Magnesium in PDB 4r4p: Crystal Structure of the Vs Ribozyme-A756G Mutant

The structure of Crystal Structure of the Vs Ribozyme-A756G Mutant, PDB code: 4r4p 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)	41.47 / 3.07
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.680, 102.680, 211.021, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 26.9

The binding sites of Magnesium atom in the Crystal Structure of the Vs Ribozyme-A756G Mutant (pdb code 4r4p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Vs Ribozyme-A756G Mutant, PDB code: 4r4p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Vs Ribozyme-A756G Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Vs Ribozyme-A756G Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:1.0 occ:1.00 O A:HOH906 2.2 0.3 1.0 O A:HOH905 2.2 0.9 1.0 O A:HOH903 2.2 93.4 1.0 O A:HOH907 2.2 0.1 1.0 O A:HOH902 2.2 0.1 1.0 O A:HOH904 2.2 0.5 1.0 H1 A:HOH906 2.8 0.1 1.0 H1 A:HOH903 2.8 0.1 1.0 H1 A:HOH905 2.8 0.9 1.0 H1 A:HOH907 2.8 0.7 1.0 H1 A:HOH902 2.8 0.1 1.0 H1 A:HOH904 2.8 1.0 1.0 H42 A:C758 3.4 0.1 1.0 H62 A:A759 3.8 0.1 1.0 H5 A:C758 4.1 0.1 1.0 N4 A:C758 4.2 0.4 1.0 N6 A:A759 4.5 0.2 1.0 H61 A:A759 4.6 0.1 1.0 H41 A:C758 4.7 0.1 1.0 H42 A:C760 4.9 0.4 1.0 C5 A:C758 4.9 0.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Vs Ribozyme-A756G Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Vs Ribozyme-A756G Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:0.0 occ:1.00 O A:HOH910 2.2 0.1 1.0 O A:HOH908 2.2 0.8 1.0 O A:HOH912 2.2 76.3 1.0 O A:HOH909 2.2 87.8 1.0 O A:HOH913 2.2 0.2 1.0 O A:HOH911 2.2 0.3 1.0 H1 A:HOH910 2.8 0.1 1.0 H1 A:HOH908 2.8 1.0 1.0 H1 A:HOH912 2.8 91.6 1.0 H1 A:HOH909 2.8 0.4 1.0 H1 A:HOH913 2.8 0.8 1.0 H1 A:HOH911 2.8 0.2 1.0 H42 A:C748 3.5 0.4 1.0 N4 A:C748 4.2 0.7 1.0 H41 A:C748 4.3 0.4 1.0 H42 A:C726 4.3 99.7 1.0 H41 A:C726 4.6 99.7 1.0 H42 A:C747 4.6 1.0 1.0 N4 A:C726 4.8 83.0 1.0 H5 A:C747 4.9 0.3 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