Magnesium in PDB 9cxf: Cryo-Em Structure of the Rail Rna Motif

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Rail Rna Motif (pdb code 9cxf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 22 binding sites of Magnesium where determined in the Cryo-Em Structure of the Rail Rna Motif, PDB code: 9cxf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg300 b:74.5 occ:1.00 N7 A:G20 3.8 80.9 1.0 C8 A:G20 4.5 80.9 1.0 OP2 A:A22 4.5 78.8 1.0 O6 A:G20 4.6 80.9 1.0 C5 A:G20 4.6 80.9 1.0 OP2 A:U19 4.8 82.5 1.0 OP1 A:A22 4.8 78.8 1.0 C6 A:G20 4.9 80.9 1.0 OP2 A:G20 4.9 80.9 1.0

Magnesium binding site 2 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:62.0 occ:1.00 N7 A:G17 4.4 80.9 1.0 O6 A:G17 4.5 80.9 1.0 OP1 A:G24 4.7 66.8 1.0 O2' A:A23 4.8 71.5 1.0 O4 A:U18 4.9 82.4 1.0

Magnesium binding site 3 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:64.4 occ:1.00 OP1 A:C80 2.0 59.8 1.0 OP1 A:U82 2.6 57.0 1.0 P A:C80 3.3 59.8 1.0 OP2 A:C80 3.7 59.8 1.0 P A:U82 3.8 57.0 1.0 OP2 A:U82 4.2 57.0 1.0 O5' A:C80 4.3 59.8 1.0 O3' A:G79 4.3 64.8 1.0 C5' A:C80 4.5 59.8 1.0 O5' A:U82 4.6 57.0 1.0 C5' A:U82 4.7 57.0 1.0 O6 A:G84 4.9 57.6 1.0 O3' A:A81 5.0 58.2 1.0

Magnesium binding site 4 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:53.4 occ:1.00 OP2 A:U82 1.9 57.0 1.0 P A:U82 3.3 57.0 1.0 O5' A:U82 3.7 57.0 1.0 OP1 A:U50 3.9 59.0 1.0 O3' A:A81 4.2 58.2 1.0 OP2 A:U50 4.3 59.0 1.0 O2' A:A33 4.3 58.1 1.0 OP1 A:U82 4.3 57.0 1.0 N7 A:G84 4.4 57.6 1.0 O6 A:G84 4.5 57.6 1.0 OP1 A:C51 4.6 60.2 1.0 P A:U50 4.6 59.0 1.0 OP2 A:C80 4.8 59.8 1.0 O2' A:A81 4.8 58.2 1.0

Magnesium binding site 5 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:68.6 occ:1.00 OP1 A:G79 2.8 64.8 1.0 OP1 A:C51 3.4 60.2 1.0 P A:G79 4.2 64.8 1.0 C5' A:C51 4.4 60.2 1.0 O3' A:A78 4.5 69.3 1.0 O3' A:U50 4.5 59.0 1.0 P A:C51 4.6 60.2 1.0 OP2 A:C52 4.6 67.2 1.0 OP1 A:U50 4.9 59.0 1.0 C5' A:U50 4.9 59.0 1.0 OP2 A:G79 4.9 64.8 1.0

Magnesium binding site 6 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:57.0 occ:1.00 OP2 A:C51 2.2 60.2 1.0 P A:C51 3.7 60.2 1.0 OP1 A:G83 4.3 57.3 1.0 O2' A:U82 4.3 57.0 1.0 O5' A:C51 4.4 60.2 1.0 C3' A:U50 4.5 59.0 1.0 OP1 A:C51 4.5 60.2 1.0 OP2 A:G185 4.5 64.9 1.0 O3' A:U50 4.6 59.0 1.0 N3 A:A81 4.6 58.2 1.0 O3' A:A184 4.8 60.2 1.0 O4' A:A184 4.9 60.2 1.0 C2' A:U82 4.9 57.0 1.0 C6 A:U50 5.0 59.0 1.0 C1' A:A184 5.0 60.2 1.0

Magnesium binding site 7 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:49.1 occ:1.00 OP2 A:G83 4.1 57.3 1.0 OP2 A:A49 4.1 57.0 1.0 O4' A:G84 4.6 57.6 1.0 OP2 A:G185 4.6 64.9 1.0 O4 A:U50 4.8 59.0 1.0 C1' A:G84 4.9 57.6 1.0 P A:G83 4.9 57.3 1.0 O5' A:G83 5.0 57.3 1.0

Magnesium binding site 8 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:59.2 occ:1.00 OP1 A:U85 2.1 55.1 1.0 P A:U85 3.5 55.1 1.0 O3' A:G84 3.9 57.6 1.0 O5' A:U85 4.5 55.1 1.0 OP2 A:U85 4.5 55.1 1.0 C5' A:U85 4.5 55.1 1.0 C4' A:U85 4.6 55.1 1.0 C5' A:A156 4.8 69.7 1.0

Magnesium binding site 9 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:46.1 occ:1.00 OP2 A:A33 4.5 58.1 1.0 O6 A:G86 4.5 53.0 1.0 O4 A:U85 4.6 55.1 1.0 N4 A:C87 4.7 54.1 1.0 N7 A:G86 4.9 53.0 1.0 C4 A:U85 4.9 55.1 1.0 C5 A:U85 5.0 55.1 1.0 N4 A:C36 5.0 59.7 1.0

Magnesium binding site 10 out of 22 in the Cryo-Em Structure of the Rail Rna Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of the Rail Rna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg309 b:49.5 occ:1.00 O6 A:G88 4.1 57.5 1.0 N7 A:G88 4.3 57.5 1.0 O6 A:G89 4.6 62.7 1.0 N4 A:C90 4.8 68.9 1.0 C6 A:G88 4.8 57.5 1.0 O6 A:G34 4.9 65.1 1.0 C5 A:G88 4.9 57.5 1.0 O4 A:U35 5.0 63.1 1.0

D.B.Haack, B.Rudolfs, S.Jin, K.M.Weeks, N.Toor, A.Khitun. Scaffold-Enabled High-Resolution Cryo-Em Structure Determination of Rna Nat Commun 2025.
ISSN: ESSN 2041-1723
PubMed: 38915706
DOI: 10.1038/S41467-024-55699-5