Magnesium in PDB 7szu: Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6

The structure of Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6, PDB code: 7szu was solved by H.C.Rees, J.A.Piccirilli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.90 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.609, 96.992, 148.255, 90, 90, 90
R / Rfree (%)	21.9 / 26.3

The structure of Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6 (pdb code 7szu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6, PDB code: 7szu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6


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 Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6 within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg101 b:74.0 occ:1.00 O R:HOH352 2.0 77.8 1.0 O R:HOH290 2.0 73.0 1.0 OP2 R:A11 2.0 78.1 1.0 O R:HOH339 2.1 78.5 1.0 O R:HOH274 2.1 79.8 1.0 O R:HOH296 2.2 77.8 1.0 O R:HOH237 3.2 77.2 1.0 P R:A11 3.4 90.3 1.0 H3' R:C10 3.7 105.2 1.0 O5' R:A11 3.7 88.6 1.0 O R:HOH278 3.8 74.8 1.0 H62 R:A12 4.0 77.8 1.0 H8 R:A11 4.0 86.3 1.0 OP1 R:G18 4.2 71.2 1.0 O4 R:U13 4.3 66.1 1.0 O3' R:C10 4.4 95.2 1.0 OP1 R:C10 4.4 95.4 1.0 OP1 R:A11 4.4 87.0 1.0 N7 R:A12 4.4 69.9 1.0 C8 R:A11 4.4 73.7 1.0 C3' R:C10 4.5 89.4 1.0 N7 R:A11 4.5 74.7 1.0 OP2 R:C10 4.5 87.7 1.0 O5' R:C10 4.5 86.4 1.0 O R:HOH239 4.6 69.2 1.0 H3' R:A11 4.6 103.6 1.0 P R:C10 4.7 98.7 1.0 N6 R:A12 4.8 66.5 1.0 OP2 R:A12 5.0 81.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6


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 Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6 within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg102 b:48.7 occ:1.00 O R:HOH226 1.8 55.0 1.0 OP2 R:C52 1.8 58.2 1.0 OP2 R:U53 1.8 67.8 1.0 O R:HOH224 2.0 49.7 1.0 O R:HOH265 2.0 53.9 1.0 N7 R:G54 2.0 60.3 1.0 C5 R:G54 3.0 53.0 1.0 C8 R:G54 3.1 64.3 1.0 O6 R:G54 3.1 67.0 1.0 P R:C52 3.2 63.4 1.0 P R:U53 3.3 71.5 1.0 H5 R:U53 3.3 78.4 1.0 H5'' R:C52 3.4 87.7 1.0 H8 R:G54 3.4 75.4 1.0 C6 R:G54 3.4 61.1 1.0 H3' R:C52 3.5 83.3 1.0 OP1 R:C52 3.7 69.3 1.0 O3' R:C52 3.9 69.7 1.0 O5' R:C52 4.0 73.8 1.0 C5' R:C52 4.1 74.2 1.0 C3' R:C52 4.1 70.5 1.0 O5' R:U53 4.2 72.5 1.0 C5 R:U53 4.2 66.6 1.0 C4 R:G54 4.2 56.0 1.0 O3' R:A51 4.2 59.3 1.0 N9 R:G54 4.3 52.4 1.0 H6 R:U53 4.3 78.0 1.0 O R:HOH350 4.3 61.9 1.0 OP1 R:U53 4.3 73.7 1.0 C6 R:U53 4.7 66.2 1.0 C4' R:C52 4.7 68.6 1.0 N1 R:G54 4.8 58.5 1.0 H5' R:C52 4.9 87.7 1.0

H.C.Rees, W.Gogacz, N.S.Li, D.Koirala, J.A.Piccirilli. Structural Basis For Fluorescence Activation By Pepper Rna. Acs Chem.Biol. V. 17 1866 2022.
ISSN: ESSN 1554-8937
PubMed: 35759696
DOI: 10.1021/ACSCHEMBIO.2C00290