Zinc in PDB 5dh8: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+

The structure of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+, PDB code: 5dh8 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)	28.34 / 3.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.937, 86.012, 103.368, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ (pdb code 5dh8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+, PDB code: 5dh8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:78.6 occ:1.00 N7 A:G29 2.2 78.2 1.0 C5 A:G29 3.1 67.9 1.0 C8 A:G29 3.2 76.9 1.0 O6 A:G29 3.2 82.9 1.0 H8 A:G29 3.4 92.3 1.0 C6 A:G29 3.5 73.7 1.0 C4 A:G29 4.3 67.0 1.0 N9 A:G29 4.4 67.7 1.0 H5 A:U28 4.4 83.9 1.0 OP2 A:G29 4.5 73.7 1.0 OP2 A:U28 4.6 77.4 1.0 OP2 A:G31 4.7 72.7 1.0 C5 A:U28 4.7 69.9 1.0 OP1 A:G31 4.8 76.4 1.0 H3' A:U28 4.9 0.8 1.0 N1 A:G29 4.9 75.1 1.0 H6 A:U28 5.0 80.9 1.0

Zinc binding site 2 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:82.5 occ:1.00 N7 A:G18 2.2 65.9 1.0 C8 A:G18 3.1 78.0 1.0 H8 A:G18 3.2 93.6 1.0 C5 A:G18 3.2 70.2 1.0 O6 A:G18 3.6 84.6 1.0 HO2' A:U17 3.7 77.5 1.0 C6 A:G18 3.8 73.2 1.0 H61 A:A19 4.3 75.4 1.0 N9 A:G18 4.3 76.3 1.0 HO2' B:U6 4.3 73.7 1.0 O2' A:U17 4.3 64.6 1.0 C4 A:G18 4.4 69.4 1.0 O2' B:U6 4.4 61.4 1.0 N6 A:A19 4.5 62.8 1.0 H62 A:A19 4.6 75.4 1.0 O3' A:U17 4.8 87.8 1.0 OP1 A:G18 4.9 59.5 1.0

Zinc binding site 3 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:86.2 occ:1.00 N7 A:G30 2.1 71.8 1.0 C5 A:G30 2.9 61.6 1.0 O6 A:G30 2.9 80.4 1.0 C8 A:G30 3.2 75.0 1.0 C6 A:G30 3.2 67.1 1.0 H8 A:G30 3.5 90.0 1.0 O6 A:G31 4.1 62.8 1.0 C4 A:G30 4.1 58.4 1.0 HO2' A:G29 4.2 92.7 1.0 N9 A:G30 4.3 67.1 1.0 O2' A:G29 4.3 77.2 1.0 N1 A:G30 4.6 64.7 1.0 C6 A:G31 4.7 61.8 1.0 O3' A:G29 4.9 86.0 1.0 OP1 A:G30 4.9 98.2 1.0

Zinc binding site 4 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:87.0 occ:0.50 N7 A:G1 2.1 95.6 1.0 C5 A:G1 3.0 89.9 1.0 C8 A:G1 3.1 98.0 1.0 O6 A:G1 3.2 94.4 1.0 H8 A:G1 3.3 0.6 1.0 C6 A:G1 3.5 86.5 1.0 OP1 A:G1 3.8 92.7 1.0 C4 A:G1 4.2 72.4 1.0 N9 A:G1 4.3 99.0 1.0 O5' A:G1 4.8 0.0 1.0 N1 A:G1 4.8 78.7 1.0 P A:G1 4.9 0.3 1.0

Zinc binding site 5 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:0.2 occ:1.00 N7 A:G2 2.2 83.5 1.0 C8 A:G2 3.0 86.1 1.0 H8 A:G2 3.2 0.4 1.0 C5 A:G2 3.2 74.0 1.0 O6 A:G2 3.6 72.0 1.0 OP2 A:G2 3.7 0.4 1.0 C6 A:G2 3.7 69.1 1.0 N9 A:G2 4.2 79.3 1.0 H3' A:G1 4.2 0.4 1.0 C4 A:G2 4.3 72.3 1.0 C5 A:G1 4.4 89.9 1.0 C6 A:G1 4.5 86.5 1.0 N7 A:G3 4.6 56.7 1.0 C4 A:G1 4.6 72.4 1.0 O5' A:G2 4.6 0.7 1.0 N1 A:G1 4.7 78.7 1.0 N7 A:G1 4.7 95.6 1.0 H2' A:G1 4.8 0.2 1.0 P A:G2 4.8 0.6 1.0 O6 A:G1 4.9 94.4 1.0 N3 A:G1 4.9 72.4 1.0 C2 A:G1 5.0 78.8 1.0

Zinc binding site 6 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:98.6 occ:1.00 H62 A:A39 3.9 79.5 1.0 OP2 B:U6 4.1 72.7 1.0 H42 B:DC7 4.2 77.0 1.0 OP2 A:C38 4.2 97.5 1.0 N6 A:A39 4.7 66.2 1.0 N7 A:A39 4.7 68.8 1.0 OP1 A:C38 4.8 86.7 1.0 OP1 B:G5 4.8 77.5 1.0 N4 B:DC7 4.9 64.2 1.0 P A:C38 4.9 0.5 1.0 OP2 B:G5 5.0 88.5 1.0

Zinc binding site 7 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:95.0 occ:1.00 N7 A:G11 2.4 69.2 1.0 C8 A:G11 3.3 64.8 1.0 H8 A:G11 3.4 77.8 1.0 C5 A:G11 3.4 62.1 1.0 H42 A:C12 3.6 71.9 1.0 O6 A:G11 3.7 72.2 1.0 C6 A:G11 3.9 63.9 1.0 H5'' A:A10 3.9 82.3 1.0 H4' A:A10 4.0 73.4 1.0 OP2 A:G11 4.2 70.6 1.0 H5' A:A10 4.2 82.3 1.0 N4 A:C12 4.3 59.9 1.0 H5 A:C12 4.4 72.5 1.0 C5' A:A10 4.4 68.6 1.0 N9 A:G11 4.5 63.3 1.0 C4 A:G11 4.5 62.1 1.0 H41 A:C12 4.7 71.9 1.0 H5' A:G34 4.7 0.5 1.0 C4' A:A10 4.7 61.2 1.0

Zinc binding site 8 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn108 b:0.4 occ:1.00 N7 A:G23 2.2 94.5 1.0 C8 A:G23 3.1 92.8 1.0 H8 A:G23 3.2 0.4 1.0 C5 A:G23 3.3 89.8 1.0 O6 A:G23 3.6 87.1 1.0 C6 A:G23 3.8 85.6 1.0 OP2 A:A22 4.2 0.4 1.0 N9 A:G23 4.3 86.0 1.0 C4 A:G23 4.4 87.2 1.0 N7 A:A22 4.5 84.8 1.0 O4 A:U24 4.6 78.7 1.0 H5 A:U24 4.7 0.3 1.0 H62 A:A22 4.7 94.6 1.0 C5 A:A22 5.0 73.7 1.0

Zinc binding site 9 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:83.7 occ:1.00 N7 B:G10 2.4 71.9 1.0 O6 B:G10 3.1 66.3 1.0 C5 B:G10 3.2 63.8 1.0 C8 B:G10 3.4 71.6 1.0 C6 B:G10 3.5 70.0 1.0 H8 B:G10 3.7 85.9 1.0 N7 B:G9 4.2 70.5 1.0 C4 B:G10 4.4 59.6 1.0 N9 B:G10 4.5 67.0 1.0 C8 B:G9 4.6 76.6 1.0 C5 B:G9 4.6 65.7 1.0 OP2 B:G10 4.7 84.0 1.0 H8 B:G9 4.8 91.9 1.0 H3' B:G9 4.8 96.0 1.0 N1 B:G10 4.9 63.6 1.0

Zinc binding site 10 out of 13 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction- G12A Mutant in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:96.5 occ:1.00 N1 B:A13 2.9 58.7 1.0 H61 B:A13 3.2 77.1 1.0 H2 B:A13 3.6 74.5 1.0 C2 B:A13 3.7 62.1 1.0 C6 B:A13 3.7 58.8 1.0 N6 B:A13 3.7 64.2 1.0 H1' A:U8 3.8 72.4 1.0 O2' A:U8 4.1 67.7 1.0 H62 B:A13 4.5 77.1 1.0 HO2' A:U8 4.6 81.2 1.0 C1' A:U8 4.7 60.3 1.0 N3 B:A13 4.9 63.3 1.0 O2 A:U8 4.9 68.5 1.0 C5 B:A13 4.9 58.9 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