Magnesium in PDB 8jk9: SP1746 in Complex with Gdp

All present enzymatic activity of SP1746 in Complex with Gdp:
3.6.1.41;

The structure of SP1746 in Complex with Gdp, PDB code: 8jk9 was solved by Y.Jin, J.Ke, L.Niu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.63 / 1.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.302, 69.302, 88.561, 90, 90, 120
R / Rfree (%)	18.1 / 21.1

The structure of SP1746 in Complex with Gdp also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the SP1746 in Complex with Gdp (pdb code 8jk9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the SP1746 in Complex with Gdp, PDB code: 8jk9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SP1746 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SP1746 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:26.5 occ:1.00 OG1 A:THR118 2.7 16.1 1.0 N A:GLY92 2.8 17.4 1.0 MG A:MG307 2.8 26.9 1.0 O A:ASN88 2.9 17.8 1.0 O A:VAL89 2.9 17.8 1.0 CA A:GLY92 3.3 17.9 1.0 CB A:THR118 3.3 16.1 1.0 C A:VAL89 3.6 18.2 1.0 ND1 A:HIS91 3.6 17.6 1.0 CE1 A:HIS91 3.7 17.6 1.0 N A:MET93 3.7 18.2 1.0 N A:HIS91 3.9 17.9 1.0 C A:ASN88 4.0 17.9 1.0 C A:HIS91 4.0 17.5 1.0 C A:GLY92 4.0 18.2 1.0 CA A:VAL89 4.0 17.9 1.0 CG A:HIS91 4.1 17.3 1.0 CG2 A:THR118 4.2 16.5 1.0 CE1 A:HIS117 4.2 15.7 1.0 NE2 A:HIS91 4.3 17.3 1.0 C A:TRP90 4.3 18.6 1.0 CA A:HIS91 4.4 17.6 1.0 N A:TRP90 4.4 18.4 1.0 N A:VAL89 4.5 17.7 1.0 N A:THR118 4.5 16.0 1.0 CG A:MET93 4.5 20.9 1.0 CA A:THR118 4.5 16.3 1.0 CD2 A:HIS91 4.5 17.4 1.0 O A:GLU115 4.6 17.6 1.0 ND1 A:HIS117 4.7 16.1 1.0 NE2 A:HIS117 4.7 15.7 1.0 O A:ASN87 4.8 18.3 1.0 O A:TRP90 4.8 19.5 1.0 CB A:HIS91 4.9 17.3 1.0 CA A:TRP90 4.9 18.7 1.0 CA A:MET93 4.9 18.7 1.0 CB A:MET93 5.0 20.2 1.0

Magnesium binding site 2 out of 2 in the SP1746 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SP1746 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:26.9 occ:1.00 O A:GLU115 2.7 17.6 1.0 MG A:MG306 2.8 26.5 1.0 N A:THR118 3.0 16.0 1.0 CB A:THR118 3.3 16.1 1.0 C A:ILE116 3.4 16.4 1.0 N A:HIS117 3.5 16.2 1.0 OG1 A:THR118 3.5 16.1 1.0 CA A:ILE116 3.5 16.5 1.0 N A:VAL119 3.6 16.5 1.0 CA A:THR118 3.6 16.3 1.0 C A:GLU115 3.6 17.4 1.0 CG A:MET93 3.7 20.9 1.0 CG2 A:VAL119 3.9 17.9 1.0 N A:ILE116 4.0 16.8 1.0 O A:ILE116 4.0 16.6 1.0 N A:MET93 4.0 18.2 1.0 C A:HIS117 4.1 16.4 1.0 CA A:GLY92 4.1 17.9 1.0 C A:THR118 4.1 16.6 1.0 SD A:MET93 4.3 23.9 1.0 CA A:HIS117 4.3 15.8 1.0 C A:GLY92 4.4 18.2 1.0 O A:VAL89 4.4 17.8 1.0 O A:ILE114 4.5 17.7 1.0 ND1 A:HIS117 4.5 16.1 1.0 CG1 A:VAL119 4.5 17.7 1.0 CB A:VAL119 4.5 17.3 1.0 CG2 A:THR118 4.6 16.5 1.0 CA A:VAL119 4.6 17.3 1.0 N A:GLY92 4.7 17.4 1.0 CA A:MET93 4.8 18.7 1.0 CG A:HIS117 4.8 15.9 1.0 CB A:MET93 4.8 20.2 1.0 CE1 A:HIS117 4.8 15.7 1.0 CB A:ILE116 4.9 16.9 1.0 CA A:GLU115 5.0 17.1 1.0

Y.Jin, J.Ke, L.Niu. Structural and Biochemical Characterization of A Novel Hydrolase From Streptococcus Pneumoniae To Be Published.