US-led forces and Iran-backed militias exchanged fire for the second day in a row, but the Biden administration said the fighting would not affect nuclear negotiations with Tehran.

US Central Command said the two bases, Conoco and Green Village, used for the US-led mission against the Islamic State (IS) had come under rocket attack on Wednesday evening, but there were no serious injuries. The US struck back with attack helicopters, killing “two or three suspected Iran-backed militants conducting one of the attacks” and destroying vehicles.

“The response was proportional and deliberate,” a CentCom statement said. “The United States does not seek conflict with Iran, but we will continue to take the measures necessary to protect and defend our people.”

US officials have stressed there is no connection between the fighting between the US and alleged Iranian proxies, and the delicate endgame of negotiations to revive a 2015 agreement between Iran and major powers which has largely disintegrated since Donald Trump withdrew the US in 2018.

The state department confirmed that the US had sent a response on Wednesday to Iranian proposals on ways to return to the deal.

Iran said that it had received the US response and was studying it. Both the US and Iran responses follow a proposed EU blueprint for restarting the nuclear deal, by which Iran would roll back its nuclear program in return for sanctions relief.

John Kirby, spokesman for the US national security council said Iran had made some concessions which had closed the distance between the negotiating positions but added: “Gaps remain. We’re not there yet.”

As the nuclear negotiations appeared to end the final stretch, fighting flared up in Syria, where the US-led anti-IS coalition are in close proximity to Tehran-supported militia in Syria and Iraq. Wednesday’s clash came a day after US airstrikes against targets in Deir Azzour, which Washington said were arms bunkers used by militias affiliated to Iran’s Islamic Revolutionary Guard Corps (IRGC). That action was taken in retaliation for drone attacks on US military outposts on 15 August.

Kahl said Tuesday’s US strikes had struck nine bunkers, and had originally targeted 11 but people had been seen near two of them. The aim was not to cause casualties but to send a deterrent message, he said.

“Our response was extraordinarily carefully calibrated. It was meant to be proportional to the attacks that the Iran-backed groups carried out on 15 August. It was very precise,” he said.

There have been a succession of attacks on the residual US military mission in Syria, left behind to monitor and contain the remnants of IS. Kahl said the decision was taken to strike back after the 15 August drone attack in part because wreckage from a downed drone could be traced back directly to Tehran. He added that US airstrikes were also a cumulative response to a series of attacks by Iranian-based militias.

“We don’t want Iran to draw the wrong conclusion that they can continue just doing this and get away with it,” he said.

He insisted the US military operations in Syria were not linked to negotiations on the nuclear deal, known as the Joint Comprehensive Plan of Action (JCPOA).

“Whether the JCPOA is reborn or not, it actually has nothing to do with our willingness and resolve to defend ourselves,” Kahl said. “I think the strike last night was a pretty clear communication to the Iranians that these things are on different tracks.”

Ellie Geranmayeh, a senior policy fellow at the European Council on Foreign Relations, said there were signs of anticipation on both sides of a deal being clinched.

“The US and Iranian governments have begun shifting the message for their audiences in expectation of something happening,” Geranmayeh said.

The Iranian press has noticeably changed tone over recent weeks, swapping nationalistic and anti-western views for more neutral positions on the deal, which Iranian leaders have framed as a pillar of sovereignty.

The Israeli government, which has struggled to prevent the JCPOA being reborn, struck a defiant tone as the prospect of a new deal rose.

“We are not prepared to live with a nuclear threat above our heads from an extremist, violent Islamist regime,” the prime minister, Yair Lapid, said. “This will not happen, because we will not let it happen.”