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Magnesium in PDB 5dun: The Crystal Structure of Ome Substituted Twister Ribozyme

Protein crystallography data

The structure of The Crystal Structure of Ome Substituted Twister Ribozyme, PDB code: 5dun was solved by A.Ren, D.J.Patel, R.Micura, K.R.Rajashankar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.52 / 2.64
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 46.819, 46.819, 143.751, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 25.2

Other elements in 5dun:

The structure of The Crystal Structure of Ome Substituted Twister Ribozyme also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 5dun

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Magnesium binding site 1 out of 8 in the The Crystal Structure of Ome Substituted Twister Ribozyme


Mono view


Stereo pair view

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

b:29.9
occ:1.00
 O A:HOH218 2.1 37.3 1.0
O A:HOH206 2.1 33.5 1.0
O A:HOH210 2.1 32.9 1.0
OP1 A:A6 2.1 32.5 1.0
OP2 A:A7 2.1 36.2 1.0
O4 A:U8 2.1 40.4 1.0
C4 A:U8 3.2 33.9 1.0
P A:A7 3.4 33.5 1.0
P A:A6 3.5 40.8 1.0
C5 A:U8 3.7 34.1 1.0
OP1 A:A7 3.8 49.5 1.0
C5' A:A6 3.9 34.9 1.0
O5' A:A6 4.0 41.5 1.0
N6 A:A47 4.2 32.1 1.0
C3' A:A6 4.2 29.1 1.0
O3' A:OMU5 4.2 40.2 1.0
O3' A:A6 4.3 31.1 1.0
N3 A:U8 4.4 34.6 1.0
C4' A:A6 4.4 29.5 1.0
O6 A:G9 4.5 38.9 1.0
O5' A:A7 4.6 34.8 1.0
OP2 A:A6 4.6 38.4 1.0
N2 A:G48 4.7 32.5 1.0
O4 A:U45 4.7 20.0 1.0

Magnesium binding site 2 out of 8 in 5dun

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Magnesium binding site 2 out of 8 in the The Crystal Structure of Ome Substituted Twister Ribozyme


Mono view


Stereo pair view

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

b:21.3
occ:1.00
 O A:HOH203 2.1 34.5 1.0
O A:HOH214 2.1 32.6 1.0
O A:HOH207 2.1 30.7 1.0
O A:HOH204 2.1 32.3 1.0
OP2 A:A42 2.1 35.8 1.0
OP2 A:A43 2.1 31.9 1.0
P A:A42 3.4 37.2 1.0
P A:A43 3.6 34.5 1.0
O5' A:A42 3.8 29.2 1.0
O3' A:U41 4.0 38.0 1.0
OP2 A:C39 4.3 34.4 1.0
OP1 A:A43 4.3 46.8 1.0
O3' A:A42 4.4 32.1 1.0
C3' A:A42 4.4 33.1 1.0
C5' A:A42 4.5 35.0 1.0
OP2 A:C40 4.5 30.6 1.0
O5' A:A43 4.6 34.7 1.0
OP1 A:A42 4.6 47.8 1.0
N7 A:A43 4.9 31.0 1.0
C8 A:A43 5.0 34.6 1.0

Magnesium binding site 3 out of 8 in 5dun

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Magnesium binding site 3 out of 8 in the The Crystal Structure of Ome Substituted Twister Ribozyme


Mono view


Stereo pair view

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

b:31.9
occ:1.00
 O A:HOH212 2.1 31.1 1.0
O4 A:U30 2.1 34.3 1.0
OP2 A:A35 2.1 31.0 1.0
C4 A:U30 3.3 28.6 1.0
P A:A35 3.6 35.9 1.0
C5 A:U30 4.1 26.5 1.0
OP1 A:A35 4.4 34.4 1.0
O5' A:A35 4.4 29.4 1.0
N3 A:U30 4.4 28.8 1.0
O6 A:G29 4.5 33.2 1.0
N7 A:A6 4.6 31.7 1.0
N7 A:G29 4.6 32.5 1.0
O3' A:A34 4.6 34.5 1.0
C8 A:A35 4.8 29.4 1.0

Magnesium binding site 4 out of 8 in 5dun

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Magnesium binding site 4 out of 8 in the The Crystal Structure of Ome Substituted Twister Ribozyme


Mono view


Stereo pair view

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

b:41.5
occ:1.00
 N7 A:G27 1.9 29.1 1.0
O A:HOH220 2.1 28.2 1.0
O A:HOH217 2.1 32.9 1.0
O A:HOH202 2.1 28.6 1.0
O A:HOH215 2.1 24.8 1.0
O A:HOH209 2.1 36.4 1.0
O6 A:G27 2.1 41.6 1.0
C5 A:G27 2.5 26.5 1.0
C6 A:G27 2.6 32.1 1.0
C8 A:G27 3.2 31.7 1.0
C4 A:G27 3.8 31.0 1.0
N7 A:A26 3.9 33.0 1.0
O6 A:G28 4.0 34.7 1.0
N1 A:G27 4.0 31.9 1.0
C5 A:A26 4.1 29.7 1.0
N9 A:G27 4.1 31.2 1.0
OP2 A:A26 4.2 32.3 1.0
N6 A:A26 4.2 29.7 1.0
C6 A:A26 4.3 31.8 1.0
N7 A:G28 4.3 27.3 1.0
C8 A:A26 4.5 33.6 1.0
C6 A:G28 4.7 31.6 1.0
N4 A:C40 4.8 29.7 1.0
C4 A:A26 4.8 27.6 1.0
C5 A:G28 4.9 28.5 1.0
OP2 A:G27 4.9 34.1 1.0
N3 A:G27 5.0 33.3 1.0
C2 A:G27 5.0 31.7 1.0

Magnesium binding site 5 out of 8 in 5dun

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Magnesium binding site 5 out of 8 in the The Crystal Structure of Ome Substituted Twister Ribozyme


Mono view


Stereo pair view

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

b:50.6
occ:1.00
 O A:HOH211 2.1 39.3 1.0
O A:HOH216 2.1 30.5 1.0
O A:HOH219 2.1 36.5 1.0
O6 A:G52 2.1 40.5 1.0
C6 A:G52 3.2 33.4 1.0
O6 A:G51 3.6 34.4 1.0
N7 A:G52 3.6 36.9 1.0
C5 A:G52 3.8 35.0 1.0
O6 A:G53 3.9 40.9 1.0
C6 A:G51 4.2 32.4 1.0
N7 A:G51 4.3 35.6 1.0
O4 A:U3 4.4 34.8 1.0
N1 A:G52 4.5 33.2 1.0
C5 A:G51 4.5 33.0 1.0
N4 A:C31 4.7 29.9 1.0
C6 A:G53 4.8 38.3 1.0
C8 A:G52 4.9 37.3 1.0
C4 A:U3 5.0 30.3 1.0

Magnesium binding site 6 out of 8 in 5dun

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Magnesium binding site 6 out of 8 in the The Crystal Structure of Ome Substituted Twister Ribozyme


Mono view


Stereo pair view

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

b:44.1
occ:1.00
 O A:HOH208 2.1 30.5 1.0
OP1 A:C32 2.1 33.1 1.0
OP2 A:U30 2.1 29.5 1.0
O3' A:C31 2.1 34.5 1.0
P A:C32 2.5 31.2 1.0
P A:U30 3.3 35.2 1.0
C3' A:C31 3.5 31.0 1.0
OP2 A:C32 3.5 32.3 1.0
O5' A:U30 3.6 33.2 1.0
O5' A:C32 3.7 34.5 1.0
C5' A:C32 3.9 29.4 1.0
C5 A:U30 4.1 26.5 1.0
C4' A:C31 4.1 26.3 1.0
OP1 A:U30 4.2 38.9 1.0
C6 A:U30 4.3 27.1 1.0
O2' A:C31 4.4 30.5 1.0
C5' A:C31 4.4 27.1 1.0
C2' A:C31 4.5 32.2 1.0
O3' A:G29 4.6 38.4 1.0
C3' A:G29 4.9 32.8 1.0
N6 A:A6 5.0 32.4 1.0
C5' A:U30 5.0 30.0 1.0

Magnesium binding site 7 out of 8 in 5dun

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Magnesium binding site 7 out of 8 in the The Crystal Structure of Ome Substituted Twister Ribozyme


Mono view


Stereo pair view

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

b:43.7
occ:1.00
 OP1 A:A7 2.1 49.5 1.0
OP2 A:U8 2.1 42.5 1.0
O5' A:A7 2.2 34.8 1.0
P A:A7 2.7 33.5 1.0
C5' A:A7 3.3 31.5 1.0
P A:U8 3.4 34.3 1.0
O3' A:A7 3.6 32.6 1.0
OP2 A:A7 3.7 36.2 1.0
C3' A:A7 3.8 32.1 1.0
O3' A:A6 3.9 31.1 1.0
C4' A:A7 4.0 33.2 1.0
O A:HOH206 4.1 33.5 1.0
C5 A:U8 4.4 34.1 1.0
O5' A:U8 4.4 40.3 1.0
OP1 A:U8 4.5 33.7 1.0
C6 A:U8 4.9 37.9 1.0
C4' A:A35 4.9 32.3 1.0

Magnesium binding site 8 out of 8 in 5dun

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Magnesium binding site 8 out of 8 in the The Crystal Structure of Ome Substituted Twister Ribozyme


Mono view


Stereo pair view

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

b:43.4
occ:1.00
 OP2 A:A55 2.1 34.8 1.0
P A:A55 3.5 39.2 1.0
OP1 A:A55 4.2 37.4 1.0
O5' A:A54 4.3 32.0 1.0
O3' A:A54 4.3 37.8 1.0
OP1 A:A54 4.5 39.2 1.0
OP2 A:A54 4.6 34.3 1.0
O5' A:A55 4.7 31.3 1.0
P A:A54 4.7 35.5 1.0
C3' A:A54 4.7 30.9 1.0
C5' A:A54 5.0 30.0 1.0

Reference:

M.Kosutic, S.Neuner, A.Ren, S.Flur, C.Wunderlich, E.Mairhofer, N.Vusurovic, J.Seikowski, K.Breuker, C.Hobartner, D.J.Patel, C.Kreutz, R.Micura. A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of This Ribozyme Class. Angew.Chem.Int.Ed.Engl. V. 54 15128 2015.
ISSN: ESSN 1521-3773
PubMed: 26473980
DOI: 10.1002/ANIE.201506601
Page generated: Mon Dec 14 20:13:17 2020

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