Iodine 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:

Magnesium

(Mg)

3 atoms

The binding sites of Iodine 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 Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structure of Adp-Dependent Glucokinase From Methanocaldococcus Jannaschii, PDB code: 5od2:
Jump to Iodine binding site number: 1; 2; 3;

Iodine 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 Iodine with other atoms in the I 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:I502 b:34.0 occ:1.00 IAE A:5ID502 0.0 34.0 1.0 C7 A:5ID502 2.2 25.7 1.0 C8 A:5ID502 3.2 26.2 1.0 C5 A:5ID502 3.2 25.4 1.0 O A:SER195 3.4 21.6 1.0 N6 A:5ID502 3.4 25.6 1.0 C6 A:5ID502 3.6 25.6 1.0 CG2 A:THR437 3.8 22.9 1.0 O A:HOH636 3.9 25.3 1.0 CG2 A:ILE350 4.0 31.5 1.0 O A:HOH655 4.2 29.2 1.0 N9 A:5ID502 4.4 25.6 1.0 CE1 A:TYR430 4.4 33.3 1.0 C4 A:5ID502 4.4 26.0 1.0 CD1 A:LEU440 4.5 20.1 1.0 OH A:TYR430 4.5 41.5 1.0 C A:SER195 4.5 22.2 1.0 CB A:THR437 4.7 23.7 1.0 CB A:SER195 4.7 26.3 1.0 CG A:PRO434 4.7 30.3 1.0 CB A:ILE350 4.8 31.6 1.0 CZ A:TYR430 4.8 36.4 1.0 N1 A:5ID502 4.9 25.6 1.0

Iodine 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 Iodine with other atoms in the I 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:I502 b:29.9 occ:1.00 IAE B:5ID502 0.0 29.9 1.0 C7 B:5ID502 2.2 22.8 1.0 C8 B:5ID502 3.2 23.1 1.0 C5 B:5ID502 3.2 22.2 1.0 O B:SER195 3.4 17.9 1.0 N6 B:5ID502 3.6 21.9 1.0 O B:HOH706 3.6 27.9 1.0 O B:HOH869 3.7 28.5 1.0 C6 B:5ID502 3.7 22.5 1.0 CG2 B:THR437 3.8 17.3 1.0 O B:HOH640 3.8 20.9 1.0 CG2 B:ILE350 4.0 24.8 1.0 CE1 B:TYR430 4.3 37.7 1.0 O B:HOH610 4.3 23.6 1.0 N9 B:5ID502 4.4 21.8 1.0 C4 B:5ID502 4.4 22.8 1.0 OH B:TYR430 4.5 36.4 1.0 CD1 B:LEU440 4.5 14.8 1.0 C B:SER195 4.5 17.4 1.0 CB B:SER195 4.7 19.0 1.0 CB B:THR437 4.7 16.7 1.0 CG B:PRO434 4.7 25.8 1.0 CB B:ILE350 4.8 23.2 1.0 CZ B:TYR430 4.8 39.8 1.0 N1 B:5ID502 5.0 22.6 1.0

Iodine 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 Iodine with other atoms in the I 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:I502 b:30.7 occ:1.00 IAE C:5ID502 0.0 30.7 1.0 C7 C:5ID502 2.2 27.1 1.0 C8 C:5ID502 3.2 26.4 1.0 C5 C:5ID502 3.2 23.8 1.0 O C:SER195 3.4 18.9 1.0 N6 C:5ID502 3.5 23.5 1.0 C6 C:5ID502 3.6 24.5 1.0 CG2 C:ILE350 3.8 22.1 1.0 CG2 C:THR437 3.9 15.6 1.0 O C:HOH723 4.0 25.1 1.0 O C:HOH608 4.0 26.0 1.0 CE1 C:TYR430 4.2 36.8 1.0 O C:HOH779 4.4 27.4 1.0 C4 C:5ID502 4.4 21.8 1.0 N9 C:5ID502 4.4 22.6 1.0 C C:SER195 4.5 19.2 1.0 CB C:ILE350 4.5 23.0 1.0 CD1 C:LEU440 4.5 17.0 1.0 OH C:TYR430 4.6 41.7 1.0 CB C:SER195 4.7 20.2 1.0 CB C:THR437 4.7 15.3 1.0 CG C:PRO434 4.8 24.7 1.0 CZ C:TYR430 4.9 35.7 1.0 N1 C:5ID502 4.9 22.5 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