Magnesium in PDB 5ktj: Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme

The structure of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme, PDB code: 5ktj was solved by L.A.Nguyen, J.Wang, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.27 / 2.97
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	85.190, 85.190, 256.540, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.7

The structure of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme also contains other interesting chemical elements:

Cobalt	(Co)	10 atoms
Samarium	(Sm)	10 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme (pdb code 5ktj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 19 binding sites of Magnesium where determined in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme, PDB code: 5ktj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


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 Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:0.6 occ:1.00 OP1 A:U3 3.8 0.9 1.0

Magnesium binding site 2 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


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 Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:0.8 occ:1.00 OP2 A:G24 3.6 0.0 1.0 OP2 A:A23 3.7 0.6 1.0 N7 A:G24 4.0 0.7 1.0 OP1 A:U26 4.4 0.6 1.0 SM A:SM102 4.5 0.6 1.0 C8 A:G24 4.7 0.8 1.0 OP2 A:U26 5.0 0.1 1.0

Magnesium binding site 3 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:0.9 occ:1.00 OP1 A:A19 3.9 0.1 1.0 SM A:SM105 4.0 0.9 1.0 OP2 A:A19 4.2 0.2 1.0 C5' A:U18 4.4 0.8 1.0 P A:A19 4.5 0.6 1.0

Magnesium binding site 4 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:99.8 occ:1.00 N7 A:G33 2.4 0.2 1.0 C8 A:G33 3.3 0.2 1.0 O4 A:U6 3.3 0.1 1.0 C5 A:G33 3.4 1.0 1.0 O6 A:G33 3.7 0.3 1.0 C6 A:G33 3.9 0.3 1.0 O5' B:U11 4.0 0.8 1.0 OP2 A:G33 4.1 98.6 1.0 C5' B:U11 4.2 0.4 1.0 C4 A:U6 4.3 0.0 1.0 OP2 A:U35 4.4 97.1 1.0 O2' A:G32 4.4 0.1 1.0 N9 A:G33 4.5 0.7 1.0 C4 A:G33 4.5 0.3 1.0 C5 A:U6 4.5 0.4 1.0 P B:U11 5.0 0.4 1.0

Magnesium binding site 5 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg115 b:0.3 occ:1.00 O A:HOH213 2.2 95.5 1.0 O B:HOH202 2.2 0.4 1.0 O A:HOH210 2.2 92.7 1.0 O B:HOH203 2.2 97.2 1.0 OP1 A:A37 4.1 0.9 1.0 OP2 B:C13 4.6 0.0 1.0

Magnesium binding site 6 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg116 b:0.1 occ:1.00 O A:HOH218 2.2 0.2 1.0 O B:HOH207 2.2 0.4 1.0 O A:HOH228 2.2 0.8 1.0 O A:HOH229 2.2 0.2 1.0 O B:HOH208 2.2 0.6 1.0 O A:HOH226 2.2 0.4 1.0 O B:HOH204 4.5 0.4 1.0

Magnesium binding site 7 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg117 b:0.9 occ:1.00 O A:HOH202 2.2 0.6 1.0 O A:HOH201 2.2 0.5 1.0 O A:HOH207 2.2 0.2 1.0 O A:HOH203 2.2 0.4 1.0 O2' A:A44 3.3 0.1 1.0 O A:HOH214 3.4 0.4 1.0 O A:HOH206 3.6 0.3 1.0 N7 A:A31 3.7 0.1 1.0 C8 A:A31 4.1 0.2 1.0 C5 A:A31 4.5 0.2 1.0 MG A:MG118 4.5 0.3 1.0 O A:HOH217 4.6 0.6 1.0 C2' A:A44 4.7 0.8 1.0 OP1 A:A31 4.9 0.3 1.0 N6 A:A31 5.0 0.9 1.0

Magnesium binding site 8 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg118 b:0.3 occ:1.00 O A:HOH217 2.2 0.6 1.0 O A:HOH206 2.2 0.3 1.0 O A:HOH214 2.2 0.4 1.0 O A:HOH202 3.2 0.6 1.0 O3' A:A44 4.1 0.2 1.0 OP1 A:G45 4.4 0.9 1.0 MG A:MG117 4.5 0.9 1.0 O A:HOH207 4.6 0.2 1.0 P A:G45 4.9 0.1 1.0

Magnesium binding site 9 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg119 b:0.0 occ:1.00 O A:HOH204 2.2 0.7 1.0 O A:HOH209 2.2 0.1 1.0 O A:HOH227 2.2 0.2 1.0 O A:HOH221 2.2 0.0 1.0 O A:HOH220 2.2 0.8 1.0 O A:HOH223 2.2 0.6 1.0 N7 A:G5 4.6 0.0 1.0 OP2 A:U7 4.8 0.3 1.0

Magnesium binding site 10 out of 19 in the Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg105 b:0.8 occ:1.00 O4' C:A31 3.3 1.0 1.0 C8 C:A31 3.6 88.8 1.0 C1' C:A31 3.7 95.9 1.0 N9 C:A31 3.8 88.7 1.0 N7 C:A31 4.3 82.9 1.0 C4' C:A44 4.5 98.8 1.0 C5' C:A44 4.5 0.4 1.0 C4 C:A31 4.6 81.9 1.0 C4' C:A31 4.6 93.9 1.0 OP1 C:A31 4.6 0.7 1.0 O5' C:A31 4.7 92.6 1.0 O3' C:A44 4.8 0.4 1.0 C5 C:A31 4.8 79.8 1.0 C5' C:A31 5.0 92.9 1.0

L.A.Nguyen, J.Wang, T.A.Steitz. Crystal Structure of Pistol, A Class of Self-Cleaving Ribozyme. Proc. Natl. Acad. Sci. V. 114 1021 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28096403
DOI: 10.1073/PNAS.1611191114