Magnesium in PDB 3wyi: Structure of S. Aureus Undecaprenyl Diphosphate Synthase

The structure of Structure of S. Aureus Undecaprenyl Diphosphate Synthase, PDB code: 3wyi was solved by J.Gao, T.P.Ko, C.H.Huang, E.Oldfield, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	62.080, 62.080, 133.486, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.7

The binding sites of Magnesium atom in the Structure of S. Aureus Undecaprenyl Diphosphate Synthase (pdb code 3wyi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of S. Aureus Undecaprenyl Diphosphate Synthase, PDB code: 3wyi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of S. Aureus Undecaprenyl Diphosphate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of S. Aureus Undecaprenyl Diphosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:50.8 occ:1.00 OE2 A:GLU168 2.6 67.4 1.0 CE1 A:HIS187 2.7 41.5 1.0 OE1 A:GLU168 2.8 66.7 1.0 CD A:GLU168 3.0 67.0 1.0 NE2 A:HIS187 3.4 41.9 1.0 O A:HOH539 3.5 55.4 1.0 ND1 A:HIS187 3.7 42.6 1.0 CG A:GLU168 4.5 66.6 1.0 CD2 A:HIS187 4.5 38.9 1.0 CG A:HIS187 4.7 38.9 1.0

Magnesium binding site 2 out of 2 in the Structure of S. Aureus Undecaprenyl Diphosphate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of S. Aureus Undecaprenyl Diphosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:21.8 occ:1.00 NE A:ARG46 3.2 27.2 1.0 OD1 A:ASN35 3.3 24.7 1.0 O A:HOH417 3.3 20.7 1.0 ND1 A:HIS50 3.4 29.8 1.0 NH1 A:ARG46 3.5 25.9 1.0 O A:MET93 3.5 30.1 1.0 CB A:HIS50 3.5 26.0 1.0 CB A:ASN35 3.6 23.8 1.0 O A:HOH449 3.7 29.0 1.0 CA A:HIS50 3.7 26.6 1.0 CZ A:ARG46 3.8 28.4 1.0 CG A:ASN35 3.9 27.0 1.0 CG A:HIS50 3.9 27.1 1.0 CB A:MET93 4.0 33.5 1.0 CG A:ARG46 4.2 29.0 1.0 N A:HIS50 4.3 23.9 1.0 CD A:ARG46 4.3 31.4 1.0 C A:MET93 4.3 30.0 1.0 SD A:MET93 4.5 47.1 1.0 OD1 A:ASN94 4.5 24.1 1.0 CE1 A:HIS50 4.6 29.5 1.0 CA A:MET93 4.8 31.1 1.0 O A:HOH401 4.8 21.6 1.0 O A:HOH567 4.9 32.5 1.0 CG A:MET93 4.9 40.8 1.0 O A:ARG46 4.9 27.6 1.0 C A:HIS50 5.0 27.6 1.0

W.Zhu, Y.Wang, K.Li, J.Gao, C.H.Huang, C.C.Chen, T.P.Ko, Y.Zhang, R.T.Guo, E.Oldfield. Antibacterial Drug Leads: Dna and Enzyme Multitargeting. J.Med.Chem. 2015.
ISSN: ISSN 0022-2623
PubMed: 25574764
DOI: 10.1021/JM501449U