Magnesium in PDB 5dh6: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+

The structure of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+, PDB code: 5dh6 was solved by A.Mir, J.Chen, D.Neau, B.L.Golden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.41 / 2.78
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.405, 85.964, 102.969, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.2

The binding sites of Magnesium atom in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+ (pdb code 5dh6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+, PDB code: 5dh6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:65.5 occ:1.00 O6 A:G29 3.3 60.3 1.0 OP1 A:G31 3.5 49.8 1.0 N7 A:G29 3.9 48.5 1.0 C6 A:G29 4.0 54.1 1.0 C5 A:G29 4.2 45.5 1.0 P A:G31 4.6 47.8 1.0 OP2 A:G31 4.6 46.6 1.0

Magnesium binding site 2 out of 5 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:56.5 occ:1.00 O6 A:G30 2.7 61.2 1.0 O6 A:G31 3.1 45.7 1.0 N7 A:G30 3.3 56.5 1.0 C6 A:G30 3.6 48.9 1.0 C5 A:G30 3.8 46.1 1.0 C6 A:G31 3.9 41.1 1.0 H1 A:G31 4.2 51.0 1.0 HO2' A:G29 4.3 64.4 1.0 N1 A:G31 4.4 42.5 1.0 O2' A:G29 4.5 53.7 1.0 C8 A:G30 4.6 52.3 1.0 C5 A:G31 4.8 43.8 1.0 N1 A:G30 4.9 45.5 1.0 H8 A:G30 4.9 62.8 1.0

Magnesium binding site 3 out of 5 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:58.5 occ:1.00 OP2 A:A41 2.5 67.3 1.0 H62 A:A42 3.4 53.2 1.0 P A:A41 3.6 66.3 1.0 O5' A:A41 3.7 55.7 1.0 N7 A:A42 3.7 48.5 1.0 H8 A:A41 3.8 64.6 1.0 C8 A:A41 4.2 53.8 1.0 H3' A:A41 4.3 71.7 1.0 N7 A:A41 4.3 56.1 1.0 N6 A:A42 4.3 44.4 1.0 H3' A:A40 4.3 71.0 1.0 OP2 A:A42 4.4 65.3 1.0 OP1 A:A41 4.4 64.3 1.0 H41 A:C43 4.5 47.8 1.0 C8 A:A42 4.7 47.8 1.0 H8 A:A42 4.7 57.4 1.0 C5 A:A42 4.7 42.4 1.0 O3' A:A40 4.8 62.9 1.0 H61 A:A42 4.9 53.2 1.0 C6 A:A42 5.0 41.5 1.0

Magnesium binding site 4 out of 5 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:59.6 occ:1.00 H41 A:C35 4.4 60.3 1.0 H5 A:C35 4.4 63.7 1.0 H62 A:A37 4.4 70.2 1.0 N4 A:C35 4.8 50.2 1.0 O6 A:G36 4.8 59.2 1.0 C5 A:C35 4.9 53.1 1.0 N7 A:G36 4.9 54.5 1.0

Magnesium binding site 5 out of 5 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-G12A Mutant in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:72.3 occ:1.00 O6 B:G3 2.8 46.8 1.0 O6 B:G2 3.1 54.2 1.0 H42 A:C45 3.5 50.3 1.0 C6 B:G3 3.8 46.5 1.0 H41 A:C45 4.0 50.3 1.0 C6 B:G2 4.0 53.6 1.0 N4 A:C45 4.1 41.9 1.0 N7 B:G3 4.3 55.9 1.0 N7 B:G2 4.3 56.1 1.0 H42 A:C46 4.4 57.4 1.0 C5 B:G3 4.4 50.1 1.0 H41 B:C4 4.4 52.6 1.0 H42 B:C4 4.5 52.6 1.0 C5 B:G2 4.5 58.2 1.0 O6 A:G44 4.5 50.1 1.0 N4 B:C4 4.6 43.8 1.0 N4 A:C46 5.0 47.8 1.0

A.Mir, J.Chen, K.Robinson, E.Lendy, J.Goodman, D.Neau, B.L.Golden. Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction. Biochemistry V. 54 6369 2015.
ISSN: ISSN 0006-2960
PubMed: 26398724
DOI: 10.1021/ACS.BIOCHEM.5B00824