Johnson was the acting street deputy at the time and signed off on official police reports after Christian Green was killed.
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Officer Robert Gonzalez says the 17-year old pointed a gun at him. But an attorney for Green's family says the teen was not armed and was running away from police when the shooting happened.
On July 4 2013, Chicago police officers alleged they chased the 17-year-old and Green tried to throw a weapon in a trash can, missed and came back to get it.
Surveillance video just released on Thursday showed some of the pursuit but not the shooting.
The attorney for Green's estate contends the officers' accounts were lies and a weapon was not found near Green.
On Thursday, the superintendent testified that he spoke with each officer involved.
"Mr. Green turned running, pointing a handgun in their direction. Turned away, but turned at them," he said. "At that point, Officer Gonzalez had fear of his life and discharged his weapon"
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"If a person has a gun in his hand, he can use it to shoot you and kill you. At that point you have a right to defend yourself," Johnson said.
The Superintendent tilted his head to the jury and pointed to the back of his head and said, "I have a constant reminder that someone can fire at you when they are running."
Earlier on Thursday, Officer George Hernandez testified that Green pointed a gun at him and his partner Officer Robert Gonzalez.
During a quiet moment in court, Green's mother became emotional. The judge asked that she leave the courtroom.
An autopsy revealed the teen was shot in the back.