Magnesium in PDB 4jej: Gggps From Flavobacterium Johnsoniae

The structure of Gggps From Flavobacterium Johnsoniae, PDB code: 4jej was solved by D.Peterhoff, B.Beer, C.Rajendran, E.P.Kumpula, E.Kapetaniou, H.Guldan, R.K.Wierenga, R.Sterner, P.Babinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.06 / 1.52
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.270, 43.010, 75.927, 90.00, 117.41, 90.00
R / Rfree (%)	17.7 / 19.8

The binding sites of Magnesium atom in the Gggps From Flavobacterium Johnsoniae (pdb code 4jej). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Gggps From Flavobacterium Johnsoniae, PDB code: 4jej:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Gggps From Flavobacterium Johnsoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gggps From Flavobacterium Johnsoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:26.0 occ:1.00 H A:GLY209 2.0 21.6 1.0 H A:ILE211 2.4 26.6 1.0 O3P A:1GP301 2.6 18.7 1.0 HB A:ILE211 2.7 28.5 1.0 O A:VAL229 2.8 18.1 1.0 N A:GLY209 2.9 18.0 1.0 HD13 A:ILE230 3.1 26.5 1.0 HA A:ILE230 3.2 20.1 1.0 HG13 A:ILE211 3.2 27.4 1.0 N A:ILE211 3.2 22.1 1.0 H11 A:1GP301 3.3 24.3 1.0 O1P A:1GP301 3.4 18.8 1.0 HA2 A:GLY208 3.4 20.7 1.0 CB A:ILE211 3.4 23.8 1.0 CA A:GLY209 3.5 17.1 1.0 P A:1GP301 3.5 18.8 1.0 HA2 A:GLY209 3.5 20.5 1.0 H A:GLY210 3.5 23.8 1.0 C A:GLY209 3.5 20.2 1.0 N A:GLY210 3.6 19.8 1.0 HD12 A:ILE211 3.6 30.0 1.0 CG1 A:ILE211 3.7 22.9 1.0 O2P A:1GP301 3.8 18.8 1.0 C1 A:1GP301 3.8 20.3 1.0 CA A:ILE211 3.9 22.8 1.0 C A:GLY208 3.9 18.1 1.0 H A:GLY231 3.9 22.3 1.0 MG A:MG305 3.9 28.6 1.0 C A:VAL229 4.0 16.6 1.0 O A:ILE211 4.0 24.5 1.0 CA A:GLY208 4.0 17.2 1.0 CD1 A:ILE230 4.1 22.1 1.0 O A:GLY209 4.1 20.1 1.0 CA A:ILE230 4.1 16.8 1.0 HA3 A:GLY208 4.2 20.7 1.0 CD1 A:ILE211 4.2 25.0 1.0 C A:GLY210 4.3 24.1 1.0 HD12 A:ILE230 4.4 26.5 1.0 H12 A:1GP301 4.4 24.3 1.0 HA3 A:GLY209 4.4 20.5 1.0 C A:ILE211 4.4 24.6 1.0 CA A:GLY210 4.5 20.9 1.0 HD11 A:ILE230 4.5 26.5 1.0 N A:ILE230 4.5 16.4 1.0 HG12 A:ILE211 4.6 27.4 1.0 N A:GLY231 4.6 18.6 1.0 HA A:ILE211 4.7 27.4 1.0 HD11 A:ILE211 4.7 30.0 1.0 O A:HOH530 4.7 27.7 1.0 CG2 A:ILE211 4.7 24.7 1.0 HB A:VAL229 4.8 21.9 1.0 O3 A:1GP301 4.8 18.8 1.0 HG23 A:ILE230 4.8 22.6 1.0 HG21 A:ILE211 4.9 29.6 1.0 HD13 A:ILE211 4.9 30.0 1.0 O4P A:1GP301 4.9 22.5 1.0 C2 A:1GP301 4.9 16.3 1.0 HG22 A:ILE211 4.9 29.6 1.0 C A:ILE230 4.9 16.8 1.0 HG13 A:VAL228 5.0 20.1 1.0 CG1 A:ILE230 5.0 18.4 1.0

Magnesium binding site 2 out of 2 in the Gggps From Flavobacterium Johnsoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gggps From Flavobacterium Johnsoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:28.6 occ:1.00 H A:ALA233 2.0 24.9 1.0 O A:ILE211 2.6 24.5 1.0 O3P A:1GP301 2.7 18.7 1.0 HB2 A:ALA233 2.8 27.6 1.0 N A:ALA233 2.8 20.7 1.0 HG23 A:ILE230 2.9 22.6 1.0 HB A:THR232 2.9 30.7 1.0 O A:HOH530 3.0 27.7 1.0 HB3 A:ALA233 3.1 27.6 1.0 H A:GLY231 3.3 22.3 1.0 CB A:ALA233 3.3 23.0 1.0 H A:THR232 3.3 25.7 1.0 N A:THR232 3.5 21.4 1.0 CA A:ALA233 3.6 20.9 1.0 CB A:THR232 3.7 25.6 1.0 P A:1GP301 3.7 18.8 1.0 HA A:ILE230 3.7 20.1 1.0 C A:ILE211 3.8 24.6 1.0 C A:THR232 3.8 23.6 1.0 HD12 A:ILE230 3.8 26.5 1.0 CG2 A:ILE230 3.8 18.8 1.0 CA A:THR232 3.8 24.5 1.0 N A:GLY231 3.9 18.6 1.0 HA A:VAL212 3.9 29.6 1.0 O2P A:1GP301 3.9 18.8 1.0 HG22 A:ILE230 3.9 22.6 1.0 H A:ILE211 3.9 26.6 1.0 MG A:MG304 3.9 26.0 1.0 HD13 A:ILE230 4.0 26.5 1.0 HG11 A:VAL212 4.0 46.5 1.0 C A:GLY231 4.1 20.8 1.0 HA A:ALA233 4.1 25.1 1.0 HB1 A:ALA233 4.2 27.6 1.0 N A:ILE211 4.3 22.1 1.0 CD1 A:ILE230 4.3 22.1 1.0 O4P A:1GP301 4.3 22.5 1.0 HG21 A:ILE230 4.4 22.6 1.0 H A:PHE234 4.4 28.5 1.0 HB A:ILE211 4.4 28.5 1.0 HG22 A:THR232 4.4 40.0 1.0 CA A:ILE230 4.4 16.8 1.0 HG1 A:THR232 4.5 32.5 1.0 CA A:GLY231 4.5 16.6 1.0 CA A:ILE211 4.6 22.8 1.0 C A:ILE230 4.6 16.8 1.0 CG2 A:THR232 4.6 33.3 1.0 CB A:ILE230 4.6 19.6 1.0 O A:GLY231 4.7 21.3 1.0 OG1 A:THR232 4.7 27.0 1.0 N A:VAL212 4.7 26.0 1.0 H A:GLY210 4.7 23.8 1.0 CA A:VAL212 4.7 24.7 1.0 C A:ALA233 4.8 26.7 1.0 HA A:THR232 4.8 29.4 1.0 CG1 A:VAL212 4.9 38.8 1.0 N A:PHE234 4.9 23.7 1.0 HA3 A:GLY231 4.9 19.9 1.0 HG21 A:THR232 4.9 40.0 1.0 O A:THR232 4.9 27.9 1.0 C A:GLY210 5.0 24.1 1.0

D.Peterhoff, B.Beer, C.Rajendran, E.P.Kumpula, E.Kapetaniou, H.Guldan, R.K.Wierenga, R.Sterner, P.Babinger. A Comprehensive Analysis of the Geranylgeranylglyceryl Phosphate Synthase Enzyme Family Identifies Novel Members and Reveals Mechanisms of Substrate Specificity and Quaternary Structure Organization. Mol.Microbiol. V. 92 885 2014.
ISSN: ISSN 0950-382X
PubMed: 24684232
DOI: 10.1111/MMI.12596