The bottleneck radius showed a deviation of about ± 0.23 Å (less than 15%).
Channels were calculated using MOLE 2.0 with parameters set as follows: minimal bottleneck radius 1.25 Å, probe radius 3 Å, surface cover radius 10 Å and origin radius 5 Å.
Channels belonging to the 2× family (mainly channels 2a, 2f, and in the case of BM3, channel 2b) were predicted to have bottleneck radii large enough to allow substrates/products to pass (> 2 Å) in both the CAM and BM3 structures, i.e., comparable or even larger than the solvent channel bottleneck radius (> 1.4 Å, radius of water molecule).
From a geometrical perspective, the most open channels were usually found within the open CAM structures, particularly 2a channels, which have a bottleneck radius larger than 2.6 Å.
In NdCld, the chlorite access channel has a length of 1.5 nm with a bottleneck radius of 0.28 nm.
Thus, despite the differences in overall and subunit structure, NdCld and NwCld have access channels of similar length and bottleneck radius.
The substrate channels to heme b of both NwCld subunits have calculated averages for the bottleneck radius of 2.6 ± 0.05 Å, for the length of 15.7 ± 1.7 Å, and for the volume of 389 ± 27 Å.
These values compare with the average values of the substrate channels for all five NdCld subunits (bottleneck radius of 2.8 ± 0.01 Å, length of 15.1 ± 0.9 Å, and volume of 518 ± 44 Å).
For the two most important tunnels in NdCld, characteristics reveal throughput-values of 0.89 and 0.86, bottleneck radii of 3.2 and 2.6, and lengths of 11.2 Å, respectively.
In addition to almost identical E°′ values, the substrate access channels of NdCld and NwCld have similar lengths (15.1 and 15.7 Å, respectively) and bottleneck radii (2.8 and 2.6 Å, respectively).
