Table 1 Predicted binding pockets of nitrate reductase and their characteristics.
Volume (ų) | Functional domain | Key residues | Functional role | |
|---|---|---|---|---|
Pocket 1 | 1089 | Molybdenum cofactor (MoCo) binding site | His84, Arg89, Asp213, Asp221, Cys237, Trp238, Phe18, Tyr230, Phe236 | Largest cavity; catalytic MoCo active site, stabilizes catalytic center, supports redox activity, positions nitrate substrate, and disulfide potential suggests redox regulation. |
Pocket 2 | 511 | FAD/NADPH-binding domain | Arg2, Lys3, Lys5, Arg124, Trp117, Tyr121, Asp122 | Binds NADPH phosphate groups; aromatic residues stack with FAD’s isoalloxazine ring, and Asp122 that may hydrogen-bond to NADPH. |
Pocket 3 | 173 | Allosteric regulation site | Arg192, Glu194, Lys199, Trp203 | Charged cluster suggests potential phosphorylation site; Trp203 mediates protein–protein interactions. |
Pocket 4 | 154 | Proton relay/substrate channel | Asp164, Glu165, Asp254, His163 | Acidic residues (Asp164, Glu165, Asp254) facilitate proton transfer, and His163 acts as a proton shuttle during catalysis. |
Pocket 5 | 142 | Redox-sensing disulfide | Cys41, Tyr52 | Potential disulfide bond formation under oxidative stress and electron transfer roles. |
Pocket 6 | 129 | Substrate access channel | Asp46, Lys47, Tyr53, Trp117 | Charged (Asp46, Lys47) and aromatic (Tyr53, Trp117) residues guide nitrate into Pocket 1. |
Pocket 7 | 122 | Heme-binding interface | Arg146, Asp151, Tyr147, Tyr150 | Heme propionate coordination and stabilization. |
Pocket 8 | 118 | Solvent-exposed electrostatic patch | Arg25, Lys29, Arg35 | Basic residues potentially anchor nitrate reductase to membranes or interacting partner proteins. |
