Magnesium in PDB 8io7: Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum in Dimeric Assembly

The binding sites of Magnesium atom in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum in Dimeric Assembly (pdb code 8io7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum in Dimeric Assembly, PDB code: 8io7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum in Dimeric 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 Phosphoketolase From Bifidobacterium Longum in Dimeric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:90.2 occ:1.00 O2B A:TPP900 2.0 95.5 1.0 OD1 A:ASN215 2.0 85.9 1.0 O1A A:TPP900 2.1 95.5 1.0 OD1 A:ASP182 2.2 88.0 1.0 CG A:ASN215 2.7 85.9 1.0 O A:TYR217 2.8 88.7 1.0 ND2 A:ASN215 2.8 85.9 1.0 PB A:TPP900 2.8 95.5 1.0 O3A A:TPP900 3.0 95.5 1.0 PA A:TPP900 3.1 95.5 1.0 CG A:ASP182 3.2 88.0 1.0 O1B A:TPP900 3.3 95.5 1.0 OD2 A:ASP182 3.6 88.0 1.0 C A:TYR217 3.9 88.7 1.0 O2A A:TPP900 4.0 95.5 1.0 NZ A:LYS300 4.1 84.0 1.0 N A:GLY183 4.2 92.5 1.0 CB A:ASN215 4.2 85.9 1.0 N A:ASP182 4.2 88.0 1.0 O3B A:TPP900 4.2 95.5 1.0 O7 A:TPP900 4.3 95.5 1.0 O A:HIS213 4.3 84.2 1.0 N A:TYR217 4.4 88.7 1.0 CB A:ASP182 4.5 88.0 1.0 N A:ASN215 4.6 85.9 1.0 N A:GLY216 4.7 86.8 1.0 CE A:LYS300 4.8 84.0 1.0 CA A:ASN215 4.8 85.9 1.0 CG2 A:THR223 4.8 91.8 1.0 CA A:TYR217 4.8 88.7 1.0 N A:LYS218 4.8 92.5 1.0 CA A:ASP182 4.8 88.0 1.0 C A:ASN215 4.9 85.9 1.0 CD A:LYS300 4.9 84.0 1.0 CA A:GLY181 5.0 88.8 1.0 C A:ASP182 5.0 88.0 1.0 C A:GLY181 5.0 88.8 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum in Dimeric 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 Phosphoketolase From Bifidobacterium Longum in Dimeric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:90.1 occ:1.00 O1B B:TPP900 2.0 95.4 1.0 OD1 B:ASN215 2.0 85.7 1.0 O2A B:TPP900 2.1 95.4 1.0 OD1 B:ASP182 2.2 88.0 1.0 CG B:ASN215 2.7 85.7 1.0 O B:TYR217 2.8 88.7 1.0 ND2 B:ASN215 2.8 85.7 1.0 PB B:TPP900 2.8 95.4 1.0 O3A B:TPP900 3.0 95.4 1.0 PA B:TPP900 3.1 95.4 1.0 CG B:ASP182 3.2 88.0 1.0 O2B B:TPP900 3.3 95.4 1.0 OD2 B:ASP182 3.6 88.0 1.0 C B:TYR217 3.9 88.7 1.0 O1A B:TPP900 4.0 95.4 1.0 NZ B:LYS300 4.1 84.0 1.0 N B:GLY183 4.2 92.3 1.0 CB B:ASN215 4.2 85.7 1.0 N B:ASP182 4.2 88.0 1.0 O3B B:TPP900 4.2 95.4 1.0 O7 B:TPP900 4.3 95.4 1.0 O B:HIS213 4.3 84.4 1.0 N B:TYR217 4.4 88.7 1.0 CB B:ASP182 4.5 88.0 1.0 N B:ASN215 4.6 85.7 1.0 N B:GLY216 4.7 86.8 1.0 CE B:LYS300 4.8 84.0 1.0 CA B:ASN215 4.8 85.7 1.0 CG2 B:THR223 4.8 91.7 1.0 CA B:TYR217 4.8 88.7 1.0 N B:LYS218 4.8 92.4 1.0 CA B:ASP182 4.8 88.0 1.0 C B:ASN215 4.9 85.7 1.0 CD B:LYS300 4.9 84.0 1.0 CA B:GLY181 5.0 88.8 1.0 C B:ASP182 5.0 88.0 1.0 C B:GLY181 5.0 88.8 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