Potassium in PDB 5dqk: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+

The structure of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+, PDB code: 5dqk 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)	26.07 / 2.71
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.764, 86.070, 103.338, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.8

The structure of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+ also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

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

Potassium binding site 1 out of 4 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:79.1 occ:1.00 O6 A:G11 3.0 6.9 1.0 O B:HOH210 3.5 19.2 1.0 H41 A:C12 3.6 20.3 1.0 H42 B:C12 3.6 19.6 1.0 H42 A:C12 3.7 20.3 1.0 N4 A:C12 3.9 16.9 1.0 C6 A:G11 4.0 8.1 1.0 O6 B:G11 4.1 18.1 1.0 H41 B:C12 4.2 19.6 1.0 N4 B:C12 4.2 16.4 1.0 N7 A:G11 4.4 11.3 1.0 C5 A:G11 4.6 9.3 1.0

Potassium binding site 2 out of 4 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:58.4 occ:1.00 H4' A:G44 2.9 15.7 1.0 O2' A:G44 3.1 10.1 1.0 O3' A:G44 3.4 14.8 1.0 HO2' A:G44 3.5 12.1 1.0 C4' A:G44 3.8 13.1 1.0 H5' A:C45 3.8 11.8 1.0 C3' A:G44 4.0 13.8 1.0 C2' A:G44 4.1 8.9 1.0 H5'' A:G44 4.5 20.1 1.0 O A:HOH205 4.6 16.6 1.0 P A:C45 4.6 5.4 1.0 O4' A:G44 4.6 11.5 1.0 OP1 A:C45 4.6 9.4 1.0 C5' A:C45 4.7 9.9 1.0 C5' A:G44 4.8 16.8 1.0 H1' A:G44 4.8 17.0 1.0 C1' A:G44 4.8 14.2 1.0 H2' A:G44 4.8 10.6 1.0 H3' A:G44 4.9 16.6 1.0 O5' A:C45 4.9 7.5 1.0 H5'' A:C45 5.0 11.8 1.0

Potassium binding site 3 out of 4 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:70.6 occ:1.00 OP2 A:C45 3.1 23.1 1.0 H5 A:C46 3.1 16.8 1.0 OP2 A:C46 3.1 13.4 1.0 H3' A:C45 3.3 10.2 1.0 O5' A:C45 3.7 7.5 1.0 P A:C45 3.8 5.4 1.0 H6 A:C45 3.9 12.4 1.0 C5 A:C46 4.0 14.0 1.0 H5 A:C45 4.0 13.4 1.0 H41 A:C46 4.0 19.0 1.0 C6 A:C45 4.1 10.3 1.0 C5 A:C45 4.2 11.2 1.0 C3' A:C45 4.2 8.5 1.0 OP1 A:C45 4.4 9.4 1.0 P A:C46 4.4 10.9 1.0 H6 A:C46 4.6 17.0 1.0 H5'' A:C45 4.6 11.8 1.0 C5' A:C45 4.6 9.9 1.0 O3' A:C45 4.7 10.5 1.0 N4 A:C46 4.7 15.9 1.0 C6 A:C46 4.8 14.2 1.0 N1 A:C45 4.9 11.8 1.0 C4 A:C46 4.9 16.6 1.0 C4' A:C45 5.0 9.4 1.0 H2' A:C45 5.0 15.2 1.0

Potassium binding site 4 out of 4 in the Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:46.6 occ:1.00 O6 B:G14 2.6 7.6 1.0 O4 B:U15 3.0 7.1 1.0 C6 B:G14 3.4 4.5 1.0 N7 B:G14 3.7 3.2 1.0 C5 B:G14 3.8 3.4 1.0 C4 B:U15 4.1 5.4 1.0 N1 B:G14 4.5 4.3 1.0 H1 B:G14 4.7 5.2 1.0 H5 B:U15 4.8 4.1 1.0 H3 B:U15 4.9 6.9 1.0 C8 B:G14 4.9 3.7 1.0 C5 B:U15 4.9 3.4 1.0 H62 B:A16 5.0 8.2 1.0 N3 B:U15 5.0 5.8 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