0
N3 A:DC54 3.6 24.0 1.0
N3 A:A9 4.1 21.3 1.0
O A:HOH323 4.4 23.2 1.0
O A:HOH320 4.4 28.4 1.0
N1 A:DC54 4.4 26.1 1.0
C4 A:A9 4.4 20.5 1.0
C1' A:A9 4.5 20.8 1.0
N9 A:A9 4.6 20.3 1.0
C2 A:A9 4.7 21.3 1.0
C1' A:DC54 4.7 27.9 1.0
C2' A:DC54 5.0 30.2 1.0
C4 A:DC54 5.0 24.7 1.0

Magnesium binding site 2 out of 9 in 5t5a

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Magnesium binding site 2 out of 9 in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:24.4
occ:1.00
 O A:HOH210 2.1 19.8 1.0
O A:HOH312 2.1 23.7 1.0
O A:HOH260 2.2 17.2 1.0
O A:HOH315 2.2 22.4 1.0
O A:HOH311 2.2 20.1 1.0
OP2 A:G27 2.2 22.5 1.0
P A:G27 3.5 22.1 1.0
O A:HOH245 4.0 19.9 1.0
OP1 A:G27 4.1 22.4 1.0
O A:HOH331 4.1 34.8 1.0
O A:HOH284 4.2 27.9 1.0
O A:HOH325 4.2 35.7 1.0
O A:HOH274 4.2 26.4 1.0
OP2 A:C28 4.2 19.8 1.0
C5' A:G27 4.2 22.7 1.0
O5' A:G27 4.3 21.4 1.0
O6 A:G21 4.4 19.4 1.0
N4 A:C20 4.4 19.4 1.0
O A:HOH278 4.6 22.9 1.0
O3' A:A26 4.6 22.1 1.0
O A:HOH302 4.7 39.6 1.0
C3' A:A26 4.7 21.0 1.0
C2' A:A26 4.8 21.2 1.0
N4 A:C29 4.9 16.3 1.0

Magnesium binding site 3 out of 9 in 5t5a

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Magnesium binding site 3 out of 9 in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:24.0
occ:1.00
 O A:HOH279 2.2 20.4 1.0
O A:HOH281 2.2 24.4 1.0
OP2 A:G10 2.2 19.6 1.0
O A:HOH259 2.2 28.6 1.0
O A:HOH226 2.2 22.6 1.0
OP2 A:A9 2.2 19.7 1.0
P A:A9 3.5 19.6 1.0
P A:G10 3.5 20.1 1.0
O5' A:A9 3.8 19.6 1.0
O5' A:G10 4.0 20.2 1.0
N4 A:C28 4.0 21.6 1.0
N3 A:C28 4.2 20.1 1.0
N7 A:G10 4.2 20.1 1.0
O A:HOH243 4.3 26.3 1.0
C3' A:A9 4.4 20.0 1.0
O A:HOH293 4.4 30.6 1.0
OP1 A:A9 4.4 19.6 1.0
C8 A:G10 4.4 20.2 1.0
O A:HOH227 4.4 28.1 1.0
O3' A:A9 4.5 20.2 1.0
O3' A:A8 4.5 19.4 1.0
C3' A:A8 4.5 19.8 1.0
OP1 A:G10 4.6 19.4 1.0
C4 A:C28 4.6 21.3 1.0
O A:HOH257 4.6 31.4 1.0
C5' A:A9 4.8 20.1 1.0
C8 A:A9 5.0 20.0 1.0
C4' A:A8 5.0 18.8 1.0

Magnesium binding site 4 out of 9 in 5t5a

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Magnesium binding site 4 out of 9 in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:36.0
occ:1.00
 O A:HOH294 2.2 38.5 1.0
O A:HOH267 2.2 45.4 1.0
O A:HOH253 2.2 34.2 1.0
O A:HOH224 2.2 33.9 1.0
OP2 A:G5 2.3 35.6 1.0
OP2 A:C52 2.3 25.9 1.0
P A:C52 3.5 25.7 1.0
P A:G5 3.7 33.8 1.0
O3' A:G51 3.9 25.4 1.0
O5' A:G5 4.2 33.0 1.0
O6 A:G6 4.2 28.8 1.0
N7 A:G5 4.4 26.5 1.0
OP1 A:C52 4.4 25.0 1.0
OP2 A:U53 4.4 23.6 1.0
C8 A:G5 4.4 27.2 1.0
N4 A:C7 4.4 24.8 1.0
N7 A:G6 4.4 27.9 1.0
OP1 A:G5 4.5 34.3 1.0
O5' A:C52 4.6 24.9 1.0
O3' A:G4 4.6 33.5 1.0
C3' A:G4 4.7 33.9 1.0
O2' A:G51 4.8 24.9 1.0
O5' A:G4 4.8 38.3 1.0
C3' A:G51 4.9 26.2 1.0
OP2 A:G4 4.9 37.8 1.0

Magnesium binding site 5 out of 9 in 5t5a

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Magnesium binding site 5 out of 9 in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:23.0
occ:1.00
 O A:HOH300 2.1 20.5 1.0
O A:HOH217 2.1 21.0 1.0
O A:HOH272 2.1 16.1 1.0
O A:HOH236 2.1 16.2 1.0
O A:HOH222 2.2 22.3 1.0
OP1 A:C28 2.3 19.9 1.0
P A:C28 3.5 20.2 1.0
O A:HOH223 3.9 26.6 1.0
O A:HOH278 3.9 22.9 1.0
O A:HOH220 4.0 25.6 1.0
N7 A:G30 4.2 18.2 1.0
OP2 A:G48 4.2 26.7 1.0
O6 A:G31 4.2 19.2 1.0
O A:HOH213 4.2 25.8 1.0
O5' A:C28 4.3 20.0 1.0
OP2 A:C28 4.3 19.8 1.0
O6 A:G30 4.4 17.9 1.0
N7 A:G31 4.4 18.8 1.0
O A:HOH218 4.5 29.9 1.0
O3' A:G27 4.5 21.5 1.0
C5' A:C28 4.5 20.8 1.0
N4 A:C29 4.7 16.3 1.0
O3' A:C47 4.7 25.1 1.0
C5 A:G30 4.9 17.9 1.0
C6 A:G30 5.0 18.1 1.0
C5 A:C29 5.0 17.9 1.0
C4 A:C29 5.0 18.5 1.0

Magnesium binding site 6 out of 9 in 5t5a

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Magnesium binding site 6 out of 9 in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:62.2
occ:1.00
 O A:HOH330 2.2 53.2 1.0
O A:HOH326 2.2 54.3 1.0
O A:HOH263 2.2 43.7 1.0
O A:HOH334 2.2 46.5 1.0
O A:HOH273 2.2 38.4 1.0
O A:HOH256 2.2 40.7 1.0
O A:HOH268 3.8 20.9 1.0
O A:HOH213 3.8 25.8 1.0
OP1 A:G48 3.9 26.8 1.0
O A:HOH262 4.0 31.9 1.0
O A:HOH307 4.0 42.3 1.0
O A:HOH258 4.0 32.4 1.0
O A:HOH218 4.2 29.9 1.0
N6 A:A33 4.4 24.0 1.0
N7 A:A33 4.7 26.5 1.0

Magnesium binding site 7 out of 9 in 5t5a

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Magnesium binding site 7 out of 9 in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:73.0
occ:1.00
 O A:HOH202 2.2 52.9 1.0
O A:HOH204 2.2 31.0 1.0
O A:HOH333 2.2 57.0 1.0
O A:HOH328 2.2 53.1 1.0
O A:HOH332 2.2 63.5 1.0
O A:HOH248 2.2 33.0 1.0
O6 A:G43 3.9 26.7 1.0
N7 A:G43 3.9 26.5 1.0
O A:HOH295 4.0 46.6 1.0
O A:HOH247 4.1 32.2 1.0
O6 A:G44 4.4 27.2 1.0
N7 A:G44 4.5 26.4 1.0
C5 A:G43 4.5 25.9 1.0
C6 A:G43 4.5 26.7 1.0
C8 A:G43 5.0 26.5 1.0

Magnesium binding site 8 out of 9 in 5t5a

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Magnesium binding site 8 out of 9 in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:35.5
occ:1.00
 OP1 A:C29 2.5 23.2 1.0
O A:HOH240 2.5 23.2 1.0
O6 A:G51 2.5 24.2 1.0
O A:HOH310 2.6 28.9 1.0
O A:HOH318 2.6 43.6 1.0
OP1 A:C7 2.7 25.1 1.0
O3' A:C28 3.6 22.4 1.0
P A:C29 3.6 23.9 1.0
C6 A:G51 3.7 23.7 1.0
P A:C7 3.7 25.9 1.0
O A:HOH211 3.7 44.1 1.0
OP1 A:A8 4.0 20.6 1.0
OP2 A:C7 4.2 25.8 1.0
O5' A:C7 4.2 25.2 1.0
O A:HOH271 4.3 22.6 1.0
N1 A:G51 4.4 23.6 1.0
O5' A:C29 4.5 24.6 1.0
C5' A:C29 4.5 24.0 1.0
C5' A:C7 4.6 24.8 1.0
C5 A:G51 4.7 24.1 1.0
O2' A:C28 4.8 21.2 1.0
OP2 A:C29 4.8 23.3 1.0
C3' A:C28 4.9 21.2 1.0

Magnesium binding site 9 out of 9 in 5t5a

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Magnesium binding site 9 out of 9 in the Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Twister Sister (Ts) Ribozyme at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg109

b:30.8
occ:1.00
 O A:HOH257 2.4 31.4 1.0
O A:HOH225 2.4 21.3 1.0
O6 A:G49 2.5 23.0 1.0
O2 A:C28 2.5 20.7 1.0
O A:HOH271 2.6 22.6 1.0
O A:HOH219 2.7 29.5 1.0
C6 A:G49 3.5 23.8 1.0
C2 A:C28 3.6 21.3 1.0
N4 A:C50 3.8 27.5 1.0
N7 A:G49 3.9 24.2 1.0
O A:HOH228 3.9 21.2 1.0
O A:HOH259 3.9 28.6 1.0
C5 A:G49 4.0 24.1 1.0
N3 A:C28 4.1 20.1 1.0
O6 A:G48 4.2 21.6 1.0
O A:HOH310 4.4 28.9 1.0
O A:HOH243 4.4 26.3 1.0
O6 A:G11 4.4 18.7 1.0
N4 A:C12 4.4 20.6 1.0
C4 A:C50 4.5 27.8 1.0
N1 A:C28 4.6 21.6 1.0
C1' A:C28 4.7 21.3 1.0
N1 A:G49 4.8 23.9 1.0
C5 A:C50 4.8 28.4 1.0
C6 A:G48 5.0 21.9 1.0

Reference:

Y.Liu, T.J.Wilson, D.M.Lilley. The Structure of A Nucleolytic Ribozyme That Employs A Catalytic Metal Ion. Nat. Chem. Biol. V. 13 508 2017.
ISSN: ESSN 1552-4469
PubMed: 28263963
DOI: 10.1038/NCHEMBIO.2333
Page generated: Mon Sep 30 04:43:46 2024

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