Potassium in PDB 4r4v: Crystal Structure of the Vs Ribozyme - G638A Mutant

The structure of Crystal Structure of the Vs Ribozyme - G638A Mutant, PDB code: 4r4v was solved by J.A.Piccirilli, N.B.Suslov, S.Dasgupta, H.Huang, D.M.J.Lilley, P.A.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.07 / 3.07
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.229, 102.229, 215.020, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.4

The structure of Crystal Structure of the Vs Ribozyme - G638A Mutant also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Potassium atom in the Crystal Structure of the Vs Ribozyme - G638A Mutant (pdb code 4r4v). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of the Vs Ribozyme - G638A Mutant, PDB code: 4r4v:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Vs Ribozyme - G638A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:K802 b:82.0 occ:1.00 O A:HOH902 3.4 33.2 1.0 H4' A:A661 3.7 49.3 1.0 H22 A:G714 3.7 37.1 1.0 HO2' A:C660 3.8 71.5 1.0 O2' A:C660 3.9 59.6 1.0 H1' A:A715 4.0 37.6 1.0 H21 A:G714 4.1 37.1 1.0 O4' A:A661 4.1 42.6 1.0 N2 A:G714 4.2 30.9 1.0 O2 A:C660 4.3 38.3 1.0 H1' A:A661 4.3 44.6 1.0 C4' A:A661 4.3 41.1 1.0 H5' A:A661 4.3 47.3 1.0 H2' A:C660 4.6 62.9 1.0 N7 A:A761 4.7 62.0 1.0 H8 A:A761 4.8 76.0 1.0 O2' A:A715 4.8 38.7 1.0 C1' A:A661 4.8 37.2 1.0 C2' A:C660 4.8 52.4 1.0 C5' A:A661 4.9 39.4 1.0 H1' A:C660 4.9 56.1 1.0 C1' A:A715 4.9 31.4 1.0 O2' A:A661 5.0 36.2 1.0 C8 A:A761 5.0 63.4 1.0

Potassium binding site 2 out of 5 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Vs Ribozyme - G638A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:K804 b:92.6 occ:1.00 O4 A:U669 2.7 31.0 1.0 C4 A:U669 3.7 29.7 1.0 O2' A:A673 3.8 48.8 1.0 H61 A:A677 3.8 37.3 1.0 H5 A:U669 3.8 38.5 1.0 O6 A:G670 3.8 43.5 1.0 HO2' A:A673 4.0 58.6 1.0 C5 A:U669 4.2 32.0 1.0 H62 A:A668 4.2 30.2 1.0 H41 A:C676 4.5 40.5 1.0 N6 A:A677 4.5 31.1 1.0 OP1 A:A675 4.6 41.6 1.0 H42 A:C676 4.6 40.5 1.0 H62 A:A677 4.7 37.3 1.0 N7 A:A668 4.7 30.3 1.0 H2' A:A673 4.7 61.8 1.0 N6 A:A668 4.8 25.2 1.0 N3 A:U669 4.8 27.2 1.0 C2' A:A673 4.9 51.5 1.0 H3 A:U669 4.9 32.7 1.0 N4 A:C676 4.9 33.8 1.0

Potassium binding site 3 out of 5 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Vs Ribozyme - G638A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:K809 b:71.6 occ:1.00 O A:HOH901 2.8 45.5 1.0 O2' A:G704 3.2 50.9 1.0 O4' A:U705 3.7 47.8 1.0 H2' A:G704 3.7 63.1 1.0 H5' A:U705 3.7 63.6 1.0 HO2' A:G704 3.8 61.1 1.0 C2' A:G704 3.9 52.6 1.0 H1' A:G704 3.9 62.1 1.0 H22 A:G704 3.9 63.3 1.0 H4' A:U705 4.0 58.1 1.0 N3 A:G704 4.0 50.2 1.0 C4' A:U705 4.3 48.4 1.0 H1' A:U705 4.4 57.9 1.0 H1' A:G683 4.4 62.0 1.0 C1' A:G704 4.4 51.8 1.0 C5' A:U705 4.5 53.0 1.0 C1' A:U705 4.6 48.3 1.0 N2 A:G704 4.7 52.7 1.0 C2 A:G704 4.8 49.6 1.0 C4 A:G704 5.0 46.7 1.0

Potassium binding site 4 out of 5 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the Vs Ribozyme - G638A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:K810 b:83.1 occ:1.00 H22 A:G740 2.6 47.2 1.0 H1' A:C741 3.2 37.6 1.0 N2 A:G740 3.5 39.4 1.0 O4' A:C741 3.6 38.5 1.0 C1' A:C741 3.8 31.3 1.0 H4' A:C741 3.9 37.1 1.0 H21 A:G740 4.0 47.2 1.0 H61 A:A739 4.1 46.1 1.0 N3 A:G740 4.2 32.1 1.0 O2' A:G740 4.3 32.3 1.0 C4' A:C741 4.3 30.9 1.0 O2' A:C741 4.3 33.9 1.0 C2 A:G740 4.3 34.8 1.0 HO2' A:G740 4.5 38.8 1.0 H2' A:G740 4.5 38.1 1.0 N6 A:A739 4.5 38.5 1.0 N1 A:A739 4.5 32.5 1.0 C2' A:C741 4.7 28.5 1.0 C6 A:A739 4.8 34.6 1.0 H5' A:C741 4.8 32.2 1.0 N1 A:C741 4.9 30.7 1.0 C2' A:G740 4.9 31.8 1.0 H62 A:A739 4.9 46.1 1.0

Potassium binding site 5 out of 5 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the Vs Ribozyme - G638A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:K811 b:98.3 occ:1.00 O2' A:C764 3.5 48.7 1.0 HO2' A:C764 3.6 58.4 1.0 H1' A:C658 3.7 54.6 1.0 HO2' A:A657 3.8 67.6 1.0 O2' A:A657 4.1 56.4 1.0 O4' A:C658 4.1 54.7 1.0 C1' A:C658 4.4 45.5 1.0 H1' A:C764 4.5 58.7 1.0 H4' A:C658 4.5 59.5 1.0 O4' A:C765 4.6 42.1 1.0 C2' A:C764 4.6 47.9 1.0 O2 A:C764 4.6 38.8 1.0 H2' A:C764 4.7 57.5 1.0 H1' A:C765 4.8 48.3 1.0 H4' A:C765 4.9 46.9 1.0 C4' A:C658 4.9 49.6 1.0 O2' A:C658 4.9 44.3 1.0 H22 A:G763 4.9 58.1 1.0 H22 A:G655 5.0 46.4 1.0

N.B.Suslov, S.Dasgupta, H.Huang, J.R.Fuller, D.M.Lilley, P.A.Rice, J.A.Piccirilli. Crystal Structure of the Varkud Satellite Ribozyme. Nat.Chem.Biol. V. 11 840 2015.
ISSN: ISSN 1552-4450
PubMed: 26414446
DOI: 10.1038/NCHEMBIO.1929