Manganese in PDB 6ufk: Pistol Ribozyme Product Crystal Soaked in MN2+

The structure of Pistol Ribozyme Product Crystal Soaked in MN2+, PDB code: 6ufk 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)	19.93 / 3.20
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.346, 90.346, 121.732, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Manganese atom in the Pistol Ribozyme Product Crystal Soaked in MN2+ (pdb code 6ufk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 22 binding sites of Manganese where determined in the Pistol Ribozyme Product Crystal Soaked in MN2+, PDB code: 6ufk:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:0.4 occ:1.00 N7 A:G33 2.3 1.0 1.0 O6 A:G33 3.0 0.2 1.0 C5 A:G33 3.0 0.9 1.0 OC1 B:23G10 3.2 0.0 1.0 C6 A:G33 3.3 0.7 1.0 C8 A:G33 3.4 0.7 1.0 O4 A:U6 4.1 0.2 1.0 C4 A:G33 4.2 0.0 1.0 N9 A:G33 4.4 0.5 1.0 OP2 A:G33 4.5 0.9 1.0 N1 A:G33 4.6 0.7 1.0 OP2 A:U35 4.6 0.3 1.0 O2' A:A32 4.7 0.1 1.0 PC B:23G10 4.8 0.4 1.0

Manganese binding site 2 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:0.3 occ:1.00 N7 A:A38 2.0 0.6 1.0 C5 A:A38 3.0 0.2 1.0 C8 A:A38 3.0 0.4 1.0 N6 A:A38 3.2 0.4 1.0 C6 A:A38 3.5 0.6 1.0 OC2 B:23G10 4.0 0.5 1.0 N9 A:A38 4.2 0.0 1.0 C4 A:A38 4.2 0.3 1.0 OP2 A:A37 4.4 0.5 1.0 N7 A:A37 4.4 0.8 1.0 C8 A:A37 4.6 0.1 1.0 N7 A:A39 4.7 0.5 1.0 OP2 A:A38 4.9 0.2 1.0 N1 A:A38 4.9 0.7 1.0

Manganese binding site 3 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:1.0 occ:1.00 O6 A:G11 3.6 0.2 1.0 O6 A:G5 3.7 0.3 1.0 N7 A:G11 4.0 0.5 1.0 N6 A:A10 4.0 1.0 1.0 N4 A:C12 4.1 0.9 1.0 N7 A:A10 4.4 0.8 1.0 C6 A:G11 4.5 0.9 1.0 C5 A:G11 4.6 1.0 1.0 C6 A:G5 4.7 0.2 1.0 C6 A:A10 4.8 0.5 1.0 C5 A:A10 4.9 0.1 1.0

Manganese binding site 4 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:0.5 occ:1.00 OP2 C:G15 4.0 0.9 1.0 OP2 A:A14 4.2 0.4 1.0 O6 A:G15 4.3 0.8 1.0 N7 C:G15 4.5 0.1 1.0 N7 A:G15 4.6 0.5 1.0 N7 A:A14 4.7 0.8 1.0

Manganese binding site 5 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:0.5 occ:0.89 OP2 A:A23 1.9 1.0 1.0 P A:A23 3.2 0.9 1.0 O6 A:G24 3.5 0.7 1.0 N7 A:G24 3.6 0.1 1.0 C5' A:C22 3.6 0.6 1.0 O5' A:A23 3.6 0.0 1.0 C3' A:C22 3.8 0.1 1.0 C4' A:C22 3.8 0.4 1.0 O3' A:C22 4.0 0.1 1.0 C6 A:G24 4.2 0.7 1.0 C5 A:G24 4.2 0.3 1.0 O5' A:C22 4.3 0.1 1.0 OP1 A:A23 4.4 0.3 1.0 C8 A:A23 4.5 0.7 1.0 N7 A:A23 4.5 0.8 1.0 C8 A:G24 4.7 0.2 1.0 OP2 A:G24 4.9 0.0 1.0 C5' A:A23 5.0 0.9 1.0

Manganese binding site 6 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn106 b:0.8 occ:0.71 OP1 A:U26 1.6 0.3 1.0 P A:U26 2.8 0.5 1.0 O3' A:C25 3.0 0.8 1.0 OP2 A:G24 3.4 0.0 1.0 OP1 A:A23 3.7 0.3 1.0 O5' A:U26 3.7 0.2 1.0 C5' A:U26 3.8 0.9 1.0 OP2 A:U26 3.9 0.0 1.0 OP1 A:G24 4.4 0.0 1.0 P A:G24 4.4 0.2 1.0 C3' A:C25 4.4 0.5 1.0 P A:A23 4.7 0.9 1.0 OP2 A:A23 4.9 1.0 1.0

Manganese binding site 7 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:0.9 occ:1.00 N7 A:G27 3.4 0.9 1.0 O6 A:G28 3.7 0.7 1.0 O6 A:G27 3.7 0.7 1.0 N7 A:G28 4.0 0.5 1.0 C5 A:G27 4.2 0.1 1.0 O4 A:U26 4.3 0.1 1.0 C6 A:G27 4.3 0.9 1.0 C4 A:U26 4.4 0.3 1.0 C5 A:U26 4.4 0.4 1.0 C8 A:G27 4.4 0.4 1.0 C6 A:G28 4.4 0.8 1.0 C5 A:G28 4.6 0.3 1.0

Manganese binding site 8 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn108 b:0.9 occ:1.00 OP2 A:C41 2.1 0.6 1.0 OP2 A:G42 2.7 0.2 1.0 P A:C41 3.6 0.1 1.0 N7 A:G43 3.9 0.8 1.0 C8 A:G42 4.1 0.5 1.0 N7 A:G42 4.1 0.6 1.0 P A:G42 4.1 0.2 1.0 C5' A:G42 4.3 0.5 1.0 O3' A:G40 4.3 0.3 1.0 OP2 A:G43 4.4 0.4 1.0 OP1 A:C41 4.4 0.3 1.0 O2' A:G40 4.4 0.8 1.0 O5' A:G42 4.4 0.0 1.0 O5' A:C41 4.5 0.2 1.0 C8 A:G43 4.6 0.8 1.0 C3' A:C41 4.8 0.2 1.0 O3' A:C41 4.9 0.9 1.0

Manganese binding site 9 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn109 b:0.0 occ:1.00 OP2 A:G5 2.8 1.0 1.0 OP1 A:U7 2.9 0.9 1.0 OP2 A:C4 3.2 0.0 1.0 O5' A:C4 3.3 1.0 1.0 OP1 A:C4 3.4 0.7 1.0 P A:C4 3.4 0.5 1.0 P A:G5 4.0 0.6 1.0 P A:U7 4.0 0.1 1.0 OP2 A:U7 4.1 0.1 1.0 C5' A:C4 4.2 0.6 1.0 C3' A:C4 4.2 0.0 1.0 O3' A:C4 4.2 0.7 1.0 OP1 A:G5 4.6 0.1 1.0 O3' A:U6 4.7 0.1 1.0 C4' A:C4 4.8 0.1 1.0 OP2 A:U8 5.0 0.3 1.0 O3' A:U3 5.0 0.9 1.0

Manganese binding site 10 out of 22 in the Pistol Ribozyme Product Crystal Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Pistol Ribozyme Product Crystal Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn101 b:0.7 occ:0.26 N7 E:G15 2.9 0.8 1.0 C8 E:G15 3.4 0.1 1.0 C5 E:G15 4.1 0.3 1.0 OP2 E:G15 4.3 0.0 1.0 O6 E:G15 4.7 0.9 1.0 N9 E:G15 4.7 0.3 1.0 C6 E:G15 4.8 0.6 1.0 N7 E:A14 4.9 0.0 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