Magnesium in PDB 5od2: Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii

All present enzymatic activity of Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii:
2.7.1.146; 2.7.1.147;

The structure of Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii, PDB code: 5od2 was solved by M.Wisniewska, P.Tokarz, P.Grudnik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 1.98
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	154.565, 154.565, 50.483, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 22.4

The structure of Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii also contains other interesting chemical elements:

Iodine

(I)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii (pdb code 5od2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii, PDB code: 5od2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii


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 Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:19.2 occ:1.00 O A:HOH648 2.0 19.0 1.0 O A:HOH654 2.1 13.4 1.0 O1 A:PO4504 2.1 20.7 1.0 O A:HOH680 2.1 18.0 1.0 O A:HOH661 2.1 18.9 1.0 O A:HOH689 2.1 15.3 1.0 P A:PO4504 3.3 19.3 1.0 O A:HOH682 3.6 17.9 1.0 O3 A:PO4504 3.6 17.4 1.0 O2 A:PO4504 3.8 20.5 1.0 O A:PHE273 4.0 19.9 1.0 OE2 A:GLU272 4.1 18.7 1.0 OE2 A:GLU302 4.1 20.2 1.0 NE2 A:HIS348 4.1 17.7 1.0 OE1 A:GLU302 4.3 18.4 1.0 OD1 A:ASP442 4.4 22.8 1.0 O A:HOH697 4.4 24.1 1.0 O A:HOH781 4.5 21.2 1.0 O4 A:PO4504 4.5 19.4 1.0 CA A:GLY441 4.6 18.1 1.0 CD A:GLU302 4.7 19.0 1.0 CE1 A:HIS348 4.7 18.6 1.0 CA A:ALA274 4.9 18.3 1.0 O A:HOH784 4.9 27.4 1.0 NE2 A:GLN108 4.9 19.2 1.0 C A:PHE273 5.0 19.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii


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 Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:14.0 occ:1.00 O B:HOH652 2.1 11.1 1.0 O B:HOH702 2.1 10.2 1.0 O B:HOH643 2.1 11.4 1.0 O2 B:PO4504 2.1 12.6 1.0 O B:HOH700 2.1 11.3 1.0 O B:HOH660 2.1 9.7 1.0 P B:PO4504 3.3 14.6 1.0 O1 B:PO4504 3.6 10.8 1.0 O B:HOH665 3.6 11.1 1.0 O3 B:PO4504 3.9 12.6 1.0 NE2 B:HIS348 4.0 13.3 1.0 OE2 B:GLU272 4.0 13.5 1.0 O B:PHE273 4.0 15.3 1.0 OE2 B:GLU302 4.1 14.1 1.0 OE1 B:GLU302 4.3 13.4 1.0 O B:HOH849 4.3 14.2 1.0 OD1 B:ASP442 4.4 13.4 1.0 O B:HOH720 4.4 20.4 1.0 CA B:GLY441 4.5 11.7 1.0 O4 B:PO4504 4.6 12.4 1.0 CE1 B:HIS348 4.6 12.8 1.0 CD B:GLU302 4.7 15.2 1.0 O B:HOH847 4.9 21.4 1.0 CA B:ALA274 4.9 15.3 1.0 C B:GLY441 4.9 11.7 1.0 NE2 B:GLN108 5.0 11.9 1.0 CD B:GLU272 5.0 13.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii


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 Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:14.3 occ:1.00 O2 C:PO4504 2.0 15.1 1.0 O C:HOH689 2.1 16.1 1.0 O C:HOH743 2.1 15.4 1.0 O C:HOH618 2.1 11.1 1.0 O C:HOH648 2.1 10.6 1.0 O C:HOH692 2.2 14.6 1.0 P C:PO4504 3.3 15.7 1.0 O1 C:PO4504 3.5 13.5 1.0 O C:HOH717 3.8 10.2 1.0 O3 C:PO4504 3.9 13.4 1.0 NE2 C:HIS348 4.1 17.2 1.0 O C:PHE273 4.1 14.3 1.0 OE2 C:GLU302 4.1 15.0 1.0 OE2 C:GLU272 4.2 14.2 1.0 O C:HOH679 4.3 17.8 1.0 OE1 C:GLU302 4.4 16.0 1.0 O C:HOH795 4.4 18.2 1.0 O4 C:PO4504 4.5 14.9 1.0 OD1 C:ASP442 4.5 17.6 1.0 CA C:GLY441 4.6 15.2 1.0 CE1 C:HIS348 4.7 17.8 1.0 CD C:GLU302 4.7 14.0 1.0 O C:HOH794 4.8 24.4 1.0 CA C:ALA274 4.9 15.3 1.0 NH2 C:ARG197 5.0 18.1 1.0 NE2 C:GLN108 5.0 15.4 1.0

P.Tokarz, M.Wisniewska, M.M.Kaminski, G.Dubin, P.Grudnik. Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii in Complex with 5-Iodotubercidin Reveals Phosphoryl Transfer Mechanism. Protein Sci. V. 27 790 2018.
ISSN: ESSN 1469-896X
PubMed: 29352744
DOI: 10.1002/PRO.3377