Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) to catalyze the transfer of a sulfo group to heparan sulfate. Unlike 3-OST-1, does not convert non-anticoagulant heparan sulfate to anticoagulant heparan sulfate. 3'-phosphoadenylyl sulfate + alpha-D-glucosaminyl-[heparan sulfate](n) = 3-sulfo-alpha-D-glucosaminyl-[heparan sulfate](n) + adenosine 3',5'-bisphosphate + H(+) Expressed in liver and kidney, followed by heart, brain, lung and testis. Belongs to the sulfotransferase 1 family.