Magnesium in PDB 8dht: Crystal Structure of A Typeiii Rubisco

All present enzymatic activity of Crystal Structure of A Typeiii Rubisco:
4.1.1.39;

The structure of Crystal Structure of A Typeiii Rubisco, PDB code: 8dht was solved by H.Qingqiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.38 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.329, 116.206, 83.285, 90, 96.32, 90
R / Rfree (%)	14.4 / 17.7

The binding sites of Magnesium atom in the Crystal Structure of A Typeiii Rubisco (pdb code 8dht). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Typeiii Rubisco, PDB code: 8dht:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Typeiii Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Typeiii Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:14.8 occ:1.00 O3 A:3PG503 2.0 18.6 1.0 OD1 A:ASP188 2.0 15.8 1.0 OE1 A:GLU189 2.1 13.7 1.0 OQ2 A:KCX186 2.1 14.9 1.0 O2 A:3PG502 2.2 16.1 1.0 O2 A:3PG503 2.2 14.9 1.0 C1 A:3PG503 2.8 15.7 1.0 C2 A:3PG503 2.8 19.6 1.0 C1 A:3PG502 3.1 16.0 1.0 CD A:GLU189 3.2 15.9 1.0 CX A:KCX186 3.2 14.9 1.0 CG A:ASP188 3.2 18.2 1.0 O1 A:3PG502 3.5 16.7 1.0 OQ1 A:KCX186 3.6 17.1 1.0 OE2 A:GLU189 3.6 15.0 1.0 ND2 C:ASN108 3.8 14.2 1.0 OD2 A:ASP188 3.9 21.1 1.0 NZ A:LYS160 3.9 15.8 1.0 N A:GLU189 3.9 13.4 1.0 NE2 A:HIS278 4.0 15.1 1.0 NZ A:LYS162 4.0 21.8 1.0 O1 A:3PG503 4.0 19.6 1.0 C3 A:3PG503 4.1 18.0 1.0 CA A:ASP188 4.3 15.5 1.0 NZ A:KCX186 4.3 13.2 1.0 CB A:ASP188 4.3 12.5 1.0 C2 A:3PG502 4.3 20.5 1.0 CG A:GLU189 4.5 15.9 1.0 CB A:GLU189 4.6 14.2 1.0 CG1 A:VAL158 4.7 14.6 1.0 C A:ASP188 4.7 15.2 1.0 CD2 A:HIS278 4.7 13.5 1.0 O1P A:3PG503 4.8 14.2 1.0 CE1 A:HIS278 4.8 13.9 1.0 CG2 A:VAL158 4.9 13.7 1.0 CA A:GLU189 4.9 12.6 1.0 CE A:LYS162 5.0 19.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Typeiii Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Typeiii Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:15.8 occ:1.00 O3 B:3PG503 2.0 19.7 1.0 OD1 B:ASP188 2.0 17.2 1.0 OE1 B:GLU189 2.1 16.6 1.0 OQ1 B:KCX186 2.1 14.4 1.0 O1 B:3PG503 2.2 20.0 1.0 O1 B:3PG502 2.2 16.6 1.0 C1 B:3PG503 2.8 17.2 1.0 C2 B:3PG503 2.8 23.7 1.0 C1 B:3PG502 3.1 20.7 1.0 CD B:GLU189 3.2 19.5 1.0 CX B:KCX186 3.2 16.6 1.0 CG B:ASP188 3.2 16.8 1.0 O2 B:3PG502 3.5 19.2 1.0 OE2 B:GLU189 3.6 19.4 1.0 OQ2 B:KCX186 3.6 16.1 1.0 NZ B:LYS160 3.9 20.8 1.0 NZ B:LYS162 3.9 17.1 1.0 NE2 B:HIS278 3.9 15.1 1.0 OD2 B:ASP188 3.9 23.6 1.0 N B:GLU189 3.9 13.9 1.0 O2 B:3PG503 4.0 23.3 1.0 C3 B:3PG503 4.1 20.3 1.0 CA B:ASP188 4.2 13.0 1.0 CB B:ASP188 4.3 13.6 1.0 NZ B:KCX186 4.3 14.2 1.0 C2 B:3PG502 4.4 19.6 1.0 CG B:GLU189 4.4 16.3 1.0 CB B:GLU189 4.6 12.2 1.0 CG1 B:VAL158 4.6 13.8 1.0 C B:ASP188 4.6 13.6 1.0 CD2 B:HIS278 4.7 15.3 1.0 CE1 B:HIS278 4.8 15.2 1.0 O1P B:3PG503 4.8 18.5 1.0 CG2 B:VAL158 4.9 12.9 1.0 CA B:GLU189 4.9 14.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Typeiii Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Typeiii Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:16.6 occ:1.00 OD1 C:ASP188 2.0 18.2 1.0 O3 C:3PG503 2.0 21.0 1.0 OE1 C:GLU189 2.1 16.8 1.0 OQ2 C:KCX186 2.1 18.1 1.0 O2 C:3PG502 2.1 20.1 1.0 O2 C:3PG503 2.2 20.9 1.0 C1 C:3PG503 2.8 19.3 1.0 C2 C:3PG503 2.8 20.9 1.0 C1 C:3PG502 3.1 21.5 1.0 CD C:GLU189 3.2 20.2 1.0 CG C:ASP188 3.2 18.7 1.0 CX C:KCX186 3.2 18.4 1.0 O1 C:3PG502 3.5 20.6 1.0 OE2 C:GLU189 3.6 19.4 1.0 OQ1 C:KCX186 3.6 17.8 1.0 ND2 A:ASN108 3.8 16.9 1.0 OD2 C:ASP188 3.9 22.7 1.0 NZ C:LYS160 3.9 17.8 1.0 O1 C:3PG503 4.0 23.4 1.0 N C:GLU189 4.0 14.6 1.0 NE2 C:HIS278 4.0 16.2 1.0 NZ C:LYS162 4.0 19.1 1.0 C3 C:3PG503 4.1 22.6 1.0 CA C:ASP188 4.3 11.8 1.0 CB C:ASP188 4.3 12.6 1.0 C2 C:3PG502 4.3 20.1 1.0 NZ C:KCX186 4.3 17.0 1.0 CG C:GLU189 4.5 16.6 1.0 CG1 C:VAL158 4.6 15.2 1.0 CB C:GLU189 4.7 16.4 1.0 C C:ASP188 4.7 16.3 1.0 CD2 C:HIS278 4.8 15.9 1.0 O1P C:3PG503 4.8 18.7 1.0 CE1 C:HIS278 4.8 16.0 1.0 CG2 C:VAL158 4.9 13.8 1.0 CE C:LYS162 4.9 22.9 1.0 CA C:GLU189 5.0 14.8 1.0 CG A:ASN108 5.0 17.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A Typeiii Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Typeiii Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:15.4 occ:1.00 O3 D:3PG503 2.0 15.1 1.0 OD1 D:ASP188 2.1 16.0 1.0 OE1 D:GLU189 2.1 15.7 1.0 OQ2 D:KCX186 2.1 16.0 1.0 O1 D:3PG502 2.2 16.1 1.0 O2 D:3PG503 2.2 16.5 1.0 C1 D:3PG503 2.8 13.8 1.0 C2 D:3PG503 2.8 16.6 1.0 C1 D:3PG502 3.1 16.5 1.0 CD D:GLU189 3.2 16.6 1.0 CX D:KCX186 3.2 14.9 1.0 CG D:ASP188 3.3 16.3 1.0 O2 D:3PG502 3.5 16.4 1.0 OQ1 D:KCX186 3.6 14.9 1.0 OE2 D:GLU189 3.7 16.3 1.0 NZ D:LYS160 3.9 14.2 1.0 NE2 D:HIS278 3.9 15.8 1.0 OD2 D:ASP188 3.9 19.2 1.0 N D:GLU189 4.0 12.4 1.0 O1 D:3PG503 4.0 18.1 1.0 NZ D:LYS162 4.0 17.2 1.0 C3 D:3PG503 4.1 16.4 1.0 CA D:ASP188 4.3 13.0 1.0 C2 D:3PG502 4.3 17.6 1.0 NZ D:KCX186 4.3 12.2 1.0 CB D:ASP188 4.3 13.6 1.0 CG D:GLU189 4.5 15.3 1.0 C D:ASP188 4.7 13.1 1.0 CB D:GLU189 4.7 14.9 1.0 CG1 D:VAL158 4.7 13.4 1.0 CD2 D:HIS278 4.7 13.0 1.0 CE1 D:HIS278 4.7 15.4 1.0 O1P D:3PG503 4.8 14.1 1.0 CG2 D:VAL158 4.9 12.9 1.0 CA D:GLU189 4.9 11.8 1.0 CE D:LYS162 5.0 19.2 1.0

Q.Huang, D.M.E.Szebenyi. Crystal Structure of A Type III Rubisco in Complex with Its Product 3-Phosphoglycerate. Proteins 2022.
ISSN: ESSN 1097-0134
PubMed: 36151846
DOI: 10.1002/PROT.26431