Magnesium in PDB 2n3r: uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement

The binding sites of Magnesium atom in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement (pdb code 2n3r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement, PDB code: 2n3r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:0.0 occ:1.00 O A:HOH206 1.8 0.0 1.0 O A:HOH203 1.8 0.0 1.0 O A:HOH205 1.8 0.0 1.0 O A:HOH202 1.8 0.0 1.0 O A:HOH204 1.8 0.0 1.0 O A:HOH201 1.8 0.0 1.0 H42 A:C37 4.7 0.0 1.0 O6 A:G36 4.9 0.0 1.0

Magnesium binding site 2 out of 8 in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:0.0 occ:1.00 O A:HOH212 1.8 0.0 1.0 O A:HOH208 1.8 0.0 1.0 O A:HOH209 1.8 0.0 1.0 O A:HOH211 1.8 0.0 1.0 O A:HOH207 1.8 0.0 1.0 O A:HOH210 1.8 0.0 1.0 O6 A:G34 3.9 0.0 1.0 N7 A:G34 4.1 0.0 1.0 H2' A:A6 4.2 0.0 1.0 O2' A:A6 4.7 0.0 1.0 C6 A:G34 4.7 0.0 1.0 C5 A:G34 4.8 0.0 1.0 H41 A:C45 4.8 0.0 1.0 H4' A:A33 4.9 0.0 1.0 C2' A:A6 4.9 0.0 1.0 HO2' A:A6 4.9 0.0 1.0

Magnesium binding site 3 out of 8 in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:0.0 occ:1.00 O A:HOH218 1.8 0.0 1.0 O A:HOH215 1.8 0.0 1.0 O A:HOH217 1.8 0.0 1.0 O A:HOH214 1.8 0.0 1.0 O A:HOH216 1.8 0.0 1.0 O A:HOH213 1.8 0.0 1.0 H8 A:A6 4.4 0.0 1.0 O6 A:G47 4.6 0.0 1.0 C8 A:A6 4.6 0.0 1.0 H42 A:C48 4.7 0.0 1.0 N7 A:A6 4.8 0.0 1.0 OP1 A:A6 4.8 0.0 1.0 O5' A:A6 4.8 0.0 1.0 H5' A:A6 4.9 0.0 1.0 H62 A:A46 5.0 0.0 1.0

Magnesium binding site 4 out of 8 in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:0.0 occ:1.00 O A:HOH224 1.8 0.0 1.0 O A:HOH221 1.8 0.0 1.0 O A:HOH223 1.8 0.0 1.0 O A:HOH220 1.8 0.0 1.0 O A:HOH222 1.8 0.0 1.0 O A:HOH219 1.8 0.0 1.0 O6 A:G21 4.0 0.0 1.0 H41 A:C18 4.3 0.0 1.0 H42 A:C18 4.7 0.0 1.0 N4 A:C18 4.9 0.0 1.0 C6 A:G21 5.0 0.0 1.0

Magnesium binding site 5 out of 8 in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:0.0 occ:1.00 O A:HOH227 1.8 0.0 1.0 O A:HOH229 1.8 0.0 1.0 O A:HOH226 1.8 0.0 1.0 O A:HOH230 1.8 0.0 1.0 O A:HOH228 1.8 0.0 1.0 O A:HOH225 1.8 0.0 1.0 N7 A:G26 4.1 0.0 1.0 OP2 A:A25 4.3 0.0 1.0 O6 A:G26 4.4 0.0 1.0 H62 A:A27 4.5 0.0 1.0 C5 A:G26 4.9 0.0 1.0

Magnesium binding site 6 out of 8 in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:0.0 occ:1.00 O A:HOH236 1.8 0.0 1.0 O A:HOH233 1.8 0.0 1.0 O A:HOH232 1.8 0.0 1.0 O A:HOH235 1.8 0.0 1.0 O A:HOH234 1.8 0.0 1.0 O A:HOH231 1.8 0.0 1.0 H41 A:C50 4.1 0.0 1.0 H42 A:C50 4.4 0.0 1.0 OP2 A:G53 4.5 0.0 1.0 N4 A:C50 4.6 0.0 1.0

Magnesium binding site 7 out of 8 in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:0.0 occ:1.00 O A:HOH239 1.8 0.0 1.0 O A:HOH242 1.8 0.0 1.0 O A:HOH238 1.8 0.0 1.0 O A:HOH241 1.8 0.0 1.0 O A:HOH237 1.8 0.0 1.0 O A:HOH240 1.8 0.0 1.0 H41 A:C56 3.0 0.0 1.0 H42 A:C5 3.1 0.0 1.0 N4 A:C5 3.3 0.0 1.0 H41 A:C5 3.4 0.0 1.0 H42 A:C56 3.5 0.0 1.0 N4 A:C56 3.6 0.0 1.0 O6 A:G7 3.6 0.0 1.0 C4 A:C5 4.0 0.0 1.0 H5 A:C5 4.4 0.0 1.0 O6 A:G57 4.4 0.0 1.0 C6 A:G7 4.5 0.0 1.0 C5 A:C5 4.5 0.0 1.0 N3 A:C5 4.7 0.0 1.0 H1 A:G7 4.7 0.0 1.0 C4 A:C56 4.8 0.0 1.0

Magnesium binding site 8 out of 8 in the uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Vs Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:0.0 occ:1.00 O A:HOH245 1.8 0.0 1.0 O A:HOH248 1.8 0.0 1.0 O A:HOH244 1.8 0.0 1.0 O A:HOH246 1.8 0.0 1.0 O A:HOH247 1.8 0.0 1.0 O A:HOH243 1.8 0.0 1.0 H62 A:A10 3.6 0.0 1.0 N7 A:G9 3.7 0.0 1.0 O6 A:G9 3.7 0.0 1.0 N6 A:A10 3.8 0.0 1.0 C5 A:G9 3.9 0.0 1.0 C6 A:G9 4.0 0.0 1.0 H61 A:A10 4.2 0.0 1.0 C6 A:A10 4.3 0.0 1.0 H1 A:G53 4.3 0.0 1.0 C8 A:G9 4.5 0.0 1.0 N7 A:A10 4.5 0.0 1.0 C5 A:A10 4.5 0.0 1.0 O6 A:G53 4.7 0.0 1.0 C4 A:G9 4.9 0.0 1.0 H8 A:G9 4.9 0.0 1.0 N1 A:G9 4.9 0.0 1.0 H41 A:C54 5.0 0.0 1.0

E.Bonneau, N.Girard, S.Lemieux, P.Legault. The uc(Nmr) Structure of the II-III-VI Three-Way Junction From the Neurospora Vs Ribozyme Reveals A Critical Tertiary Interaction and Provides New Insights Into the Global Ribozyme Structure. Rna V. 21 1621 2015.
ISSN: ISSN 1355-8382
PubMed: 26124200
DOI: 10.1261/RNA.052076.115