I finally find the issue !
What I do :
Edit /etc/apache2/apache2.conf and change the Timeout value to 600
systemctl restart apache2
Edit /etc/mysql/my.cnf and change value like this :
[client]
port=3306
socket=/var/run/mysqld/mysqld.sock
[mysqld_safe]
socket=/var/run/mysqld/mysqld.sock
[mysqld]
user=mysql
pid-file=/var/run/mysqld/mysqld.pid
socket=/var/run/mysqld/mysqld.sock
port=3306
basedir=/usr
datadir=/var/lib/mysql
tmpdir=/tmp
lc-messages-dir=/usr/share/mysql
log_error=/var/log/mysql/error.log
sql_mode=""
symbolic-links=0
local-infile=0
skip-external-locking
key_buffer_size = 16M
#max_allowed_packet = 1M
max_allowed_packet = 100M
table_open_cache = 10
sort_buffer_size = 64K
read_buffer_size = 256K
read_rnd_buffer_size = 256K
net_buffer_length = 2K
thread_stack = 240K
#innodb_use_native_aio = 0
innodb_file_per_table
max_connections=30
max_user_connections=20
wait_timeout=100
interactive_timeout=50
long_query_time=5
!includedir /etc/mysql/conf.d/
And finally 
systemctl restart mysql
I think I had two limits which cause the issue : one under apache2 and another one with mysql
Thanks for all your answers, it’s help me to dig further