Proper evaluation of the ionic structure of biomolecular systems remains challenging in X ray and cryo-EM techniques but is essential for advancing our understanding of complex structure/activity/solvent relationships. However, numerous studies overestimate the number of MgProper evaluation of the ionic structure of biomolecular systems remains challenging in X ray and cryo-EM techniques but is essential for advancing our understanding of complex structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg2+ in the deposited structures and underrate the importance of stereochemical rules to correctly assign these ions. Herein, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure and establish that stereochemical principles need consideration when evaluating ion binding features, even when K+ anomalous signals are available as it is the case for 6QNR. Assignment errors can result in misleading conceptions of the solvent structure of ribosomes and other RNA systems and should therefore be avoided. Our analysis resulted in a significant decrease of the number of bound Mg2+ in the 6QNR structure, suggesting that K+ and not Mg2+ is the prevalent ion in the ribosome 1st solvation shell. We stress that the use of proper stereochemical guidelines is critical for deflating the current Mg2+ bubble witnessed in many ribosome and other RNA structures. Herewith, we would like to draw the attention of the researchers interested in the ionic structure of biomolecular systems on the importance and complementarity of stereochemistry and other ion identification techniques such as those pertaining to the detection of anomalous signals of transition metals and K+ We also stress that for the identification of lighter ions such as Mg2+, Na+, , stereochemistry coupled with high resolution structures remain the best currently available option. in the deposited structures and underrate the importance of stereochemical rules to correctly assign these ions. Herein, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure and establish that stereochemical principles need consideration when evaluating ion binding features, even when K+ anomalous signals are available as it is the case for 6QNR. Assignment errors can result in misleading conceptions of the solvent structure of ribosomes and other RNA systems and should therefore be avoided. Our analysis resulted in a significant decrease of the number of bound Mg2+ in the 6QNR structure, suggesting that K+ and not Mg2+ is the prevalent ion in the ribosome 1st solvation shell. We stress that the use of proper stereochemical guidelines is critical for deflating the current Mg2+ bubble witnessed in many ribosome and other RNA structures. Herewith, we would like to draw the attention of the researchers interested in the ionic structure of biomolecular systems on the importance and complementarity of stereochemistry and other ion identification techniques such as those pertaining to the detection of anomalous signals of transition metals and K+ We also stress that for the identification of lighter ions such as Mg2+, Na+, , stereochemistry coupled with high resolution structures remain the best currently available option.

中文翻译：

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缩小 RNA Mg2+ 气泡。立体化学来救援！


在 X 射线和冷冻电镜技术中，正确评估生物分子系统的离子结构仍然具有挑战性，但对于增进我们对复杂结构/活性/溶剂关系的理解至关重要。然而，许多研究高估了 Mg 的数量。对生物分子系统离子结构的正确评估在 X 射线和冷冻电镜技术中仍然具有挑战性，但对于增进我们对复杂结构/活性/溶剂关系的理解至关重要。然而，许多研究高估了沉积结构中 Mg2+ 的数量，并低估了正确分配这些离子的立体化学规则的重要性。在此，我们重新评估核糖体离子结构的 PDBid 6QNR 和 6SJ6 模型，并确定在评估离子结合特征时需要考虑立体化学原理，即使 K+ 异常信号可用（如 6QNR 的情况）。分配错误可能会导致对核糖体和其他 RNA 系统的溶剂结构的误导性概念，因此应避免。我们的分析导致 6QNR 结构中结合的 Mg2+ 数量显着减少，表明核糖体第一溶剂化壳中的普遍离子是 K+ 而不是 Mg2+。我们强调，使用正确的立体化学指南对于缩小许多核糖体和其他 RNA 结构中当前出现的 Mg2+ 气泡至关重要。 在此，我们想提请对生物分子系统离子结构感兴趣的研究人员注意立体化学和其他离子识别技术（例如与过渡金属和 K+ 异常信号检测相关的技术）的重要性和互补性，我们还强调对于鉴定较轻的离子（例如 Mg2+、Na+），立体化学与高分辨率结构相结合仍然是目前最好的选择。并低估了立体化学规则对正确分配这些离子的重要性。在此，我们重新评估核糖体离子结构的 PDBid 6QNR 和 6SJ6 模型，并确定在评估离子结合特征时需要考虑立体化学原理，即使 K+ 异常信号可用（如 6QNR 的情况）。分配错误可能会导致对核糖体和其他 RNA 系统的溶剂结构的误导性概念，因此应避免。我们的分析导致 6QNR 结构中结合的 Mg2+ 数量显着减少，表明核糖体第一溶剂化壳中的普遍离子是 K+ 而不是 Mg2+。我们强调，使用正确的立体化学指南对于缩小许多核糖体和其他 RNA 结构中当前出现的 Mg2+ 气泡至关重要。 在此，我们想提请对生物分子系统离子结构感兴趣的研究人员注意立体化学和其他离子识别技术（例如与过渡金属和 K+ 异常信号检测相关的技术）的重要性和互补性，我们还强调对于鉴定较轻的离子（例如 Mg2+、Na+），立体化学与高分辨率结构相结合仍然是目前最好的选择。