Differential atomic interactions upon nucleotide binding obtained from X-ray structures and MD simulations.

The average difference in distance () is shown for each of the three calculations; between X-ray t and r″ (column 1), MD simulations of t with and without ATP (column 2), and X-ray t and ATP bound t conformers (column 3). Negative values (above mid rule) depict interactions present (or closer) in the nucleotide free state (unliganded), while positive values (below mid rule) depict interactions closer in the nucleotide bound state.本结果展示了三种计算方案各自的距离平均差值：分别为X射线（X-ray）结构中的t与r''（第一列）、添加与不添加三磷酸腺苷（ATP）时针对t的分子动力学（MD）模拟（第二列），以及X射线结构中的t与结合ATP的t构象体（第三列）。负值（位于中线之上）代表在无核苷酸的未配体结合状态下存在（或距离更短）的相互作用；正值（位于中线之下）则代表在核苷酸结合状态下相互作用距离更短。