Magnesium in PDB 2bk9: Drosophila Melanogaster Globin

The structure of Drosophila Melanogaster Globin, PDB code: 2bk9 was solved by D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Ponassi, M.Nardini, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.75 / 1.2
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.752, 55.835, 56.163, 90.00, 90.00, 90.00
R / Rfree (%)	10.1 / 13.4

The structure of Drosophila Melanogaster Globin also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Drosophila Melanogaster Globin (pdb code 2bk9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Drosophila Melanogaster Globin, PDB code: 2bk9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Drosophila Melanogaster Globin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Drosophila Melanogaster Globin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1156 b:11.6 occ:1.00 OD2 A:ASP147 2.0 7.8 1.0 O A:HOH2294 2.1 14.2 1.0 O A:HOH2306 2.2 13.8 1.0 H1 A:HOH2294 2.7 14.2 1.0 H1 A:HOH2306 2.7 13.8 1.0 CG A:ASP147 3.1 7.4 1.0 HB3 A:ASP147 3.4 6.2 1.0 HB2 A:ASP147 3.5 6.2 1.0 CB A:ASP147 3.6 6.2 1.0 HB2 A:ASN151 3.7 5.3 1.0 H2 A:HOH2301 4.2 14.7 1.0 O A:HOH2144 4.2 18.6 1.0 OD1 A:ASP147 4.2 6.6 1.0 O A:HOH2302 4.3 18.6 1.0 O A:ALA152 4.3 7.8 1.0 OD1 A:ASN151 4.5 9.3 1.0 H2 A:HOH2144 4.5 18.6 1.0 H2 A:HOH2302 4.5 18.6 1.0 OXT A:LYS153 4.6 13.0 1.0 H1 A:HOH2302 4.6 18.6 1.0 CB A:ASN151 4.6 5.4 1.0 H1 A:HOH2311 4.6 27.1 1.0 O A:HOH2301 4.7 14.7 1.0 HB3 A:ASN151 4.8 5.3 1.0 HA A:LYS153 4.8 8.8 1.0 H2 A:HOH2312 4.9 15.9 0.5 CG A:ASN151 5.0 5.3 1.0

Magnesium binding site 2 out of 2 in the Drosophila Melanogaster Globin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Drosophila Melanogaster Globin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1157 b:6.3 occ:1.00 O A:HOH2332 2.1 7.3 1.0 O A:HOH2333 2.1 9.2 1.0 O A:HOH2330 2.1 7.2 1.0 O A:HOH2328 2.1 8.4 1.0 O A:HOH2331 2.1 7.2 1.0 O A:HOH2329 2.1 7.3 1.0 O A:HOH2337 2.6 7.2 0.0 O A:HOH2339 2.6 8.1 1.0 O A:HOH2338 2.6 9.1 0.0 O A:HOH2336 2.6 7.2 0.0 O A:HOH2335 2.6 7.1 0.0 O A:HOH2334 2.7 7.5 0.0 H2 A:HOH2326 3.4 9.9 1.0 HD22 A:ASN151 3.5 4.5 0.0 H2 A:HOH2325 3.6 10.5 1.0 H2 A:HOH2324 3.6 9.8 1.0 H1 A:HOH2301 3.9 14.7 1.0 H1 A:HOH2321 4.1 11.4 1.0 H1 A:HOH2324 4.1 9.8 1.0 O A:HOH2325 4.1 10.5 1.0 O A:HOH2321 4.2 11.4 1.0 O A:HOH2323 4.2 9.9 1.0 O A:HOH2324 4.2 9.8 1.0 H2 A:HOH2321 4.2 11.4 1.0 O A:HOH2301 4.2 14.7 1.0 O A:HOH2326 4.3 9.9 1.0 O A:HOH2322 4.3 7.0 1.0 HG23 A:THR100 4.3 7.2 1.0 ND2 A:ASN151 4.3 4.6 1.0 O A:HOH2327 4.4 18.4 1.0 OD1 A:ASN151 4.4 9.3 1.0 H1 A:HOH2323 4.4 9.9 1.0 H2 A:HOH2322 4.5 7.0 1.0 CG A:ASN151 4.7 5.3 1.0 H1 A:HOH2326 4.8 9.9 1.0 H2 A:HOH2327 4.9 18.4 1.0 H1 A:HOH2327 4.9 18.4 1.0

D.De Sanctis, S.Dewilde, C.Vonrhein, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Ponassi, M.Nardini, M.Bolognesi. Bishistidyl Heme Hexacoordination, A Key Structural Property in Drosophila Melanogaster Hemoglobin J.Biol.Chem. V. 280 27222 2005.
ISSN: ISSN 0021-9258
PubMed: 15917230
DOI: 10.1074/JBC.M503814200