Magnesium in PDB 5k9b: Azotobacter Vinelandii Flavodoxin II

The structure of Azotobacter Vinelandii Flavodoxin II, PDB code: 5k9b was solved by D.C.Rees, H.M.Segal, T.Spatzal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.53 / 1.17
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	39.873, 39.873, 178.656, 90.00, 90.00, 120.00
R / Rfree (%)	15 / 16.8

The binding sites of Magnesium atom in the Azotobacter Vinelandii Flavodoxin II (pdb code 5k9b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Azotobacter Vinelandii Flavodoxin II, PDB code: 5k9b:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Azotobacter Vinelandii Flavodoxin II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Azotobacter Vinelandii Flavodoxin II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:32.3 occ:1.00 O A:HOH473 2.0 42.1 1.0 O A:HOH459 2.0 30.8 1.0 O A:HOH398 2.1 23.0 1.0 O A:HOH407 2.2 39.6 1.0 OD2 A:ASP32 4.0 27.8 1.0 O A:HOH410 4.2 23.9 1.0 O A:HOH422 4.3 23.4 1.0 OD1 A:ASP32 4.4 19.9 1.0 CG A:ASP32 4.5 20.0 1.0 OD2 A:ASP27 4.6 22.5 1.0 HB3 A:ASP27 4.6 22.2 1.0 O A:HOH328 4.7 31.6 1.0 CG A:ASP27 4.9 18.5 1.0 O A:HOH317 4.9 26.4 1.0 H A:ASP32 5.0 13.8 1.0

Magnesium binding site 2 out of 3 in the Azotobacter Vinelandii Flavodoxin II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Azotobacter Vinelandii Flavodoxin II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:21.6 occ:1.00 O A:HOH414 2.0 29.9 1.0 O A:HOH340 2.0 24.8 1.0 O A:HOH427 2.1 28.3 1.0 OD2 A:ASP26 2.2 16.7 1.0 CG A:ASP26 3.2 15.6 1.0 OD1 A:ASP26 3.5 15.3 1.0 HG1 A:THR29 3.6 16.9 1.0 HB2 A:GLU28 3.9 20.6 1.0 O A:HOH399 4.1 16.7 1.0 OG1 A:THR29 4.2 14.1 1.0 O A:HOH467 4.2 32.3 1.0 OE2 A:GLU28 4.5 58.8 1.0 O A:HOH424 4.5 10.3 1.0 CB A:ASP26 4.6 14.8 1.0 HB3 A:ASP26 4.6 17.8 1.0 CB A:GLU28 4.8 17.2 1.0 HB2 A:ASP26 4.9 17.8 1.0

Magnesium binding site 3 out of 3 in the Azotobacter Vinelandii Flavodoxin II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Azotobacter Vinelandii Flavodoxin II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:37.2 occ:1.00 O A:HOH360 2.2 34.5 1.0 OE1 A:GLU82 3.2 24.4 0.3 O A:HOH321 4.0 38.4 1.0 OE2 A:GLU82 4.1 22.5 0.7 O A:HOH416 4.3 31.7 1.0 CD A:GLU82 4.3 20.3 0.3 O A:PRO79 4.5 18.1 1.0 HG2 A:GLU82 4.5 22.9 0.3 HG3 A:GLU82 4.6 22.9 0.3 HG2 A:GLU82 4.8 20.1 0.7 CG A:GLU82 4.8 19.1 0.3 HG3 A:GLU82 5.0 20.1 0.7

H.M.Segal, T.Spatzal, M.G.Hill, A.K.Udit, D.C.Rees. Electrochemical and Structural Characterization of Azotobacter Vinelandii Flavodoxin II. Protein Sci. V. 26 1984 2017.
ISSN: ESSN 1469-896X
PubMed: 28710816
DOI: 10.1002/PRO.3236