A Level 3 sex offender allegedly raped a woman in her Beacon Hill home and then tied her to a chair and threatened to kill her if she did not provide him with the PIN for her ATM bank card, a Suffolk County prosecutor said today.

Anthony G. Williams was arraigned in Boston Municipal Court today where he pleaded not guilty to charges of aggravated rape, kidnapping, armed burglary and assault and battery with a dangerous weapon stemming from the Nov. 10 attack that led Boston police to step up patrols in a neighborhood unaccustomed to violence.

Judge Mark Hart Summerville adopted the recommendation of Suffolk Assistant District Attorney Holly Broadbent and set bail at $1 million cash for the 45-year-old Williams, who was arrested at his mother’s Boston home on Tuesday but who also lives in homeless shelters.

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At the request of his defense attorney, Erin R. Opperman, and with the backing of the prosecution, Williams did not come into the courtroom today because eyewitness identification will be a key issue in the case.

Opperman asked for $50,000 cash bail and said that Williams’s sister and his niece were in the court to support him. When Summerville set bail at $1 million cash, one of the woman broke down in tears. After the arraignment the older of the women — both of whom refused to identify themselves — expressed support in a brief comment.

“He’s innocent,’’ the older woman said.

According to Broadbent, a woman was returning to her Beacon Hill home after spending an evening with friends when Williams, wearing a tan jacket and white construction hat, came up behind her and put his hand over his mouth to keep her from screaming.

He allegedly forced the woman inside her home and once inside, stole jewelry, an iPhone, and an iPad from the woman—after he repeatedly threatened to kill her, having armed himself with a knife taken from the woman’s kitchen, Broadbent said.

At that point during the ordeal, Williams allegedly raped the woman, Broadbent said.

She said Williams then forced the woman into the kitchen where he tied her to some furniture and once again threatened to kill her as he demanded the PIN for her bank ATM card. Broadbent said the woman provided Williams with the PIN, who then left the woman’s home.

The prosecutor alleged that Williams went to an nearby ATM that morning and used the woman’s ATM card to withdraw cash, an action that was captured by bank surveillance cameras and was released by Boston police as they tried to identify the woman’s attacker.

Broadbent said that a shelter worker where Williams sometimes lived recognized Williams from the surveillance images and contacted police.

She also said that Williams was also tied to the attack by a Boston store owner who brought the stolen iPhone from him a few hours after the violent assault on Beacon Hill. Williams was captured on surveillance camera in that store conducting the transaction, but Broadbent also said the store owner knows Williams and identified him to police.

According to Broadbent, the Sex Offender Registry Board, and Essex District Attorney Jonathan Blodgett’s office, Williams’s criminal record dates back to the 1980s and includes a conviction for raping a woman in Salem early in the morning of March 20, 1996.

Williams was finally tried in 1998 and convicted even though he took the stand and told Essex Superior Court jurors that the woman had agreed to have sex with him in return for his sharing some crack cocaine with her.

The woman, however, testified she was raped by a complete stranger she chanced upon as she walked on Bridge Street in the North Shore city, a man who dragged her into an alley, said he was armed with a knife — and then apologized after the violent assault.

Williams was sentenced to 12 to 14 years in state prison and was released from the Massachusetts Treatment Center for sex offenders in Bridgewater on Oct. 31, 2009 after serving his entire sentence, officials said.

Under state law, prosecutors have the responsibility of deciding whether to seek the civil commitment of sex offenders as sexually dangerous persons, a designation under civil law that allows them to be kept in Department of Correction custody beyond their prison sentences.

In a statement, Blodgett’s office said they investigated the possibility of having Williams civilly committed as sexually dangerous person.

“The sexually dangerous persons statute requires proof beyond a reasonable doubt that the defendant suffered from a mental abnormality or personality disorder, which at the time of our review in 2009, there was no such evidence,’’ prosecutors said in the statement.

Sometime after his 2009 release from prison, Williams was classified by the Sex Offender Registry Board as a Level 3 offender, which the board describes on its website as a person who poses a high risk to reoffend.

Under state law, Williams was required to regularly inform police and the board of his address and where he was working if he had a job. However, Williams failed to register as required and was arrested and arraigned in the BMC on a charge of failing to register.

This year, Williams was twice before judges in the BMC on the failing to register charge and also on a separate assault and battery charge, but in each instance, Williams was released from custody.