Magnesium in PDB 7tgm: Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway

The structure of Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway, PDB code: 7tgm was solved by K.D.Patel, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.60 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	125.8, 237.4, 329.7, 90, 90, 90
R / Rfree (%)	18.9 / 22

The binding sites of Magnesium atom in the Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway (pdb code 7tgm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway, PDB code: 7tgm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway


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 Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg617 b:58.9 occ:1.00 O2P A:LMS615 2.1 54.8 1.0 O2 A:PO4616 2.1 60.3 1.0 OD1 A:ASN443 2.5 56.5 1.0 OE1 A:GLU442 2.6 56.3 1.0 OD2 A:ASP460 2.7 60.6 1.0 S A:LMS615 3.4 57.0 1.0 P A:PO4616 3.4 57.1 1.0 CG A:ASP460 3.4 59.5 1.0 CG A:ASN443 3.5 54.5 1.0 CD A:GLU442 3.6 55.8 1.0 O3 A:PO4616 3.7 54.6 1.0 C5' A:LMS615 3.8 54.0 1.0 OE2 A:GLU442 3.8 58.5 1.0 ND2 A:ASN443 3.8 52.1 1.0 O A:HOH747 3.8 55.7 1.0 CB A:ASP460 3.8 58.9 1.0 O1P A:LMS615 3.9 53.8 1.0 O5' A:LMS615 4.0 56.0 1.0 O4 A:PO4616 4.1 55.9 1.0 OD1 A:ASP460 4.4 66.1 1.0 O1 A:PO4616 4.5 52.9 1.0 NZ A:LYS459 4.6 56.1 1.0 CE1 A:HIS440 4.6 51.7 1.0 CB A:SER275 4.7 46.7 1.0 N A:LMS615 4.7 50.2 1.0 C4' A:LMS615 4.8 50.4 1.0 CB A:ASN443 4.9 51.2 1.0 NE2 A:HIS440 4.9 51.9 1.0 CG A:GLU442 5.0 53.6 1.0 OE2 A:GLU464 5.0 73.9 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway


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 Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg618 b:58.4 occ:1.00 O4 B:PO4617 2.2 58.6 1.0 O2P B:LMS616 2.3 51.9 1.0 OD1 B:ASN443 2.5 51.8 1.0 OE1 B:GLU442 2.6 52.3 1.0 OD2 B:ASP460 2.7 57.2 1.0 P B:PO4617 3.3 53.2 1.0 S B:LMS616 3.5 47.1 1.0 O2 B:PO4617 3.5 52.6 1.0 CG B:ASN443 3.5 52.3 1.0 CG B:ASP460 3.6 56.8 1.0 O5' B:LMS616 3.7 49.9 1.0 CD B:GLU442 3.7 52.6 1.0 C5' B:LMS616 3.8 48.3 1.0 CB B:ASP460 3.8 52.9 1.0 ND2 B:ASN443 3.9 51.5 1.0 O1P B:LMS616 3.9 50.5 1.0 O3 B:PO4617 4.0 52.8 1.0 OE2 B:GLU442 4.1 52.6 1.0 O B:HOH744 4.2 50.8 1.0 NZ B:LYS459 4.3 55.2 1.0 O1 B:PO4617 4.4 51.2 1.0 CE1 B:HIS440 4.5 50.7 1.0 CB B:SER275 4.5 46.5 1.0 OD1 B:ASP460 4.7 57.9 1.0 C4' B:LMS616 4.8 45.4 1.0 CB B:ASN443 4.8 51.5 1.0 N B:LMS616 4.9 48.3 1.0 NE2 B:HIS440 5.0 49.2 1.0 CG B:GLU442 5.0 47.7 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg613 b:61.2 occ:1.00 O2P C:LMS611 2.2 62.7 1.0 OD1 C:ASN443 2.4 64.4 1.0 O3 C:PO4612 2.4 63.9 1.0 OE1 C:GLU442 2.5 62.6 1.0 OD2 C:ASP460 2.8 65.9 1.0 CG C:ASN443 3.3 61.9 1.0 P C:PO4612 3.4 66.4 1.0 CG C:ASP460 3.4 65.3 1.0 O2 C:PO4612 3.5 65.3 1.0 ND2 C:ASN443 3.5 62.6 1.0 S C:LMS611 3.6 56.0 1.0 CD C:GLU442 3.6 63.0 1.0 CB C:ASP460 3.7 64.4 1.0 C5' C:LMS611 3.8 55.5 1.0 O4 C:PO4612 3.9 62.6 1.0 OE2 C:GLU442 4.0 64.9 1.0 O1P C:LMS611 4.0 64.0 1.0 O5' C:LMS611 4.1 57.1 1.0 NZ C:LYS459 4.2 64.7 1.0 OD1 C:ASP460 4.4 64.7 1.0 CE1 C:HIS440 4.5 59.4 1.0 CB C:ASN443 4.6 61.1 1.0 CB C:SER275 4.7 55.9 1.0 O1 C:PO4612 4.7 61.7 1.0 N C:LMS611 4.8 53.1 1.0 C4' C:LMS611 4.9 54.5 1.0 CG C:GLU442 4.9 59.0 1.0 NE2 C:HIS440 4.9 58.5 1.0 CA C:ASN443 4.9 63.1 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg612 b:62.9 occ:1.00 O3 E:PO4611 1.9 67.2 1.0 OD1 E:ASN443 2.4 60.2 1.0 O2P E:LMS610 2.5 65.7 1.0 OE2 E:GLU442 2.6 67.5 1.0 OD2 E:ASP460 2.6 69.2 1.0 P E:PO4611 3.2 62.1 1.0 CG E:ASP460 3.4 62.0 1.0 CG E:ASN443 3.5 61.5 1.0 O4 E:PO4611 3.6 62.6 1.0 CB E:ASP460 3.6 60.2 1.0 S E:LMS610 3.7 56.7 1.0 CD E:GLU442 3.7 65.3 1.0 ND2 E:ASN443 3.8 62.2 1.0 O1 E:PO4611 3.8 58.3 1.0 NZ E:LYS459 4.0 63.7 1.0 O5' E:LMS610 4.1 58.5 1.0 OE1 E:GLU442 4.1 68.9 1.0 O1P E:LMS610 4.1 56.1 1.0 C5' E:LMS610 4.1 57.1 1.0 O2 E:PO4611 4.4 61.3 1.0 OD1 E:ASP460 4.5 66.1 1.0 CE1 E:HIS440 4.5 59.6 1.0 CB E:SER275 4.7 56.9 1.0 CB E:ASN443 4.8 63.4 1.0 NE2 E:HIS440 4.9 59.7 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Hsc-Ams Bound Desd, the Desferrioxamine Synthetase From the Streptomyces Griseoflavus Ferrimycin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg619 b:57.5 occ:1.00 O4 D:PO4618 2.1 58.3 1.0 O2P D:LMS617 2.3 50.6 1.0 OE1 D:GLU442 2.4 52.5 1.0 OD1 D:ASN443 2.5 53.0 1.0 OD2 D:ASP460 2.8 56.8 1.0 P D:PO4618 3.4 53.4 1.0 CG D:ASN443 3.5 52.1 1.0 S D:LMS617 3.5 57.9 1.0 CG D:ASP460 3.6 57.4 1.0 CD D:GLU442 3.6 56.0 1.0 O2 D:PO4618 3.7 53.5 1.0 C5' D:LMS617 3.7 48.4 1.0 ND2 D:ASN443 3.8 51.5 1.0 O5' D:LMS617 3.8 51.1 1.0 CB D:ASP460 3.9 53.0 1.0 O3 D:PO4618 4.0 57.4 1.0 O1P D:LMS617 4.0 49.8 1.0 OE2 D:GLU442 4.1 55.8 1.0 NZ D:LYS459 4.4 53.2 1.0 CB D:SER275 4.5 49.5 1.0 O1 D:PO4618 4.5 51.9 1.0 OD1 D:ASP460 4.5 60.7 1.0 CE1 D:HIS440 4.6 49.2 1.0 C4' D:LMS617 4.7 50.0 1.0 CB D:ASN443 4.9 50.0 1.0 CG D:GLU442 4.9 52.2 1.0 N D:LMS617 4.9 51.6 1.0

J.Yang, V.S.Banas, K.D.Patel, G.S.M.Rivera, L.S.Mydy, A.M.Gulick, T.A.Wencewicz. An Acyl-Adenylate Mimic Reveals the Structural Basis For Substrate Recognition By the Iterative Siderophore Synthetase Desd. J.Biol.Chem. V. 298 02166 2022.
ISSN: ESSN 1083-351X
PubMed: 35750210
DOI: 10.1016/J.JBC.2022.102166