Manganese in PDB 5di4: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low pH

The structure of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low pH, PDB code: 5di4 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)	28.22 / 2.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.169, 85.923, 104.258, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 23.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

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 Low pH (pdb code 5di4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 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 Low pH, PDB code: 5di4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low 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 Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:91.8 occ:0.50 N7 A:G1 2.6 94.8 1.0 C8 A:G1 3.4 97.5 1.0 H8 A:G1 3.5 1.0 1.0 C5 A:G1 3.7 87.8 1.0 OP1 A:G1 3.8 89.7 1.0 O6 A:G1 3.9 88.7 1.0 C6 A:G1 4.2 87.8 1.0 N9 A:G1 4.7 89.9 1.0 C4 A:G1 4.8 83.8 1.0

Manganese binding site 2 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low 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 Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:88.9 occ:1.00 N7 A:G18 2.5 95.3 1.0 C8 A:G18 3.3 0.3 1.0 H8 A:G18 3.3 0.6 1.0 C5 A:G18 3.6 98.8 1.0 O2' A:U17 3.7 83.2 1.0 H62 A:A19 3.9 0.3 1.0 O6 A:G18 3.9 94.4 1.0 HO2' A:U17 3.9 99.8 1.0 C6 A:G18 4.1 95.1 1.0 N6 A:A19 4.3 86.1 1.0 O3' A:U17 4.4 98.7 1.0 H61 A:A19 4.5 0.3 1.0 N9 A:G18 4.6 95.3 1.0 C4 A:G18 4.7 95.8 1.0 OP1 A:G18 4.8 87.2 1.0 HO2' B:U6 4.9 89.9 1.0 H4' A:U17 4.9 0.6 1.0 O2' B:U6 4.9 74.9 1.0 C2' A:U17 5.0 87.0 1.0

Manganese binding site 3 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low 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 Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:0.6 occ:1.00 N7 A:G30 2.2 87.3 1.0 C5 A:G30 3.2 76.6 1.0 O6 A:G30 3.2 93.8 1.0 C8 A:G30 3.3 79.4 1.0 H8 A:G30 3.5 95.3 1.0 C6 A:G30 3.6 84.4 1.0 O6 A:G31 3.8 72.5 1.0 HO2' A:G29 4.1 96.1 1.0 O2' A:G29 4.2 80.1 1.0 C6 A:G31 4.3 70.0 1.0 C4 A:G30 4.4 76.5 1.0 N9 A:G30 4.5 78.5 1.0 C5 A:G31 4.9 70.9 1.0 O3' A:G29 4.9 85.2 1.0 N1 A:G30 4.9 78.3 1.0

Manganese binding site 4 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low 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 Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:0.2 occ:1.00 N7 A:G2 3.1 85.3 1.0 O6 A:G2 3.8 83.0 1.0 C5 A:G2 3.9 77.3 1.0 C8 A:G2 4.0 91.7 1.0 H8 A:G2 4.1 1.0 1.0 C6 A:G2 4.2 80.6 1.0 OP2 A:G2 4.7 89.6 1.0 N7 A:G3 4.8 66.5 1.0 N7 A:G1 4.8 94.8 1.0 O6 A:G3 5.0 74.3 1.0 C5 A:G1 5.0 87.8 1.0

Manganese binding site 5 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low 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 Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:0.4 occ:1.00 N7 A:A48 2.9 94.8 1.0 H62 A:A48 3.2 0.8 1.0 C8 A:A48 3.8 96.0 1.0 H8 A:A48 3.8 0.2 1.0 C5 A:A48 3.9 82.3 1.0 N6 A:A48 4.0 89.8 1.0 OP2 A:A48 4.0 99.2 1.0 OP2 A:C47 4.1 75.7 1.0 C6 A:A48 4.4 82.1 1.0 H61 A:A48 4.7 0.8 1.0 H3' A:C47 4.7 0.1 1.0 O5' A:C47 5.0 87.5 1.0 N9 A:A48 5.0 96.3 1.0

Manganese binding site 6 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low 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 Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn106 b:0.0 occ:1.00 OP2 A:A22 1.9 0.3 1.0 H8 A:G23 3.1 0.9 1.0 N7 A:G23 3.2 0.8 1.0 P A:A22 3.3 0.0 1.0 C8 A:G23 3.5 0.4 1.0 O5' A:A22 3.7 0.1 1.0 O3' A:G21 4.1 0.7 1.0 OP2 A:G23 4.2 0.6 1.0 H3' A:A22 4.4 0.5 1.0 OP1 A:A22 4.4 0.2 1.0 C5 A:G23 4.5 96.4 1.0 H8 A:A22 4.7 0.6 1.0 O5' A:G23 4.7 0.9 1.0 N9 A:G23 4.9 0.9 1.0

Manganese binding site 7 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low 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 Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:91.1 occ:1.00 OP2 A:A41 2.2 96.0 1.0 P A:A41 3.4 90.9 1.0 H62 A:A42 3.7 86.0 1.0 O5' A:A41 3.8 87.0 1.0 H8 A:A41 4.0 0.4 1.0 OP1 A:A41 4.1 0.8 1.0 H3' A:A40 4.2 0.3 1.0 N7 A:A42 4.3 70.2 1.0 C8 A:A41 4.5 84.5 1.0 N7 A:A41 4.6 82.1 1.0 N6 A:A42 4.6 71.7 1.0 O3' A:A40 4.7 94.3 1.0 OP2 A:A42 4.7 87.2 1.0 H3' A:A41 4.8 0.4 1.0 H41 A:C43 4.8 88.2 1.0 O5' A:A40 4.9 93.5 1.0 C3' A:A40 5.0 93.6 1.0

Manganese binding site 8 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn108 b:0.6 occ:1.00 P A:G1 2.9 0.7 1.0 OP2 A:G1 3.3 0.3 1.0 H41 B:C17 3.4 92.3 1.0 OP1 A:G1 3.7 89.7 1.0 O5' A:G1 3.9 0.8 1.0 H5'' A:G1 4.0 0.3 1.0 H62 B:A16 4.1 75.5 1.0 N4 B:C17 4.2 76.9 1.0 H42 B:C17 4.3 92.3 1.0 C5' A:G1 4.3 99.4 1.0 H5' A:G1 4.4 0.3 1.0 H5 B:U15 4.5 77.2 1.0 N7 B:A16 4.8 62.6 1.0 N6 B:A16 5.0 62.9 1.0

Manganese binding site 9 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn109 b:0.5 occ:1.00 N7 A:G29 2.4 95.5 1.0 C8 A:G29 3.3 95.2 1.0 H8 A:G29 3.4 0.3 1.0 C5 A:G29 3.4 79.8 1.0 O6 A:G29 3.7 93.5 1.0 C6 A:G29 3.9 81.2 1.0 OP2 A:G29 4.4 0.6 1.0 OP2 A:U28 4.4 0.2 1.0 N9 A:G29 4.5 83.1 1.0 C4 A:G29 4.6 79.8 1.0 H5 A:U28 4.7 0.6 1.0 OP2 A:G31 4.7 74.8 1.0 C5 A:U28 4.9 87.2 1.0 H3' A:U28 4.9 0.3 1.0

Manganese binding site 10 out of 11 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low pH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MN2+ at Low pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:0.6 occ:1.00 N7 B:G10 3.0 88.9 1.0 O6 B:G10 3.7 87.6 1.0 C5 B:G10 3.8 83.9 1.0 C8 B:G10 3.9 92.2 1.0 C6 B:G10 4.1 85.1 1.0 H8 B:G10 4.1 0.7 1.0 OP2 B:G10 4.6 92.0 1.0 N7 B:G9 4.9 89.8 1.0 C4 B:G10 5.0 83.0 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