Magnesium in PDB 6ufj: Pistol Ribozyme Product Crystal Structure

The structure of Pistol Ribozyme Product Crystal Structure, PDB code: 6ufj was solved by M.Teplova, C.Falschlunger, O.Krasheninina, D.J.Patel, R.Micura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.49 / 2.65
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.734, 90.734, 121.651, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Magnesium atom in the Pistol Ribozyme Product Crystal Structure (pdb code 6ufj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the Pistol Ribozyme Product Crystal Structure, PDB code: 6ufj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:69.9 occ:1.00 N7 A:G33 2.3 99.5 1.0 OC1 B:23G10 2.8 0.2 1.0 C8 A:G33 3.2 91.1 1.0 C5 A:G33 3.3 99.7 1.0 O6 A:G33 3.7 0.9 1.0 C6 A:G33 3.8 0.0 1.0 OP2 A:G33 4.1 97.5 1.0 O4 A:U6 4.3 79.2 1.0 PC B:23G10 4.4 0.9 1.0 N9 A:G33 4.4 86.9 1.0 O5' E:U11 4.5 0.1 1.0 C4 A:G33 4.5 94.1 1.0 OP2 A:U35 4.5 80.5 1.0 C5' E:U11 4.7 0.8 1.0 O2' B:23G10 4.9 0.3 1.0 N6 A:A39 4.9 91.8 1.0

Magnesium binding site 2 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:0.2 occ:1.00 N7 A:A38 3.3 94.5 1.0 OP2 A:A37 3.6 92.1 1.0 OC2 B:23G10 4.0 0.6 1.0 C8 A:A38 4.2 0.9 1.0 N6 A:A38 4.3 0.3 1.0 N7 A:A37 4.4 0.2 1.0 C5 A:A38 4.4 0.3 1.0 OP2 A:A38 4.7 0.4 1.0 N7 A:A39 4.7 0.1 1.0 C8 A:A37 4.7 0.1 1.0 C6 A:A38 4.8 0.3 1.0 PC B:23G10 4.8 0.9 1.0 O3' B:23G10 4.9 0.3 1.0 OC1 B:23G10 4.9 0.2 1.0 P A:A37 4.9 96.5 1.0

Magnesium binding site 3 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:71.3 occ:1.00 O6 A:G5 3.3 80.9 1.0 O6 A:G11 3.7 82.3 1.0 N4 A:C12 3.9 73.2 1.0 N7 A:G11 4.2 75.8 1.0 C6 A:G5 4.3 71.7 1.0 N6 A:A10 4.4 74.1 1.0 C6 A:G11 4.6 81.8 1.0 N4 A:C4 4.7 80.8 1.0 C5 A:G11 4.8 77.8 1.0 N7 A:A10 4.9 0.3 1.0 C4 A:C12 5.0 76.4 1.0

Magnesium binding site 4 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:81.4 occ:1.00 OP2 C:G15 4.0 84.9 1.0 OP2 A:A14 4.3 59.5 1.0 OP2 A:G15 4.4 77.1 1.0 N7 A:G15 4.5 80.9 1.0 OP2 C:A14 4.5 88.2 1.0 N7 C:G15 4.6 69.0 1.0 N7 A:A14 4.9 65.5 1.0

Magnesium binding site 5 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:99.4 occ:1.00 OP2 A:A23 2.3 88.5 1.0 C5' A:C22 3.7 93.0 1.0 P A:A23 3.7 87.9 1.0 O6 A:G24 3.8 84.2 1.0 N7 A:A23 3.8 75.4 1.0 O5' A:A23 4.0 84.9 1.0 C4' A:C22 4.1 87.7 1.0 C8 A:A23 4.1 70.2 1.0 C3' A:C22 4.1 84.3 1.0 OP2 A:C22 4.2 85.2 1.0 N7 A:G24 4.4 76.8 1.0 O2' A:A21 4.4 0.3 1.0 O3' A:C22 4.4 80.3 1.0 C6 A:G24 4.6 69.8 1.0 O5' A:C22 4.7 98.9 1.0 C5 A:G24 4.8 68.6 1.0 OP1 A:A23 4.8 93.2 1.0 C5 A:A23 4.9 68.5 1.0

Magnesium binding site 6 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:95.9 occ:1.00 OP1 A:A23 2.5 93.2 1.0 OP1 A:U26 2.5 79.7 1.0 OP2 A:G24 2.9 56.8 1.0 P A:A23 3.6 87.9 1.0 P A:U26 3.7 77.1 1.0 P A:G24 4.0 80.7 1.0 O5' A:A23 4.1 84.9 1.0 OP2 A:A23 4.1 88.5 1.0 OP2 A:U26 4.1 73.5 1.0 OP1 A:G24 4.4 78.6 1.0 O3' A:C25 4.6 67.5 1.0 O3' A:A23 4.7 56.6 1.0 C5' A:A23 4.7 78.6 1.0 O5' A:U26 4.9 81.1 1.0 O3' A:C22 4.9 80.3 1.0

Magnesium binding site 7 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:98.1 occ:1.00 OP2 A:C41 2.5 0.2 1.0 OP2 A:G42 2.7 0.9 1.0 O3' A:G40 3.5 0.1 1.0 P A:C41 3.6 0.8 1.0 N7 A:G43 3.7 97.2 1.0 N2 B:23G10 3.8 1.0 1.0 O2' A:G40 3.9 0.0 1.0 O6 A:G43 4.0 0.9 1.0 P A:G42 4.2 0.9 1.0 O5' A:C41 4.2 1.0 1.0 N7 A:G42 4.3 0.6 1.0 C5 A:G43 4.6 98.3 1.0 O5' A:G42 4.6 0.9 1.0 C6 A:G43 4.6 0.7 1.0 C3' A:G40 4.6 0.7 1.0 C8 A:G42 4.7 0.4 1.0 C8 A:G43 4.8 95.0 1.0 C2' A:G40 4.8 0.4 1.0 OP1 A:C41 4.9 0.8 1.0

Magnesium binding site 8 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:94.5 occ:1.00 OP1 A:U7 2.0 0.1 1.0 P A:U7 3.3 98.1 1.0 OP2 A:G5 3.7 71.7 1.0 OP2 A:U7 4.0 0.1 1.0 OP1 A:C4 4.1 99.1 1.0 OP2 A:C4 4.1 0.2 1.0 O3' A:U6 4.2 96.6 1.0 O5' A:U7 4.3 97.0 1.0 P A:C4 4.4 98.4 1.0 C5' A:U7 4.5 99.4 1.0 O5' A:C4 4.5 87.1 1.0 OP2 A:U8 4.6 91.8 1.0 P A:G5 4.7 85.7 1.0 OP1 A:G5 4.9 97.7 1.0

Magnesium binding site 9 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:84.7 occ:1.00 OP1 A:A32 4.0 97.0 1.0 O4 A:U30 4.4 1.0 1.0 C5 A:U30 4.4 90.6 1.0 OP2 A:A32 4.5 95.8 1.0 C4 A:U30 4.6 95.7 1.0 P A:A32 4.8 89.0 1.0

Magnesium binding site 10 out of 17 in the Pistol Ribozyme Product Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Pistol Ribozyme Product Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:75.7 occ:1.00 N7 C:G33 2.5 73.3 1.0 OC2 D:23G10 3.1 75.0 1.0 C8 C:G33 3.2 68.1 1.0 C5 C:G33 3.8 62.6 1.0 OP2 C:G33 3.8 87.0 1.0 O5' F:U11 3.8 66.3 1.0 O4 C:U6 4.1 59.9 1.0 O6 C:G33 4.3 60.2 1.0 C6 C:G33 4.4 66.3 1.0 C5' F:U11 4.5 51.9 1.0 N9 C:G33 4.5 59.5 1.0 O2' C:A32 4.6 81.3 1.0 OP2 C:U35 4.6 78.9 1.0 PC D:23G10 4.7 78.9 1.0 C4 C:G33 4.8 68.4 1.0 C4 C:U6 5.0 71.9 1.0

M.Teplova, C.Falschlunger, O.Krasheninina, M.Egger, A.Ren, D.J.Patel, R.Micura. On Crucial Roles of Two Hydrated MG2+ Ions in Reaction Catalysis of the Pistol Ribozyme. Angew.Chem.Int.Ed.Engl. 2019.
ISSN: ESSN 1521-3773
PubMed: 31804735
DOI: 10.1002/ANIE.201912522