Magnesium in PDB 5ygk: Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp

The structure of Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp, PDB code: 5ygk was solved by J.Gao, W.D.Liu, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.87 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.090, 119.308, 93.133, 90.00, 117.35, 90.00
R / Rfree (%)	18.4 / 23.6

The binding sites of Magnesium atom in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp (pdb code 5ygk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp, PDB code: 5ygk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp


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 A Synthase From Streptomyces Sp. CL190 with Dmaspp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:36.0 occ:1.00 O7 A:DST302 1.6 35.1 1.0 O7 A:DST301 2.0 39.4 1.0 O A:HOH460 2.0 33.1 1.0 O A:HOH423 2.1 38.6 1.0 O4 A:DST302 2.1 35.0 1.0 OD1 A:ASP9 2.3 32.7 1.0 P3 A:DST302 2.9 43.0 1.0 P1 A:DST302 3.1 35.2 1.0 CG A:ASP9 3.3 36.4 1.0 P3 A:DST301 3.4 48.6 1.0 O6 A:DST302 3.4 34.7 1.0 O2 A:DST302 3.4 36.4 1.0 OD2 A:ASP9 3.5 36.5 1.0 O8 A:DST301 4.0 63.9 1.0 O8 A:DST302 4.1 56.8 1.0 O6 A:DST301 4.1 50.2 1.0 S9 A:DST302 4.2 46.2 1.0 O2 A:DST301 4.2 41.0 1.0 NH1 A:ARG13 4.3 29.0 1.0 O5 A:DST302 4.4 32.2 1.0 N A:GLY10 4.5 30.3 1.0 C10 A:DST301 4.6 53.9 1.0 CB A:ASP9 4.7 28.5 1.0 C11 A:DST301 4.8 53.5 1.0 C10 A:DST302 4.8 47.9 1.0 P1 A:DST301 4.8 38.4 1.0 S9 A:DST301 4.9 60.1 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp


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 A Synthase From Streptomyces Sp. CL190 with Dmaspp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:43.9 occ:1.00 O8 B:DST302 2.0 41.7 1.0 O8 B:DST301 2.1 51.5 1.0 OD1 B:ASP9 2.2 49.1 1.0 O6 B:DST302 2.2 39.1 1.0 CG B:ASP9 3.0 42.1 1.0 OD2 B:ASP9 3.2 52.4 1.0 P1 B:DST302 3.3 42.6 1.0 P3 B:DST302 3.3 47.0 1.0 P3 B:DST301 3.5 67.1 1.0 O5 B:DST302 3.5 42.5 1.0 O2 B:DST302 3.7 43.9 1.0 O4 B:DST301 3.8 51.5 1.0 O7 B:DST301 4.2 65.2 1.0 NH1 B:ARG13 4.2 39.6 1.0 S9 B:DST302 4.2 47.9 1.0 O2 B:DST301 4.3 54.5 1.0 C10 B:DST302 4.4 60.0 1.0 C13 B:DST301 4.5 48.5 1.0 CB B:ASP9 4.5 39.0 1.0 O7 B:DST302 4.5 49.5 1.0 N B:GLY10 4.5 40.6 1.0 O4 B:DST302 4.5 42.6 1.0 C10 B:DST301 4.6 60.0 1.0 P1 B:DST301 4.6 49.9 1.0 NH2 B:ARG163 4.8 50.3 1.0 CA B:ASP9 4.9 36.2 1.0 S9 B:DST301 4.9 69.0 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp


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 A Synthase From Streptomyces Sp. CL190 with Dmaspp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:31.2 occ:1.00 O C:HOH404 2.0 33.1 1.0 O C:HOH426 2.0 33.0 1.0 O4 C:DST302 2.0 28.9 1.0 O7 C:DST302 2.1 33.4 1.0 OD1 C:ASP9 2.1 25.1 1.0 O7 C:DST301 2.2 38.7 1.0 CG C:ASP9 3.1 31.9 1.0 P1 C:DST302 3.1 27.8 1.0 P3 C:DST302 3.3 40.2 1.0 OD2 C:ASP9 3.3 33.1 1.0 O6 C:DST302 3.4 36.0 1.0 P3 C:DST301 3.5 46.9 1.0 O2 C:DST302 3.6 31.0 1.0 NH2 H:ARG211 4.0 51.5 1.0 NH1 C:ARG13 4.1 28.8 1.0 O5 C:DST301 4.1 43.8 1.0 S9 C:DST301 4.1 52.6 1.0 S9 C:DST302 4.2 39.3 1.0 C10 C:DST302 4.2 46.0 1.0 N C:GLY10 4.2 30.9 1.0 O5 C:DST302 4.3 31.5 1.0 O8 C:DST302 4.5 44.3 1.0 CB C:ASP9 4.5 25.7 1.0 O2 C:DST301 4.5 41.5 1.0 O8 C:DST301 4.5 42.1 1.0 NE H:ARG211 4.6 61.8 1.0 C10 C:DST301 4.6 37.5 1.0 CZ H:ARG211 4.7 63.3 1.0 P1 C:DST301 4.8 36.1 1.0 CA C:GLY10 4.8 25.4 1.0 CA C:ASP9 4.9 23.2 1.0 O6 C:DST301 5.0 40.3 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp


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 A Synthase From Streptomyces Sp. CL190 with Dmaspp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:41.7 occ:1.00 O8 D:DST302 2.0 50.0 1.0 O8 D:DST301 2.1 44.8 1.0 O5 D:DST302 2.1 37.2 1.0 O D:HOH411 2.1 38.8 1.0 O D:HOH421 2.2 49.5 1.0 OD1 D:ASP9 2.3 31.6 1.0 P3 D:DST302 3.2 46.3 1.0 CG D:ASP9 3.2 37.3 1.0 P1 D:DST302 3.2 34.2 1.0 OD2 D:ASP9 3.3 36.1 1.0 P3 D:DST301 3.4 57.2 1.0 O4 D:DST302 3.6 39.5 1.0 O2 D:DST302 3.6 29.1 1.0 O6 D:DST301 3.7 52.7 1.0 S9 D:DST301 4.0 58.9 1.0 C10 D:DST301 4.1 50.6 1.0 S9 D:DST302 4.2 47.3 1.0 NH1 D:ARG13 4.3 32.1 1.0 O7 D:DST302 4.4 53.2 1.0 O6 D:DST302 4.4 30.5 1.0 O2 D:DST301 4.4 46.0 1.0 O7 D:DST301 4.5 37.2 1.0 N D:GLY10 4.5 38.0 1.0 O D:HOH481 4.5 48.3 1.0 P1 D:DST301 4.6 48.0 1.0 CB D:ASP9 4.6 30.5 1.0 C10 D:DST302 4.6 58.5 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp


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 A Synthase From Streptomyces Sp. CL190 with Dmaspp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg303 b:42.4 occ:1.00 O7 E:DST302 1.5 42.2 1.0 O E:HOH455 1.9 43.2 1.0 OD1 E:ASP9 2.1 31.7 1.0 O8 E:DST301 2.2 54.3 1.0 O5 E:DST302 2.2 41.2 1.0 P3 E:DST302 2.8 48.7 1.0 P1 E:DST302 3.1 39.4 1.0 CG E:ASP9 3.1 29.4 1.0 O2 E:DST302 3.3 45.8 1.0 O6 E:DST302 3.4 49.5 1.0 OD2 E:ASP9 3.4 43.3 1.0 P3 E:DST301 3.6 58.0 1.0 S9 E:DST302 4.0 50.6 1.0 O8 E:DST302 4.0 49.5 1.0 O2 E:DST301 4.0 52.0 1.0 NH1 E:ARG13 4.0 34.0 1.0 O E:HOH407 4.1 47.9 1.0 N E:GLY10 4.3 32.3 1.0 C10 E:DST302 4.3 47.4 1.0 O4 E:DST302 4.4 38.6 1.0 O7 E:DST301 4.4 63.1 1.0 CB E:ASP9 4.5 32.9 1.0 C10 E:DST301 4.6 42.9 1.0 C11 E:DST301 4.7 41.2 1.0 CA E:ASP9 4.9 28.7 1.0 S9 E:DST301 4.9 52.1 1.0 C11 E:DST302 4.9 47.5 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg303 b:54.0 occ:1.00 O8 F:DST302 2.0 58.4 1.0 O4 F:DST302 2.0 66.0 1.0 O7 F:DST301 2.1 57.2 1.0 O F:HOH402 2.1 53.0 1.0 OD1 F:ASP9 2.5 54.7 1.0 O F:HOH431 2.5 59.6 1.0 P1 F:DST302 3.1 62.9 1.0 P3 F:DST302 3.2 69.6 1.0 P3 F:DST301 3.4 64.4 1.0 O6 F:DST302 3.4 59.2 1.0 CG F:ASP9 3.5 58.3 1.0 O2 F:DST302 3.6 62.5 1.0 O8 F:DST301 3.7 70.0 1.0 OD2 F:ASP9 3.7 58.3 1.0 NH1 F:ARG13 3.8 59.0 1.0 S9 F:DST302 4.4 57.0 1.0 O5 F:DST302 4.4 55.3 1.0 O7 F:DST302 4.4 65.7 1.0 O2 F:DST301 4.4 68.6 1.0 O5 F:DST301 4.4 60.2 1.0 N F:GLY10 4.5 60.3 1.0 C10 F:DST301 4.7 52.7 1.0 C10 F:DST302 4.7 64.5 1.0 C11 F:DST301 4.7 49.7 1.0 S9 F:DST301 4.8 60.3 1.0 CZ F:ARG13 4.8 58.7 1.0 CB F:ASP9 4.8 49.0 1.0 P1 F:DST301 4.9 57.6 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg303 b:48.1 occ:1.00 O G:HOH409 1.9 43.3 1.0 O6 G:DST302 2.0 43.4 1.0 O8 G:DST302 2.0 47.3 1.0 O8 G:DST301 2.3 56.8 1.0 OD1 G:ASP9 2.4 42.8 1.0 P1 G:DST302 3.1 41.8 1.0 P3 G:DST302 3.2 42.9 1.0 CG G:ASP9 3.3 37.3 1.0 O5 G:DST302 3.4 39.0 1.0 P3 G:DST301 3.4 76.4 1.0 OD2 G:ASP9 3.4 44.2 1.0 O2 G:DST302 3.6 42.7 1.0 O7 G:DST301 3.6 78.3 1.0 NH1 G:ARG13 4.0 39.7 1.0 S9 G:DST302 4.2 41.8 1.0 O4 G:DST302 4.4 34.6 1.0 N G:GLY10 4.4 37.3 1.0 O7 G:DST302 4.5 60.5 1.0 C10 G:DST301 4.5 48.0 1.0 O4 G:DST301 4.5 61.9 1.0 O6 G:DST301 4.6 50.8 1.0 S9 G:DST301 4.6 58.1 1.0 C10 G:DST302 4.6 45.3 1.0 CB G:ASP9 4.7 39.4 1.0 O2 G:DST301 4.8 63.0 1.0 P1 G:DST301 4.9 52.1 1.0 NH2 G:ARG163 5.0 34.3 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A Synthase From Streptomyces Sp. CL190 with Dmaspp within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg303 b:36.4 occ:1.00 O4 H:DST302 2.1 34.0 1.0 O7 H:DST301 2.1 36.1 1.0 O8 H:DST302 2.1 39.8 1.0 OD1 H:ASP9 2.3 32.0 1.0 P1 H:DST302 3.0 37.4 1.0 P3 H:DST302 3.2 46.5 1.0 CG H:ASP9 3.3 33.4 1.0 O6 H:DST302 3.3 37.8 1.0 O2 H:DST302 3.4 39.6 1.0 OD2 H:ASP9 3.5 41.0 1.0 P3 H:DST301 3.6 41.8 1.0 NH1 H:ARG13 4.1 33.2 1.0 O2 H:DST301 4.1 43.7 1.0 S9 H:DST302 4.1 46.8 1.0 O5 H:DST302 4.3 35.5 1.0 C10 H:DST302 4.3 35.5 1.0 O8 H:DST301 4.4 43.7 1.0 N H:GLY10 4.4 32.0 1.0 O7 H:DST302 4.5 43.6 1.0 C10 H:DST301 4.7 34.1 1.0 CB H:ASP9 4.7 25.4 1.0 C11 H:DST301 4.8 32.7 1.0 S9 H:DST301 5.0 44.2 1.0

S.R.Malwal, J.Gao, X.Y.Hu, Y.Y.Yang, W.D.Liu, J.W.Huang, T.P.Ko, L.P.Li, C.C.Chen, B.O'dowd, R.L.Khade, Y.Zhang, Y.H.Zhang, E.Oldfield, R.T.Guo. Crystal Structure of A Synthase From Streptomyces Sp. CL190 Acs Catalysis V. 8 4299 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B00543