Magnesium in PDB 1f27: Crystal Structure of A Biotin-Binding Rna Pseudoknot

The structure of Crystal Structure of A Biotin-Binding Rna Pseudoknot, PDB code: 1f27 was solved by J.Nix, D.Sussman, C.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.18 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	47.590, 30.960, 62.110, 90.00, 111.88, 90.00
R / Rfree (%)	19.9 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of A Biotin-Binding Rna Pseudoknot (pdb code 1f27). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of A Biotin-Binding Rna Pseudoknot, PDB code: 1f27:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of A Biotin-Binding Rna Pseudoknot


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 A Biotin-Binding Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg34 b:8.6 occ:0.49 O A:HOH200 2.0 13.9 0.7 O A:HOH201 2.0 14.3 0.7 O A:HOH171 2.0 26.4 1.0 O A:HOH163 2.1 15.4 1.0 O A:HOH43 2.2 10.0 1.0 O A:HOH199 2.5 14.2 0.4 O6 A:G19 4.0 9.8 1.0 O A:HOH83 4.1 16.8 0.8 O A:HOH103 4.2 19.9 0.8 N7 A:G18 4.2 9.2 1.0 N7 A:G19 4.4 8.4 1.0 O6 A:G18 4.4 9.1 1.0 O A:HOH198 4.5 12.4 1.0 O A:HOH197 4.6 13.9 0.5 C6 A:G19 4.9 9.0 1.0 C5 A:G18 4.9 7.5 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of A Biotin-Binding Rna Pseudoknot


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 A Biotin-Binding Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg35 b:19.3 occ:0.89 O A:HOH164 2.0 15.5 1.0 O A:HOH173 2.1 29.0 0.9 O A:HOH162 2.1 13.6 1.0 O4 A:U7 2.3 13.8 1.0 C4 A:U7 3.3 10.9 1.0 C5 A:U7 3.8 10.5 1.0 O A:HOH205 3.9 35.4 1.0 O A:HOH93 3.9 22.3 0.9 O6 A:G6 4.0 10.3 1.0 N7 A:G6 4.1 8.3 1.0 O A:HOH45 4.3 15.1 1.0 O A:HOH63 4.3 16.4 0.8 O A:HOH129 4.3 29.6 0.8 N6 A:A16 4.4 14.3 1.0 N3 A:U7 4.5 11.2 1.0 C6 A:G6 4.6 9.0 1.0 C5 A:G6 4.7 6.6 1.0 O A:HOH101 4.7 24.2 1.0 O A:HOH55 4.9 15.6 0.8

Magnesium binding site 3 out of 6 in the Crystal Structure of A Biotin-Binding Rna Pseudoknot


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 A Biotin-Binding Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg36 b:15.2 occ:0.92 OP2 A:A9 2.0 14.9 1.0 O A:HOH165 2.0 14.9 1.0 O A:HOH168 2.1 20.2 1.0 O A:HOH167 2.1 17.7 1.0 O A:HOH65 2.2 14.2 0.8 O A:HOH166 2.2 19.0 1.0 P A:A9 3.4 13.1 1.0 O A:HOH42 3.6 12.7 1.0 O A:HOH44 3.9 16.3 1.0 N7 A:G12 4.1 14.3 1.0 O A:HOH86 4.1 28.0 1.0 OP1 A:A9 4.2 15.9 1.0 O5' A:A9 4.3 16.5 1.0 O A:HOH211 4.3 39.6 1.0 O A:HOH183 4.3 38.8 1.0 C5' A:A9 4.3 21.4 1.0 OP2 A:G12 4.4 30.0 1.0 O A:HOH73 4.4 15.9 0.7 O3' A:C8 4.4 13.1 1.0 N7 A:G13 4.7 15.3 1.0 C8 A:G12 4.7 16.7 1.0 OP2 A:A11 4.8 30.0 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of A Biotin-Binding Rna Pseudoknot


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 A Biotin-Binding Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg37 b:52.2 occ:1.00 OP2 A:C8 1.9 15.1 1.0 O A:HOH203 2.0 17.8 0.5 O A:HOH202 2.0 18.2 0.5 O A:HOH172 2.1 23.7 0.8 O A:HOH170 2.2 20.5 1.0 O A:HOH105 2.3 18.1 0.7 P A:C8 3.3 13.9 1.0 O B:HOH187 3.9 43.9 1.0 O B:HOH46 4.0 17.6 1.0 C5' A:C8 4.0 12.7 1.0 O B:HOH53 4.0 15.4 1.0 O B:HOH208 4.1 45.2 1.0 OP1 A:C8 4.1 14.0 1.0 O5' A:C8 4.1 12.7 1.0 O3' A:U7 4.3 12.2 1.0 O A:HOH78 4.6 39.8 1.0 C3' A:U7 4.6 11.2 1.0 O A:HOH139 4.7 35.3 1.0 O B:HOH122 4.7 35.9 1.0 C5' A:U7 4.7 11.3 1.0 C4' A:U7 4.7 11.2 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of A Biotin-Binding Rna Pseudoknot


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 A Biotin-Binding Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg39 b:13.4 occ:0.64 O A:HOH198 2.0 12.4 1.0 O A:HOH169 2.0 26.7 1.0 O A:HOH197 2.2 13.9 0.5 O A:HOH137 3.9 39.7 1.0 O A:HOH61 3.9 19.1 1.0 O A:HOH199 3.9 14.2 0.4 O4 A:U20 4.2 9.2 1.0 O A:HOH43 4.3 10.0 1.0 O4 A:U21 4.4 9.7 1.0 C4 A:U20 5.0 8.1 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of A Biotin-Binding Rna Pseudoknot


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 A Biotin-Binding Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg38 b:8.3 occ:0.93 OP2 B:A25 2.0 10.2 1.0 O B:HOH158 2.0 9.2 1.0 O A:HOH160 2.1 9.3 1.0 O3 A:BTN33 2.1 11.3 1.0 O B:HOH161 2.1 9.7 0.9 O A:HOH159 2.1 10.9 1.0 C3 A:BTN33 3.1 10.9 1.0 P B:A25 3.3 11.3 1.0 N1 A:BTN33 3.6 12.1 1.0 O5' B:A25 3.7 11.7 1.0 N7 B:A26 4.0 10.7 1.0 O2' A:G6 4.1 9.4 1.0 OP1 B:A25 4.1 15.1 1.0 O B:HOH40 4.1 9.0 0.9 N2 A:G6 4.2 8.5 1.0 N3 A:G6 4.3 7.4 1.0 C8 B:A25 4.3 9.7 1.0 N7 B:A25 4.3 8.8 1.0 OP2 B:A24 4.3 10.9 1.0 N2 A:BTN33 4.3 12.6 1.0 O B:HOH60 4.3 18.4 1.0 OP2 B:A26 4.4 13.0 1.0 N6 B:A26 4.5 10.3 1.0 O3' B:A24 4.5 10.5 1.0 O A:HOH58 4.6 15.3 0.8 C2 A:G6 4.7 6.6 1.0 C3' B:A24 4.8 10.4 1.0 O B:HOH53 4.8 15.4 1.0 C2' A:G6 4.9 8.2 1.0 C8 B:A26 5.0 11.2 1.0 C5 B:A26 5.0 10.4 1.0

J.Nix, D.Sussman, C.Wilson. The 1.3 A Crystal Structure of A Biotin-Binding Pseudoknot and the Basis For Rna Molecular Recognition. J.Mol.Biol. V. 296 1235 2000.
ISSN: ISSN 0022-2836
PubMed: 10698630
DOI: 10.1006/JMBI.2000.3539