Magnesium in PDB 8i4q: Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum

The structure of Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum, PDB code: 8i4q was solved by H.Yu, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.84 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.004, 119.471, 153.446, 90, 90, 90
R / Rfree (%)	16.4 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum (pdb code 8i4q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum, PDB code: 8i4q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum


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 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:30.0 occ:1.00 O A:HOH837 1.8 26.8 1.0 O A:HOH667 2.0 29.4 1.0 O A:HOH923 2.0 29.6 1.0 O A:HOH750 2.1 26.0 1.0 O A:HOH732 2.2 22.6 1.0 O A:HOH776 2.3 31.5 1.0 O A:ASN141 4.1 19.3 1.0 NH2 A:ARG28 4.1 32.6 1.0 O A:ILE164 4.1 16.7 1.0 OD1 A:ASN29 4.1 23.6 1.0 ND2 A:ASN29 4.2 20.3 1.0 O A:HOH700 4.2 28.0 1.0 O A:ALA165 4.5 17.4 1.0 CG A:ASN29 4.6 23.1 1.0 OD1 A:ASN25 4.6 18.2 1.0 C A:ILE164 4.7 16.6 1.0 O A:HOH637 4.8 36.6 1.0 C A:ASN141 4.8 21.8 1.0 O A:SER163 4.8 17.4 1.0 CA A:ILE164 5.0 17.1 1.0 CA A:GLY142 5.0 17.1 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum


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 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:23.7 occ:1.00 O A:HOH792 2.1 28.2 1.0 O A:HOH645 2.1 21.5 1.0 O A:HOH601 2.1 25.5 1.0 OD2 A:ASP230 2.1 21.3 1.0 CG A:ASP230 3.0 23.6 1.0 OD1 A:ASP230 3.3 23.9 1.0 OE2 A:GLU405 3.8 40.3 1.0 O A:HOH805 4.2 20.5 1.0 OE1 A:GLU405 4.3 37.4 1.0 CD A:GLU405 4.3 30.4 1.0 CB A:ASP230 4.4 20.2 1.0 OH A:TYR401 4.5 18.4 1.0 O A:HOH602 4.8 37.2 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum


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 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:30.0 occ:1.00 O B:HOH781 1.9 28.3 1.0 O B:HOH786 2.0 25.3 1.0 O B:HOH866 2.0 25.6 1.0 O B:HOH867 2.1 26.7 1.0 O B:HOH658 2.1 27.1 1.0 O B:HOH871 2.2 32.3 1.0 NZ B:LYS350 3.9 25.2 1.0 O B:HOH845 4.1 40.6 1.0 O B:HOH730 4.1 15.6 1.0 O B:HOH694 4.1 30.0 1.0 O B:VAL360 4.2 20.3 1.0 OE2 B:GLU392 4.3 32.1 1.0 OE1 B:GLU392 4.3 28.4 1.0 O B:HOH863 4.3 22.3 1.0 O B:HOH650 4.4 18.8 1.0 CD B:GLU392 4.8 27.8 1.0 CE B:LYS350 4.8 23.9 1.0 OD1 B:ASP359 4.9 43.5 1.0 CD B:LYS350 4.9 22.0 1.0 O B:HOH904 4.9 23.7 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum


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 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:35.3 occ:1.00 O B:HOH625 2.0 30.4 1.0 O B:HOH792 2.1 29.8 1.0 O B:HOH910 2.2 36.7 1.0 O B:HOH638 2.2 36.8 1.0 O B:HOH704 2.3 27.7 1.0 O B:HOH674 2.3 25.1 1.0 NH2 B:ARG28 3.9 34.0 1.0 OD1 B:ASN29 4.0 27.4 1.0 O B:ASN141 4.0 25.1 1.0 ND2 B:ASN29 4.0 19.0 1.0 O B:ILE164 4.3 19.6 1.0 CG B:ASN29 4.4 25.2 1.0 OD1 B:ASN25 4.6 20.1 1.0 O B:ALA165 4.7 19.0 1.0 C B:ASN141 4.8 26.2 1.0 C B:ILE164 4.9 18.3 1.0 O B:SER163 4.9 20.3 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:27.8 occ:1.00 O B:HOH623 1.9 30.0 1.0 OD2 B:ASP230 2.1 21.4 1.0 O B:HOH608 2.1 26.5 1.0 O B:HOH640 2.1 22.6 1.0 CG B:ASP230 3.0 23.1 1.0 OD1 B:ASP230 3.3 23.6 1.0 OE2 B:GLU405 4.0 34.0 1.0 OE1 B:GLU405 4.1 37.8 1.0 O B:HOH798 4.1 22.6 1.0 CD B:GLU405 4.4 29.7 1.0 CB B:ASP230 4.4 20.1 1.0 OH B:TYR401 4.5 17.9 1.0 O B:HOH603 4.6 38.8 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg507 b:33.3 occ:1.00 O B:HOH620 1.9 32.5 1.0 OG B:SER52 4.2 31.6 1.0 CB B:SER52 4.8 31.4 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum within 5.0Å range:

H.Yu, J.Hong, J.Seok, Y.B.Seu, I.K.Kim, K.J.Kim. Crystal Structures of 6-Phosphogluconate Dehydrogenase From Corynebacterium Glutamicum. J Microbiol Biotechnol. V. 33 1 2023.
ISSN: ESSN 1738-8872
PubMed: 37417004
DOI: 10.4014/JMB.2305.05002