Magnesium in PDB 8ioe: Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly (pdb code 8ioe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly, PDB code: 8ioe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:174.5 occ:1.00 O3B A:TPP801 2.3 160.2 1.0 O A:TYR213 2.4 181.5 1.0 O2A A:TPP801 2.5 160.2 1.0 OD1 A:ASN211 2.5 163.9 1.0 O2B A:TPP801 2.6 160.2 1.0 PB A:TPP801 2.8 160.2 1.0 OD1 A:ASP178 2.9 161.4 1.0 ND2 A:ASN211 2.9 163.9 1.0 CG A:ASN211 3.1 163.9 1.0 O3A A:TPP801 3.3 160.2 1.0 PA A:TPP801 3.5 160.2 1.0 NZ A:LYS293 3.5 172.3 1.0 C A:TYR213 3.5 181.5 1.0 CE A:LYS293 3.6 172.3 1.0 CG A:ASP178 3.9 161.4 1.0 OD2 A:ASP178 4.1 161.4 1.0 CG2 A:THR219 4.2 172.5 1.0 O1B A:TPP801 4.3 160.2 1.0 N A:LYS214 4.3 178.8 1.0 CA A:LYS214 4.4 178.8 1.0 N A:TYR213 4.4 181.5 1.0 O7 A:TPP801 4.5 160.2 1.0 CA A:TYR213 4.6 181.5 1.0 CB A:ASN211 4.6 163.9 1.0 O1A A:TPP801 4.6 160.2 1.0 N A:GLY179 4.6 158.9 1.0 N A:ASP178 4.9 161.4 1.0 O A:HIS209 5.0 155.0 1.0

Magnesium binding site 2 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:183.3 occ:1.00 O1B B:TPP801 2.1 164.6 1.0 O1A B:TPP801 2.1 164.6 1.0 O B:TYR213 2.1 191.2 1.0 OD1 B:ASN211 2.2 172.1 1.0 OD1 B:ASP178 2.8 168.7 1.0 CG B:ASN211 2.9 172.1 1.0 ND2 B:ASN211 2.9 172.1 1.0 C B:TYR213 3.3 191.2 1.0 PB B:TPP801 3.4 164.6 1.0 PA B:TPP801 3.4 164.6 1.0 O3A B:TPP801 3.6 164.6 1.0 CG B:ASP178 3.6 168.7 1.0 NZ B:LYS293 3.6 177.1 1.0 OD2 B:ASP178 3.8 168.7 1.0 CE B:LYS293 3.8 177.1 1.0 CG2 B:THR219 3.8 177.8 1.0 N B:TYR213 4.0 191.2 1.0 N B:LYS214 4.1 182.1 1.0 O7 B:TPP801 4.1 164.6 1.0 O2B B:TPP801 4.2 164.6 1.0 CA B:TYR213 4.2 191.2 1.0 CA B:LYS214 4.2 182.1 1.0 N B:GLY179 4.3 165.8 1.0 CB B:ASN211 4.4 172.1 1.0 O3B B:TPP801 4.4 164.6 1.0 O2A B:TPP801 4.6 164.6 1.0 N B:GLY212 4.7 179.7 1.0 N B:ASP178 4.8 168.7 1.0 N B:ASN211 4.9 172.1 1.0 CB B:ASP178 4.9 168.7 1.0 O B:HIS209 4.9 159.9 1.0 CA B:GLY179 5.0 165.8 1.0

Magnesium binding site 3 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg802 b:177.3 occ:1.00 O3B C:TPP801 2.2 162.7 1.0 O C:TYR213 2.4 185.0 1.0 OD1 C:ASN211 2.4 168.8 1.0 O2A C:TPP801 2.6 162.7 1.0 O2B C:TPP801 2.8 162.7 1.0 PB C:TPP801 2.8 162.7 1.0 ND2 C:ASN211 2.8 168.8 1.0 OD1 C:ASP178 2.9 162.1 1.0 CG C:ASN211 3.0 168.8 1.0 O3A C:TPP801 3.4 162.7 1.0 NZ C:LYS293 3.4 178.2 1.0 C C:TYR213 3.5 185.0 1.0 CE C:LYS293 3.5 178.2 1.0 PA C:TPP801 3.6 162.7 1.0 CG C:ASP178 3.8 162.1 1.0 OD2 C:ASP178 4.0 162.1 1.0 O1B C:TPP801 4.3 162.7 1.0 N C:LYS214 4.3 178.5 1.0 CG2 C:THR219 4.3 172.3 1.0 N C:TYR213 4.3 185.0 1.0 CA C:LYS214 4.3 178.5 1.0 CB C:ASN211 4.5 168.8 1.0 CA C:TYR213 4.5 185.0 1.0 O7 C:TPP801 4.6 162.7 1.0 N C:GLY179 4.6 156.4 1.0 O1A C:TPP801 4.7 162.7 1.0 N C:ASP178 4.9 162.1 1.0 O C:HIS209 4.9 157.4 1.0

Magnesium binding site 4 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg802 b:180.7 occ:1.00 O2B D:TPP801 2.1 163.3 1.0 OD1 D:ASN211 2.1 169.2 1.0 O D:TYR213 2.1 186.3 1.0 O1A D:TPP801 2.3 163.3 1.0 CG D:ASN211 2.8 169.2 1.0 ND2 D:ASN211 2.8 169.2 1.0 OD1 D:ASP178 2.8 162.7 1.0 OD2 D:ASP178 3.0 162.7 1.0 C D:TYR213 3.2 186.3 1.0 CG D:ASP178 3.3 162.7 1.0 PB D:TPP801 3.4 163.3 1.0 PA D:TPP801 3.5 163.3 1.0 NZ D:LYS293 3.6 178.6 1.0 O3A D:TPP801 3.7 163.3 1.0 CG2 D:THR219 3.8 173.0 1.0 CE D:LYS293 3.8 178.6 1.0 N D:TYR213 4.0 186.3 1.0 N D:LYS214 4.0 179.7 1.0 CA D:LYS214 4.1 179.7 1.0 CA D:TYR213 4.2 186.3 1.0 O7 D:TPP801 4.2 163.3 1.0 O3B D:TPP801 4.2 163.3 1.0 CB D:ASN211 4.3 169.2 1.0 N D:GLY179 4.4 157.1 1.0 O1B D:TPP801 4.4 163.3 1.0 N D:GLY212 4.6 172.2 1.0 CB D:ASP178 4.7 162.7 1.0 O2A D:TPP801 4.7 163.3 1.0 N D:ASP178 4.8 162.7 1.0 N D:ASN211 4.9 169.2 1.0 O D:HIS209 4.9 155.5 1.0 CA D:ASN211 5.0 169.2 1.0 C D:GLY212 5.0 172.2 1.0

Magnesium binding site 5 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg802 b:182.4 occ:1.00 O3B E:TPP801 2.3 165.7 1.0 O E:TYR213 2.4 190.1 1.0 O2A E:TPP801 2.5 165.7 1.0 OD1 E:ASN211 2.5 171.4 1.0 O2B E:TPP801 2.7 165.7 1.0 PB E:TPP801 2.8 165.7 1.0 ND2 E:ASN211 2.9 171.4 1.0 OD1 E:ASP178 3.1 168.7 1.0 CG E:ASN211 3.1 171.4 1.0 O3A E:TPP801 3.3 165.7 1.0 PA E:TPP801 3.4 165.7 1.0 NZ E:LYS293 3.5 175.6 1.0 C E:TYR213 3.5 190.1 1.0 CE E:LYS293 3.6 175.6 1.0 CG E:ASP178 3.9 168.7 1.0 OD2 E:ASP178 4.0 168.7 1.0 CG2 E:THR219 4.2 177.2 1.0 O1B E:TPP801 4.3 165.7 1.0 N E:LYS214 4.3 184.0 1.0 N E:TYR213 4.3 190.1 1.0 CA E:LYS214 4.4 184.0 1.0 O7 E:TPP801 4.5 165.7 1.0 CA E:TYR213 4.5 190.1 1.0 O1A E:TPP801 4.5 165.7 1.0 N E:GLY179 4.6 166.2 1.0 CB E:ASN211 4.6 171.4 1.0 N E:ASP178 4.9 168.7 1.0 O E:HIS209 4.9 161.1 1.0

Magnesium binding site 6 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg802 b:176.2 occ:1.00 O1B F:TPP801 2.1 160.6 1.0 O F:TYR213 2.1 181.4 1.0 O1A F:TPP801 2.1 160.6 1.0 OD1 F:ASN211 2.2 163.9 1.0 OD1 F:ASP178 2.8 160.9 1.0 ND2 F:ASN211 2.9 163.9 1.0 CG F:ASN211 2.9 163.9 1.0 C F:TYR213 3.2 181.4 1.0 PB F:TPP801 3.4 160.6 1.0 PA F:TPP801 3.4 160.6 1.0 O3A F:TPP801 3.6 160.6 1.0 NZ F:LYS293 3.6 173.9 1.0 CG F:ASP178 3.6 160.9 1.0 CG2 F:THR219 3.7 170.6 1.0 CE F:LYS293 3.8 173.9 1.0 OD2 F:ASP178 3.8 160.9 1.0 N F:TYR213 4.0 181.4 1.0 N F:LYS214 4.0 178.9 1.0 CA F:LYS214 4.1 178.9 1.0 O7 F:TPP801 4.2 160.6 1.0 O2B F:TPP801 4.2 160.6 1.0 CA F:TYR213 4.2 181.4 1.0 N F:GLY179 4.3 158.6 1.0 CB F:ASN211 4.4 163.9 1.0 O3B F:TPP801 4.5 160.6 1.0 O2A F:TPP801 4.6 160.6 1.0 N F:GLY212 4.7 169.4 1.0 N F:ASP178 4.8 160.9 1.0 N F:ASN211 4.9 163.9 1.0 CB F:ASP178 5.0 160.9 1.0 C F:LYS214 5.0 178.9 1.0 O F:HIS209 5.0 153.2 1.0 CA F:GLY179 5.0 158.6 1.0

Magnesium binding site 7 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg802 b:176.0 occ:1.00 O3B G:TPP801 2.2 161.2 1.0 O G:TYR213 2.4 182.5 1.0 OD1 G:ASN211 2.5 165.2 1.0 O2A G:TPP801 2.5 161.2 1.0 O2B G:TPP801 2.7 161.2 1.0 PB G:TPP801 2.8 161.2 1.0 ND2 G:ASN211 2.9 165.2 1.0 OD1 G:ASP178 2.9 161.0 1.0 CG G:ASN211 3.1 165.2 1.0 O3A G:TPP801 3.3 161.2 1.0 PA G:TPP801 3.5 161.2 1.0 C G:TYR213 3.5 182.5 1.0 NZ G:LYS293 3.5 173.9 1.0 CE G:LYS293 3.6 173.9 1.0 CG G:ASP178 3.8 161.0 1.0 OD2 G:ASP178 4.0 161.0 1.0 CG2 G:THR219 4.2 171.8 1.0 O1B G:TPP801 4.2 161.2 1.0 N G:LYS214 4.3 180.5 1.0 N G:TYR213 4.3 182.5 1.0 CA G:LYS214 4.4 180.5 1.0 O7 G:TPP801 4.5 161.2 1.0 CA G:TYR213 4.5 182.5 1.0 N G:GLY179 4.5 158.8 1.0 O1A G:TPP801 4.6 161.2 1.0 CB G:ASN211 4.6 165.2 1.0 N G:ASP178 4.9 161.0 1.0 O G:HIS209 4.9 154.0 1.0

Magnesium binding site 8 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg802 b:181.8 occ:1.00 O1B H:TPP801 2.0 164.2 1.0 O H:TYR213 2.2 190.1 1.0 O1A H:TPP801 2.2 164.2 1.0 OD1 H:ASN211 2.3 171.3 1.0 OD1 H:ASP178 2.7 168.3 1.0 ND2 H:ASN211 2.8 171.3 1.0 CG H:ASN211 2.9 171.3 1.0 C H:TYR213 3.2 190.1 1.0 PB H:TPP801 3.4 164.2 1.0 PA H:TPP801 3.5 164.2 1.0 O3A H:TPP801 3.6 164.2 1.0 NZ H:LYS293 3.7 176.5 1.0 CG H:ASP178 3.7 168.3 1.0 CE H:LYS293 3.8 176.5 1.0 CG2 H:THR219 3.9 176.9 1.0 OD2 H:ASP178 3.9 168.3 1.0 N H:LYS214 4.0 180.4 1.0 CA H:LYS214 4.0 180.4 1.0 N H:TYR213 4.1 190.1 1.0 O2B H:TPP801 4.2 164.2 1.0 O7 H:TPP801 4.2 164.2 1.0 CA H:TYR213 4.3 190.1 1.0 N H:GLY179 4.4 164.6 1.0 CB H:ASN211 4.4 171.3 1.0 O3B H:TPP801 4.4 164.2 1.0 O2A H:TPP801 4.6 164.2 1.0 N H:GLY212 4.9 178.2 1.0 N H:ASP178 4.9 168.3 1.0 C H:LYS214 5.0 180.4 1.0 O H:HIS209 5.0 160.3 1.0

Magnesium binding site 9 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg802 b:179.8 occ:1.00 O2B I:TPP801 2.0 164.4 1.0 O2A I:TPP801 2.1 164.4 1.0 OD1 I:ASN211 2.2 170.0 1.0 O I:TYR213 2.2 186.7 1.0 OD1 I:ASP178 2.7 164.2 1.0 ND2 I:ASN211 2.7 170.0 1.0 CG I:ASN211 2.8 170.0 1.0 C I:TYR213 3.4 186.7 1.0 PB I:TPP801 3.4 164.4 1.0 PA I:TPP801 3.4 164.4 1.0 NZ I:LYS293 3.6 178.3 1.0 O3A I:TPP801 3.6 164.4 1.0 CE I:LYS293 3.7 178.3 1.0 CG I:ASP178 3.7 164.2 1.0 OD2 I:ASP178 3.9 164.2 1.0 CG2 I:THR219 3.9 174.5 1.0 O7 I:TPP801 4.1 164.4 1.0 N I:TYR213 4.1 186.7 1.0 O1B I:TPP801 4.2 164.4 1.0 N I:LYS214 4.2 180.9 1.0 CB I:ASN211 4.3 170.0 1.0 CA I:TYR213 4.3 186.7 1.0 CA I:LYS214 4.3 180.9 1.0 N I:GLY179 4.4 161.0 1.0 O3B I:TPP801 4.4 164.4 1.0 O1A I:TPP801 4.6 164.4 1.0 N I:GLY212 4.8 174.4 1.0 N I:ASP178 4.8 164.2 1.0 O I:HIS209 4.9 156.3 1.0 N I:ASN211 4.9 170.0 1.0 CA I:ASN211 5.0 170.0 1.0

Magnesium binding site 10 out of 12 in the Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Cyanobacteria Phosphoketolase in Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg802 b:176.7 occ:1.00 O2B J:TPP801 2.1 163.6 1.0 O J:TYR213 2.4 183.4 1.0 OD1 J:ASN211 2.5 167.9 1.0 O1A J:TPP801 2.5 163.6 1.0 O1B J:TPP801 2.7 163.6 1.0 PB J:TPP801 2.7 163.6 1.0 ND2 J:ASN211 2.9 167.9 1.0 CG J:ASN211 3.1 167.9 1.0 OD1 J:ASP178 3.1 162.4 1.0 O3A J:TPP801 3.3 163.6 1.0 PA J:TPP801 3.4 163.6 1.0 NZ J:LYS293 3.5 176.7 1.0 C J:TYR213 3.5 183.4 1.0 CE J:LYS293 3.6 176.7 1.0 CG J:ASP178 3.9 162.4 1.0 OD2 J:ASP178 4.0 162.4 1.0 O3B J:TPP801 4.2 163.6 1.0 CG2 J:THR219 4.2 171.0 1.0 CA J:LYS214 4.2 176.3 1.0 N J:LYS214 4.2 176.3 1.0 N J:TYR213 4.4 183.4 1.0 O7 J:TPP801 4.5 163.6 1.0 O2A J:TPP801 4.6 163.6 1.0 CB J:ASN211 4.6 167.9 1.0 CA J:TYR213 4.6 183.4 1.0 N J:GLY179 4.6 157.4 1.0 N J:ASP178 4.9 162.4 1.0 O J:HIS209 4.9 156.8 1.0

C.-W.Chang, M.-D.Tsai. An Atp-Sensitive Phosphoketolase Regulates Carbon Fixation in Cyanobacteria. Nat Metab 2023.
ISSN: ISSN 2522-5812
DOI: 10.1038/S42255-023-00831-W