The 2006 article you cite, which contains no evidence at all establishing Putin’s responsibility, just innuendo and speculation, is a bit out of date.
“In August 2011, Russian prosecutors claimed they were close to solving the murder after detaining Dmitry Pavliuchenkov, a former policeman, who they alleged was the principal organiser. The following month Kommersant Daily reported that, according to Pavlyuchenkov, Lom-Ali Gaitukayev was the one negotiating with the person who ordered the killing, and although Pavlyuchenkov did not know the name, he suspected he could be the fugitive businessman and Putin critic Boris Berezovsky.
In December 2012 Dmitry Pavliutchenkov was found guilty and sentenced to 11 years in a high security penal colony.
In May 2014 five men were convicted of murdering Politkovskaya, including three defendants who had been acquitted in a previous trial. The defendants were three Chechen brothers, one of whom was accused of shooting Politkovskaya in the lobby of her Moscow apartment building. In June 2014 the men were sentenced to prison, two of them, Lom-Ali Gaitukayev and his nephew Rustam Makhmudov, receiving life sentences. It is still unclear who ordered or paid for the contract killing.”
https://en.wikipedia.org/wiki/Anna_Politkovskaya
“According to Pavlyuchenkov, it was Boris Berezovsky and former Chechen emissary in London Akhmed Zakayev who ordered the murder.” https://www.rt.com/op-edge/165348-russia-politkovskaya-court-verdict/
“Moscow’s highest criminal court on Monday sentenced five men to prison, including two to life sentences, for the 2006 murder of the investigative journalist Anna Politkovskaya, but left unsolved the question of who ordered the killing, the highest-profile attack on a Russian journalist of the last decade.
Ms. Politkovskaya, who was known for scathing criticism of Kremlin policies in the Russian republic of Chechnya and of the local strongman Ramzan A. Kadyrov, was 48 when she was shot to death in a contract killing in her Moscow apartment block.
On Monday, Judge Pavel Melyokhin sentenced Lom-Ali Gaitukayev, the organizer of the team that murdered Ms. Politkovskaya, and his nephew Rustam Makhmudov, the gunman, to life sentences in prison.
The sentences for the men, who were convicted last month, were the toughest punishment to date in the long-running investigation into Ms. Politkovskaya’s death.
Yet that investigation has yielded little publicly about who wanted Ms. Politkovskaya killed and why.
“The case cannot be closed because it has not been solved,” Vera Politkovskaya, Ms. Politkovskaya’s daughter, said by telephone.”