Manganese in PDB 5di2: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH

The structure of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH, PDB code: 5di2 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)	39.81 / 2.99
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.625, 85.815, 103.753, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.9

The binding sites of Manganese atom in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH (pdb code 5di2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH, PDB code: 5di2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:90.1 occ:0.50 N7 A:G1 2.4 96.8 1.0 C8 A:G1 3.3 0.7 1.0 C5 A:G1 3.4 88.0 1.0 H8 A:G1 3.4 0.1 1.0 O6 A:G1 3.5 80.6 1.0 C6 A:G1 3.8 80.5 1.0 OP1 A:G1 4.3 87.7 1.0 N9 A:G1 4.6 93.1 1.0 C4 A:G1 4.6 85.0 1.0 MN A:MN106 4.7 0.3 1.0

Manganese binding site 2 out of 7 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:86.3 occ:1.00 OP2 A:A41 2.3 95.6 1.0 P A:A41 3.5 90.9 1.0 O5' A:A41 3.7 88.8 1.0 H62 A:A42 4.0 74.6 1.0 OP2 A:A40 4.1 87.2 1.0 H8 A:A41 4.2 88.5 1.0 OP1 A:A41 4.2 96.8 1.0 N7 A:A42 4.3 60.2 1.0 H3' A:A40 4.3 0.6 1.0 C8 A:A41 4.6 73.8 1.0 N7 A:A41 4.6 67.4 1.0 H3' A:A41 4.7 96.2 1.0 OP2 A:A42 4.7 82.0 1.0 O5' A:A40 4.7 96.3 1.0 O3' A:A40 4.8 92.8 1.0 N6 A:A42 4.8 62.2 1.0 H41 A:C43 4.9 72.4 1.0

Manganese binding site 3 out of 7 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:0.1 occ:1.00 N7 A:G29 2.6 80.6 1.0 C8 A:G29 3.4 81.3 1.0 H8 A:G29 3.5 97.5 1.0 C5 A:G29 3.6 70.9 1.0 O6 A:G29 3.8 77.5 1.0 C6 A:G29 4.0 76.3 1.0 OP1 A:G31 4.5 79.6 1.0 OP2 A:G31 4.6 64.3 1.0 N9 A:G29 4.6 73.4 1.0 C4 A:G29 4.7 65.6 1.0 OP2 A:G29 4.7 91.2 1.0 OP2 A:U28 4.8 90.2 1.0 H5 A:U28 5.0 90.1 1.0

Manganese binding site 4 out of 7 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:98.2 occ:1.00 N7 A:G18 2.5 79.4 1.0 C8 A:G18 3.3 81.3 1.0 H8 A:G18 3.4 97.6 1.0 C5 A:G18 3.6 74.1 1.0 O6 A:G18 3.8 70.6 1.0 C6 A:G18 4.1 67.1 1.0 H62 A:A19 4.1 85.0 1.0 O2' A:U17 4.1 74.0 1.0 HO2' A:U17 4.3 88.7 1.0 N6 A:A19 4.3 70.8 1.0 H61 A:A19 4.4 85.0 1.0 N9 A:G18 4.6 75.8 1.0 O3' A:U17 4.7 86.8 1.0 C4 A:G18 4.7 77.2 1.0 HO2' B:U6 4.8 69.2 1.0 OP1 A:G18 4.9 76.1 1.0 O2' B:U6 4.9 57.7 1.0

Manganese binding site 5 out of 7 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:0.3 occ:1.00 OP2 A:A22 2.6 95.5 1.0 N7 A:G23 3.3 0.2 1.0 O6 A:G23 3.8 88.6 1.0 P A:A22 3.9 0.2 1.0 O5' A:A22 4.2 96.9 1.0 C5 A:G23 4.2 99.3 1.0 C8 A:G23 4.4 0.7 1.0 C6 A:G23 4.4 93.7 1.0 H8 A:G23 4.5 0.3 1.0 H8 A:A22 4.5 0.8 1.0 N7 A:A22 4.5 84.5 1.0 O3' A:G21 4.6 0.1 1.0 OP2 B:U8 4.6 71.7 1.0 C8 A:A22 4.7 93.1 1.0 OP2 A:G23 4.7 0.7 1.0 H3' A:A22 4.8 0.1 1.0

Manganese binding site 6 out of 7 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn106 b:0.3 occ:1.00 N7 A:G2 3.2 82.2 1.0 O6 A:G2 3.7 75.7 1.0 C5 A:G2 4.0 76.2 1.0 C8 A:G2 4.2 82.9 1.0 C6 A:G2 4.2 75.2 1.0 H8 A:G2 4.3 99.5 1.0 N7 A:G1 4.6 96.8 1.0 OP1 A:G1 4.6 87.7 1.0 MN A:MN101 4.7 90.1 0.5 C5 A:G1 4.8 88.0 1.0 OP2 A:G2 4.9 91.8 1.0 C6 A:G1 5.0 80.5 1.0

Manganese binding site 7 out of 7 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at High pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:0.2 occ:1.00 N7 A:G39 2.4 83.2 1.0 OP2 A:C38 3.0 93.5 1.0 O6 A:G39 3.3 80.2 1.0 C5 A:G39 3.3 81.0 1.0 C8 A:G39 3.5 87.2 1.0 C6 A:G39 3.6 78.5 1.0 H8 A:G39 3.7 0.6 1.0 H5 A:C38 4.1 93.6 1.0 P A:C38 4.3 0.4 1.0 C5 B:DC7 4.3 76.0 1.0 H5'' A:C38 4.4 0.1 1.0 H6 A:C38 4.5 93.6 1.0 N4 B:DC7 4.5 76.9 1.0 C4 A:G39 4.6 78.5 1.0 OP1 A:C38 4.6 0.2 1.0 N9 A:G39 4.6 85.5 1.0 H3' A:A37 4.7 0.6 1.0 C4 B:DC7 4.7 71.2 1.0 C5 A:C38 4.7 78.0 1.0 C6 A:C38 5.0 78.0 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