This study aims to discover spatial correlations between Earth observations and atmospheric states to improve the forecasting accuracy of global atmospheric state estimation, which are usually conducted using conventional numerical weather prediction (NWP) systems and is the beginning of weather forecasting. NWP systems predict future atmospheric states at fixed locations, which are called NWP grid points, by analyzing previous atmospheric states and newly acquired Earth observations without fixed locations. Thus, surrounding meteorological context and the changing locations of the observations make spatial correlations between atmospheric states and observations over time. To handle complicated spatial correlations, which change dynamically, we employ spatiotemporal graph neural networks (STGNNs) with structure learning. However, structure learning has an inherent limitation that this can cause structural information loss and over-smoothing problem by generating excessive edges. To solve this problem, we regulate edge sampling by adaptively determining node degrees and considering the spatial distances between NWP grid points and observations. We validated the effectiveness of the proposed method by using real-world atmospheric state and observation data from East Asia. Even in areas with high atmospheric variability, the proposed method outperformed existing STGNN models with and without structure learning.