Magnesium in PDB 2y3r: Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group

The structure of Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group, PDB code: 2y3r was solved by J.C.Carlson, S.Li, S.S.Gunatilleke, Y.Anzai, D.A.Burr, L.M.Podust, D.H.Sherman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	150.68 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.088, 106.171, 151.172, 90.00, 94.63, 90.00
R / Rfree (%)	14.6 / 21.9

The structure of Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Magnesium atom in the Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group (pdb code 2y3r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group, PDB code: 2y3r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg800 b:19.1 occ:1.00 O A:HOH2344 2.0 16.9 1.0 O A:HOH2496 2.1 14.8 1.0 O5 A:TIR700 2.1 17.6 1.0 O A:HOH2342 2.2 20.6 1.0 O A:HOH2393 2.2 18.5 1.0 O6 A:TIR700 2.2 14.8 1.0 C4 A:TIR700 3.2 13.6 1.0 C22 A:TIR700 3.2 15.3 1.0 C3 A:TIR700 3.5 14.9 1.0 OD2 A:ASP330 4.0 21.2 1.0 O A:HOH2498 4.2 22.0 1.0 O A:ASP332 4.2 13.9 1.0 OD1 A:ASP330 4.3 14.8 1.0 N A:TIR700 4.5 15.3 1.0 C5 A:TIR700 4.5 13.5 1.0 CG2 A:THR405 4.5 12.2 1.0 CG A:ASP330 4.6 18.3 1.0 OG1 A:THR405 4.8 17.5 1.0 C6 A:TIR700 4.9 15.9 1.0 C1 A:GOL1500 4.9 34.9 1.0 CB A:ASP332 4.9 15.7 1.0 C2 A:TIR700 4.9 13.8 1.0 CB A:THR405 5.0 13.9 1.0 O1 A:GOL1500 5.0 30.7 1.0

Magnesium binding site 2 out of 4 in the Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg800 b:21.8 occ:1.00 O B:HOH2323 1.9 18.5 1.0 O B:HOH2381 2.1 21.0 1.0 O2 B:TRK700 2.1 16.0 1.0 O4 B:TRK700 2.1 20.0 1.0 O B:HOH2489 2.1 21.0 1.0 O B:HOH2322 2.2 16.0 1.0 C10 B:TRK700 3.0 17.1 1.0 C8 B:TRK700 3.1 16.7 1.0 C9 B:TRK700 3.4 17.6 1.0 O B:HOH2491 4.0 32.4 1.0 OD2 B:ASP330 4.1 22.2 1.0 O B:HOH2329 4.2 46.5 1.0 O B:ASP332 4.2 15.4 1.0 N B:TRK700 4.3 17.3 1.0 OD1 B:ASP330 4.3 16.1 1.0 C7 B:TRK700 4.4 18.2 1.0 CG2 B:THR405 4.4 12.6 1.0 OG1 B:THR405 4.4 18.6 1.0 CG B:ASP330 4.7 18.5 1.0 C1 B:GOL1500 4.7 31.1 1.0 C12 B:TRK700 4.7 16.2 1.0 CB B:THR405 4.8 15.0 1.0 C6 B:TRK700 4.8 17.0 1.0 CB B:ASP332 4.9 15.0 1.0

Magnesium binding site 3 out of 4 in the Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg800 b:19.5 occ:1.00 O C:HOH2361 2.0 15.6 1.0 O5 C:TIR700 2.1 16.9 1.0 O C:HOH2419 2.1 16.4 1.0 O C:HOH2531 2.1 22.4 1.0 O C:HOH2360 2.2 18.2 1.0 O6 C:TIR700 2.2 16.5 1.0 C22 C:TIR700 3.1 15.1 1.0 C4 C:TIR700 3.1 13.3 1.0 C3 C:TIR700 3.4 15.9 1.0 OD2 C:ASP330 4.1 20.9 1.0 O C:HOH2533 4.1 32.4 1.0 O C:ASP332 4.2 14.1 1.0 O2 C:GOL1501 4.3 40.5 1.0 N C:TIR700 4.4 15.1 1.0 OD1 C:ASP330 4.4 15.3 1.0 CG2 C:THR405 4.4 14.5 1.0 C5 C:TIR700 4.4 14.0 1.0 OG1 C:THR405 4.6 18.3 1.0 C1 C:GOL1501 4.6 34.5 1.0 CG C:ASP330 4.7 17.4 1.0 C2 C:TIR700 4.8 14.2 1.0 C6 C:TIR700 4.8 15.8 1.0 CB C:THR405 4.9 14.2 1.0 CB C:ASP332 4.9 14.8 1.0

Magnesium binding site 4 out of 4 in the Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Tirandamycin-Bound Fad-Dependent Tirandamycin Oxidase Taml in P21 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg800 b:23.1 occ:1.00 O D:HOH2304 2.0 14.9 1.0 O4 D:TRK700 2.1 15.5 1.0 O D:HOH2305 2.1 17.4 1.0 O D:HOH2468 2.1 22.0 1.0 O2 D:TRK700 2.2 14.6 1.0 O D:HOH2467 2.3 23.5 1.0 C8 D:TRK700 3.1 15.5 1.0 C10 D:TRK700 3.2 15.9 1.0 C9 D:TRK700 3.5 16.4 1.0 OD2 D:ASP330 4.0 22.5 1.0 O D:ASP332 4.0 13.7 1.0 O D:HOH2465 4.1 52.7 1.0 OD1 D:ASP330 4.2 15.0 1.0 O D:HOH2469 4.4 30.1 1.0 N D:TRK700 4.4 16.0 1.0 O D:HOH2303 4.4 38.5 1.0 C7 D:TRK700 4.4 14.9 1.0 CG D:ASP330 4.5 17.9 1.0 CG2 D:THR405 4.6 12.9 1.0 O2 D:GOL1501 4.7 38.6 1.0 CB D:ASP332 4.7 13.6 1.0 OG1 D:THR405 4.8 16.2 1.0 C6 D:TRK700 4.8 14.2 1.0 C2 D:GOL1501 4.8 34.6 1.0 C12 D:TRK700 4.9 16.3 1.0 C3 D:GOL1501 4.9 33.1 1.0

J.C.Carlson, S.Li, S.S.Gunatilleke, Y.Anzai, D.A.Burr, L.M.Podust, D.H.Sherman. Tirandamycin Biosynthesis Is Mediated By Co-Dependent Oxidative Enzymes Nat.Chem V. 3 628 2011.
ISSN: ISSN 1755-4330
PubMed: 21778983
DOI: 10.1038/NCHEM.1087