Magnesium in PDB 4e84: Crystal Structure of Burkholderia Cenocepacia Hlda

The structure of Crystal Structure of Burkholderia Cenocepacia Hlda, PDB code: 4e84 was solved by T.-W.Lee, M.S.Junop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.95 / 2.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.398, 90.398, 397.917, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 26.3

The structure of Crystal Structure of Burkholderia Cenocepacia Hlda also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Burkholderia Cenocepacia Hlda (pdb code 4e84). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Burkholderia Cenocepacia Hlda, PDB code: 4e84:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Burkholderia Cenocepacia Hlda


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 Burkholderia Cenocepacia Hlda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:68.3 occ:1.00 O A:HOH603 2.2 55.6 1.0 O A:HOH602 2.3 58.7 1.0 O2B A:ANP501 2.3 43.4 1.0 O A:HOH606 3.0 41.7 1.0 O A:HOH604 3.3 43.7 1.0 O A:HOH608 3.4 49.3 1.0 PB A:ANP501 3.8 41.2 1.0 OD1 A:ASP184 3.8 52.9 1.0 OD2 A:ASP184 3.9 45.0 1.0 OE2 A:GLU205 4.1 54.9 1.0 ND2 A:ASN202 4.1 34.9 1.0 CA A:GLY269 4.2 32.7 1.0 O A:HOH601 4.2 39.6 1.0 CG A:ASP184 4.3 50.0 1.0 OE1 A:GLU205 4.4 40.5 1.0 O1B A:ANP501 4.4 48.1 1.0 N3B A:ANP501 4.4 44.2 1.0 O1 A:M7B502 4.5 49.4 1.0 CD A:GLU205 4.6 45.6 1.0 OH A:TYR159 4.6 42.3 1.0 C A:GLY269 4.6 49.2 1.0 OD1 A:ASP270 4.7 48.6 1.0 N A:GLY269 4.8 34.4 1.0 O3A A:ANP501 4.8 52.4 1.0 N A:ASP270 5.0 48.1 1.0 CG A:ASN202 5.0 43.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Burkholderia Cenocepacia Hlda


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 Burkholderia Cenocepacia Hlda within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:70.0 occ:1.00 OP3 B:GMZ502 2.3 48.5 0.5 O B:HOH603 2.4 57.0 1.0 O B:HOH602 2.4 60.7 1.0 O2B B:ANP501 2.4 38.5 1.0 O B:HOH605 3.1 50.3 1.0 P1 B:GMZ502 3.4 64.7 0.5 OP1 B:GMZ502 3.4 45.0 0.5 O B:HOH606 3.6 29.4 1.0 OE2 B:GLU205 3.8 53.3 1.0 PB B:ANP501 3.9 36.9 1.0 OD2 B:ASP184 4.0 60.0 1.0 O B:HOH604 4.1 40.2 1.0 O B:HOH601 4.1 38.8 1.0 OP2 B:GMZ502 4.1 52.9 0.5 OD1 B:ASP184 4.2 49.2 1.0 ND2 B:ASN202 4.2 37.0 1.0 CA B:GLY269 4.3 35.1 1.0 O1B B:ANP501 4.4 42.3 1.0 CG B:ASP184 4.5 45.1 1.0 CD B:GLU205 4.5 47.5 1.0 OE1 B:GLU205 4.5 37.8 1.0 O1 B:GMZ502 4.6 49.4 1.0 OH B:TYR159 4.7 35.4 1.0 N3B B:ANP501 4.7 42.9 1.0 C B:GLY269 4.8 47.7 1.0 NZ B:LYS186 4.8 48.0 1.0 O3A B:ANP501 4.9 62.1 1.0 N B:GLY269 5.0 41.0 1.0

T.W.Lee, T.B.Verhey, P.A.Antiperovitch, D.Atamanyuk, N.Desroy, C.Oliveira, A.Denis, V.Gerusz, E.Drocourt, S.A.Loutet, M.A.Hamad, C.Stanetty, S.N.Andres, S.Sugiman-Marangos, P.Kosma, M.A.Valvano, F.Moreau, M.S.Junop. Structural-Functional Studies of Burkholderia Cenocepacia D-Glycero-Beta-D-Manno-Heptose 7-Phosphate Kinase (Hlda) and Characterization of Inhibitors with Antibiotic Adjuvant and Antivirulence Properties. J.Med.Chem. V. 56 1405 2013.
ISSN: ISSN 0022-2623
PubMed: 23256532
DOI: 10.1021/JM301483H