Magnesium in PDB 8za0: Crystal Structure of OR4K15 Ribozyme

The structure of Crystal Structure of OR4K15 Ribozyme, PDB code: 8za0 was solved by Y.Ren, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.96 / 1.96
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.082, 36.57, 113.94, 90, 91.29, 90
R / Rfree (%)	20.3 / 23

The binding sites of Magnesium atom in the Crystal Structure of OR4K15 Ribozyme (pdb code 8za0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of OR4K15 Ribozyme, PDB code: 8za0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of OR4K15 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 OR4K15 Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:39.3 occ:1.00 O B:HOH211 2.4 29.5 1.0 O2' A:G14 2.9 27.2 1.0 N3 A:G14 3.0 29.5 1.0 C2' A:G14 3.3 26.1 1.0 O4' A:G15 3.4 29.9 1.0 O E:HOH220 3.4 28.2 1.0 C1' A:G14 3.6 24.9 1.0 O2' E:G14 3.7 27.6 1.0 N2 A:G14 3.7 29.9 1.0 O E:HOH211 3.8 27.7 1.0 C2 A:G14 3.8 29.7 1.0 C4 A:G14 4.0 29.6 1.0 C1' A:G15 4.0 30.0 1.0 N9 A:G14 4.2 23.8 1.0 C4' A:G15 4.2 30.7 1.0 O2 B:U3 4.6 28.9 1.0 C5' A:G15 4.7 29.6 1.0 N9 A:G15 4.7 31.5 1.0 C3' A:G14 4.8 24.6 1.0 O4' A:G14 4.9 26.1 1.0 C2' E:G14 5.0 25.4 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of OR4K15 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 OR4K15 Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:41.7 occ:1.00 N7 A:G10 2.4 31.7 1.0 O A:HOH210 3.0 33.6 1.0 O6 A:G10 3.1 28.9 1.0 C5 A:G10 3.2 28.5 1.0 C8 A:G10 3.5 29.9 1.0 C6 A:G10 3.5 28.6 1.0 OP2 A:A9 3.6 35.7 1.0 N7 A:A9 3.7 33.6 1.0 C8 A:A9 4.3 31.8 1.0 C4 A:G10 4.5 30.4 1.0 C5 A:A9 4.5 33.2 1.0 N9 A:G10 4.6 30.1 1.0 N7 A:G11 4.7 26.3 1.0 OP2 A:G10 4.7 42.4 1.0 N6 A:A9 4.8 30.6 1.0 N1 A:G10 4.9 28.8 1.0 P A:A9 4.9 42.1 1.0 C6 A:A9 5.0 31.2 1.0 O5' A:A9 5.0 39.4 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of OR4K15 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 OR4K15 Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:45.7 occ:1.00 O B:HOH208 2.2 36.8 1.0 O B:HOH224 2.5 44.1 1.0 N7 B:G15 2.8 32.1 1.0 O B:HOH221 2.8 41.2 1.0 O6 B:G15 3.4 26.8 1.0 C5 B:G15 3.7 28.2 1.0 N7 B:A14 3.7 30.6 1.0 O B:HOH214 3.8 35.8 1.0 C8 B:G15 3.8 31.4 1.0 C6 B:G15 3.9 28.3 1.0 C8 B:A14 4.3 28.0 1.0 C5 B:A14 4.3 26.0 1.0 N7 B:A16 4.6 32.9 1.0 N6 B:A16 4.6 25.4 1.0 N6 B:A14 4.7 27.3 1.0 OP2 B:A14 4.7 36.6 1.0 C6 B:A14 4.8 24.8 1.0 OP2 B:G15 4.9 38.8 1.0 C4 B:G15 4.9 28.5 1.0 N9 B:G15 5.0 32.9 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of OR4K15 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 OR4K15 Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:46.7 occ:1.00 O C:HOH219 1.9 35.2 1.0 O C:HOH201 2.2 36.2 1.0 O D:HOH115 2.7 43.2 1.0 O6 C:G6 2.7 36.1 1.0 C6 C:G6 3.3 36.1 1.0 N7 C:G5 3.6 37.7 1.0 O C:HOH203 3.6 38.5 1.0 O C:HOH204 3.8 35.0 1.0 N1 C:G6 3.8 32.7 1.0 O6 C:G5 3.9 32.7 1.0 O C:HOH218 3.9 38.6 1.0 N7 C:G4 4.0 37.1 1.0 O C:HOH207 4.0 43.3 1.0 O6 C:G4 4.1 33.2 1.0 C5 C:G6 4.3 35.4 1.0 OP2 D:A10 4.4 31.7 1.0 C5 C:G5 4.4 33.2 1.0 C6 C:G5 4.5 32.4 1.0 C5 C:G4 4.6 35.9 1.0 C8 C:G5 4.6 35.0 1.0 O D:HOH121 4.7 41.5 1.0 C6 C:G4 4.7 31.4 1.0 N7 C:G6 4.8 41.6 1.0 C8 C:G4 4.9 35.8 1.0 C2 C:G6 5.0 31.1 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of OR4K15 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 OR4K15 Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:43.6 occ:1.00 O F:HOH115 1.9 32.6 1.0 N1 F:A11 3.1 37.2 1.0 N1 E:C7 3.3 41.3 1.0 C1' E:C7 3.4 46.0 1.0 C6 E:C7 3.5 38.0 1.0 N2 E:G5 3.6 31.6 1.0 N6 F:A11 3.7 33.2 1.0 C2 E:C7 3.7 38.1 1.0 C6 F:A11 3.8 34.5 1.0 O4' E:C7 3.9 48.2 1.0 C2 E:G5 3.9 32.7 1.0 C2 F:A11 4.0 36.4 1.0 C5 E:C7 4.1 38.9 1.0 O2 F:C12 4.1 33.7 1.0 O2 E:C7 4.2 40.7 1.0 O4' E:G6 4.2 47.1 1.0 N1 E:G5 4.2 27.6 1.0 N3 E:C7 4.3 37.1 1.0 C4 E:C7 4.4 36.5 1.0 N3 E:G5 4.5 34.2 1.0 C1' E:G6 4.5 40.2 1.0 C2 F:C12 4.7 30.3 1.0 N3 F:C12 4.8 27.9 1.0 C2' E:C7 4.8 47.7 1.0 C8 E:G6 5.0 39.5 1.0

Y.Ren, X.Lin, W.Liao, X.Peng, J.Deng, Z.Zhang, J.Zhan, Y.Zhou, E.Westhof, D.M.J.Lilley, J.Wang, L.Huang. A General Strategy For Engineering Gu Base Pairs to Facilitate Rna Crystallization. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 39721592
DOI: 10.1093/NAR/GKAE1218