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

Protein crystallography data

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

Other elements in 2y3r:

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

Magnesium Binding Sites:

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 2y3r

Go back to Magnesium Binding Sites List in 2y3r
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 2y3r

Go back to Magnesium Binding Sites List in 2y3r
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 2y3r

Go back to Magnesium Binding Sites List in 2y3r
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 2y3r

Go back to Magnesium Binding Sites List in 2y3r
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

Reference:

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
Page generated: Wed Aug 14 07:24:05 2024

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