Barium in PDB 8zau: Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G

The structure of Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G, PDB code: 8zau 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)	25.20 / 2.43
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	49.4, 52.588, 100.784, 90, 90, 90
R / Rfree (%)	23.9 / 28.4

The structure of Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Barium atom in the Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G (pdb code 8zau). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 5 binding sites of Barium where determined in the Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G, PDB code: 8zau:
Jump to Barium binding site number: 1; 2; 3; 4; 5;

Barium binding site 1 out of 5 in the Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba102 b:42.9 occ:1.00 HO2' A:A36 2.5 52.8 1.0 OP2 A:A37 3.0 38.4 1.0 O3' A:A36 3.1 39.0 1.0 O2' A:A36 3.2 43.8 1.0 P A:A37 3.7 41.2 1.0 H5'' A:A37 4.0 53.1 1.0 H1' A:A36 4.1 46.5 1.0 C2' A:A36 4.1 41.2 1.0 C3' A:A36 4.2 43.1 1.0 OP2 A:C35 4.5 42.5 1.0 H3' A:A36 4.6 52.1 1.0 C1' A:A36 4.7 38.5 1.0 C5' A:A37 4.7 44.0 1.0 O4 A:U7 4.7 37.5 1.0 O5' A:A37 4.7 44.5 1.0 H5' A:A37 4.7 53.1 1.0 OP1 A:A37 4.7 46.6 1.0 H2' A:A36 5.0 49.8 1.0

Barium binding site 2 out of 5 in the Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba103 b:61.3 occ:1.00 O A:HOH205 2.0 37.6 1.0 O4 A:U50 2.6 62.3 1.0 O6 A:G59 3.0 60.9 1.0 O4 A:U58 3.0 66.1 1.0 O6 A:G49 3.1 60.6 1.0 H3 A:U50 3.6 72.7 1.0 H61 A:A51 3.6 72.9 1.0 C4 A:U50 3.7 60.5 1.0 C4 A:U58 4.0 63.9 1.0 H62 A:A51 4.0 72.9 1.0 C6 A:G49 4.0 58.4 1.0 H42 A:C60 4.0 65.0 1.0 N3 A:U50 4.0 60.3 1.0 N6 A:A51 4.0 60.5 1.0 C6 A:G59 4.2 59.6 1.0 H5 A:U58 4.4 80.7 1.0 N7 A:G49 4.5 60.1 1.0 N4 A:C60 4.5 54.3 1.0 H41 A:C60 4.6 65.0 1.0 C5 A:G49 4.6 59.2 1.0 C5 A:U58 4.7 67.0 1.0 N7 A:G59 4.9 64.5 1.0 H3 A:U58 4.9 78.3 1.0 C5 A:U50 4.9 55.9 1.0 N3 A:U58 4.9 65.0 1.0 C5 A:G59 5.0 60.5 1.0

Barium binding site 3 out of 5 in the Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba104 b:89.9 occ:0.50 OP2 A:U7 5.0 45.0 1.0

Barium binding site 4 out of 5 in the Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba105 b:86.5 occ:1.00 OP2 A:G41 2.7 61.6 1.0 O4 A:U45 3.3 49.6 1.0 O A:HOH208 3.6 57.6 1.0 H5 A:U45 3.6 49.8 1.0 P A:G41 3.7 40.9 1.0 C4 A:U45 4.0 47.1 1.0 O3' A:A40 4.0 54.9 1.0 C5 A:U45 4.1 41.2 1.0 OP1 A:G41 4.2 55.4 1.0 HN9 A:GUN101 4.4 47.8 1.0 H62 A:A46 4.7 54.0 1.0 OP2 A:A44 4.8 53.9 1.0 HO2' A:A40 4.8 65.6 1.0 O2' A:A40 4.9 54.4 1.0

Barium binding site 5 out of 5 in the Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of A Methyl Transferase Ribozyme Mutant - C29U and A59G within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba106 b:85.5 occ:1.00 N7 A:G31 3.0 43.5 1.0 O6 A:G31 3.0 44.4 1.0 O A:HOH211 3.0 44.5 1.0 O A:HOH207 3.1 53.3 1.0 N7 A:G30 3.3 53.2 1.0 C5 A:G31 3.6 44.7 1.0 C6 A:G31 3.6 43.0 1.0 O A:HOH218 3.7 56.3 1.0 C5 A:G30 3.8 53.5 1.0 O6 A:G30 3.9 47.5 1.0 C8 A:G30 4.1 55.6 1.0 C6 A:G30 4.1 50.0 1.0 O A:HOH216 4.1 52.5 1.0 C8 A:G31 4.1 44.7 1.0 H8 A:G30 4.3 67.0 1.0 H8 A:G31 4.4 54.0 1.0 H41 A:C18 4.5 52.6 1.0 N7 A:G32 4.7 37.8 1.0 O6 A:G32 4.7 45.8 1.0 O A:HOH217 4.8 53.7 1.0 C4 A:G30 4.8 50.8 1.0 OP2 A:G30 4.9 64.1 1.0 N9 A:G30 4.9 51.7 1.0 C4 A:G31 5.0 46.8 1.0 N1 A:G31 5.0 41.1 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