Magnesium in PDB 3fxg: Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg

The structure of Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg, PDB code: 3fxg was solved by A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo, Newyork Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.94 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	200.898, 201.085, 82.090, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.6

The binding sites of Magnesium atom in the Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg (pdb code 3fxg). 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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg, PDB code: 3fxg:
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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg


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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:20.6 occ:1.00 OE2 A:GLU274 2.2 25.5 1.0 OD2 A:ASP221 2.2 21.5 1.0 OE2 A:GLU247 2.2 16.8 1.0 O A:HOH506 2.3 22.8 1.0 O A:HOH750 2.5 18.8 1.0 O A:HOH2059 2.8 35.5 1.0 CD A:GLU274 3.1 24.7 1.0 CG A:ASP221 3.3 19.2 1.0 CD A:GLU247 3.3 15.6 1.0 OE1 A:GLU274 3.4 24.3 1.0 OD1 A:ASP221 3.7 17.6 1.0 O A:HOH1019 3.8 18.0 1.0 NZ A:LYS184 3.8 15.6 1.0 CG A:GLU247 3.9 15.9 1.0 CD2 A:HIS324 4.1 26.5 1.0 O A:HOH487 4.2 14.4 1.0 OE1 A:GLU247 4.3 14.7 1.0 OE2 A:GLU248 4.4 21.4 1.0 CG A:GLU274 4.4 20.3 1.0 O A:HOH2780 4.5 49.2 1.0 CE A:LYS184 4.5 14.1 1.0 CB A:ASP221 4.6 17.2 1.0 NE2 A:HIS324 4.7 26.9 1.0 OE2 A:GLU344 4.9 14.3 1.0 CB A:GLU247 4.9 12.7 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg


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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:18.7 occ:1.00 OE2 B:GLU274 2.0 23.2 1.0 OD2 B:ASP221 2.2 19.0 1.0 O B:HOH494 2.2 23.2 1.0 OE2 B:GLU247 2.3 15.2 1.0 O B:HOH542 2.5 19.5 1.0 O B:HOH1404 3.0 35.7 1.0 CD B:GLU274 3.0 24.0 1.0 CG B:ASP221 3.2 16.7 1.0 CD B:GLU247 3.3 13.9 1.0 OE1 B:GLU274 3.4 24.2 1.0 OD1 B:ASP221 3.6 18.0 1.0 NZ B:LYS184 3.8 15.1 1.0 CG B:GLU247 3.8 12.1 1.0 O B:HOH469 3.9 17.0 1.0 CD2 B:HIS324 4.1 22.4 1.0 O B:HOH459 4.2 13.7 1.0 OE1 B:GLU247 4.3 13.1 1.0 CG B:GLU274 4.4 20.9 1.0 OE2 B:GLU248 4.4 19.1 1.0 CB B:ASP221 4.5 12.2 1.0 CE B:LYS184 4.5 15.2 1.0 NE2 B:HIS324 4.8 23.5 1.0 CB B:GLU247 4.9 12.0 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg


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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:19.6 occ:1.00 OD2 C:ASP221 2.1 20.9 1.0 OE2 C:GLU274 2.1 24.0 1.0 OE2 C:GLU247 2.3 16.6 1.0 O C:HOH504 2.3 21.6 1.0 O C:HOH519 2.4 18.4 1.0 O C:HOH1494 2.9 36.4 1.0 CD C:GLU274 3.1 22.0 1.0 CG C:ASP221 3.2 18.4 1.0 CD C:GLU247 3.3 14.3 1.0 OE1 C:GLU274 3.5 22.1 1.0 OD1 C:ASP221 3.7 19.2 1.0 NZ C:LYS184 3.8 14.7 1.0 CG C:GLU247 3.9 13.5 1.0 O C:HOH548 4.0 19.5 1.0 CD2 C:HIS324 4.1 22.9 1.0 O C:HOH514 4.3 13.9 1.0 OE1 C:GLU247 4.3 14.1 1.0 CE C:LYS184 4.4 13.4 1.0 CG C:GLU274 4.5 18.9 1.0 CB C:ASP221 4.5 15.1 1.0 OE2 C:GLU248 4.6 19.6 1.0 NE2 C:HIS324 4.9 23.5 1.0 CB C:GLU247 4.9 9.1 1.0 OE2 C:GLU344 5.0 16.2 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg


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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:20.7 occ:1.00 OD2 D:ASP221 2.1 19.9 1.0 OE2 D:GLU247 2.2 16.8 1.0 OE1 D:GLU274 2.3 23.0 1.0 O D:HOH1156 2.3 23.9 1.0 O D:HOH1217 2.4 25.3 1.0 O D:HOH2001 3.1 31.3 1.0 CG D:ASP221 3.2 16.4 1.0 CD D:GLU247 3.2 15.8 1.0 CD D:GLU274 3.2 23.4 1.0 OE2 D:GLU274 3.5 24.9 1.0 NZ D:LYS184 3.5 18.5 1.0 OD1 D:ASP221 3.6 18.9 1.0 O D:HOH832 3.8 18.8 1.0 CG D:GLU247 3.8 15.6 1.0 OE1 D:GLU247 4.1 16.2 1.0 CD2 D:HIS324 4.2 27.6 1.0 O D:HOH3088 4.3 16.6 1.0 CE D:LYS184 4.3 14.2 1.0 CB D:ASP221 4.4 14.7 1.0 CG D:GLU274 4.5 20.6 1.0 OE2 D:GLU248 4.6 21.1 1.0 CB D:GLU247 4.8 12.9 1.0 OE2 D:GLU344 4.9 16.0 1.0 NE2 D:HIS324 4.9 27.1 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg


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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:20.5 occ:1.00 OE2 E:GLU274 2.2 21.4 1.0 OD1 E:ASP221 2.2 22.4 1.0 OE2 E:GLU247 2.2 16.5 1.0 O E:HOH1533 2.3 20.1 1.0 O E:HOH509 2.4 25.1 1.0 O E:HOH1926 3.1 48.1 1.0 CD E:GLU274 3.1 22.8 1.0 CD E:GLU247 3.3 16.7 1.0 CG E:ASP221 3.3 19.0 1.0 OE1 E:GLU274 3.5 22.3 1.0 OD2 E:ASP221 3.8 19.7 1.0 O E:HOH978 3.8 22.1 1.0 NZ E:LYS184 3.8 15.2 1.0 CG E:GLU247 3.9 16.4 1.0 O E:HOH479 4.1 15.6 1.0 CD2 E:HIS324 4.1 25.8 1.0 OE1 E:GLU247 4.3 15.6 1.0 CG E:GLU274 4.4 19.9 1.0 OE2 E:GLU248 4.5 20.1 1.0 CE E:LYS184 4.5 13.3 1.0 CB E:ASP221 4.6 15.3 1.0 NE2 E:HIS324 4.8 24.9 1.0 CB E:GLU247 4.9 14.1 1.0 OE2 E:GLU344 5.0 18.4 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg


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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg501 b:18.9 occ:1.00 OD2 F:ASP221 2.1 20.3 1.0 OE2 F:GLU274 2.1 24.1 1.0 OE2 F:GLU247 2.2 16.8 1.0 O F:HOH522 2.3 20.2 1.0 O F:HOH1331 2.4 20.3 1.0 O F:HOH1838 2.9 36.2 1.0 CD F:GLU274 3.1 23.8 1.0 CG F:ASP221 3.2 18.2 1.0 CD F:GLU247 3.3 14.1 1.0 OE1 F:GLU274 3.5 23.7 1.0 OD1 F:ASP221 3.6 17.7 1.0 NZ F:LYS184 3.7 14.6 1.0 CG F:GLU247 3.8 12.7 1.0 O F:HOH506 4.0 17.5 1.0 CD2 F:HIS324 4.2 25.1 1.0 O F:HOH514 4.2 15.7 1.0 OE1 F:GLU247 4.2 12.7 1.0 CE F:LYS184 4.4 12.2 1.0 CB F:ASP221 4.5 16.3 1.0 CG F:GLU274 4.5 18.6 1.0 OE2 F:GLU248 4.5 18.2 1.0 NE2 F:HIS324 4.8 25.6 1.0 CB F:GLU247 4.9 10.6 1.0 OE2 F:GLU344 5.0 16.7 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg


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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg501 b:16.4 occ:1.00 OE2 G:GLU247 2.1 16.6 1.0 OD2 G:ASP221 2.1 18.1 1.0 OE2 G:GLU274 2.2 22.8 1.0 O G:HOH624 2.3 20.8 1.0 O G:HOH972 2.4 20.3 1.0 CD G:GLU274 3.2 23.5 1.0 CG G:ASP221 3.2 16.6 1.0 CD G:GLU247 3.2 14.5 1.0 O G:HOH2391 3.4 52.3 1.0 OE1 G:GLU274 3.6 23.1 1.0 OD1 G:ASP221 3.6 15.6 1.0 CG G:GLU247 3.8 13.9 1.0 NZ G:LYS184 3.8 17.9 1.0 O G:HOH1305 3.9 19.4 1.0 CD2 G:HIS324 4.1 29.1 1.0 OE1 G:GLU247 4.2 13.9 1.0 O G:HOH545 4.2 13.6 1.0 CG G:GLU274 4.5 18.5 1.0 CB G:ASP221 4.5 11.8 1.0 OE2 G:GLU248 4.5 19.6 1.0 CE G:LYS184 4.5 14.5 1.0 NE2 G:HIS324 4.8 29.5 1.0 CB G:GLU247 4.9 10.7 1.0 OE2 G:GLU344 4.9 15.7 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg


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 Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg501 b:20.8 occ:1.00 OE2 H:GLU274 2.2 18.8 1.0 OE2 H:GLU247 2.2 16.2 1.0 OD1 H:ASP221 2.2 19.6 1.0 O H:HOH467 2.4 17.6 1.0 O H:HOH495 2.4 15.4 1.0 O H:HOH1994 2.8 32.5 1.0 CD H:GLU274 3.1 21.6 1.0 CD H:GLU247 3.3 15.3 1.0 CG H:ASP221 3.3 15.7 1.0 OE1 H:GLU274 3.4 21.9 1.0 OD2 H:ASP221 3.7 17.4 1.0 NZ H:LYS184 3.8 15.8 1.0 O H:HOH773 3.8 17.9 1.0 CG H:GLU247 3.9 12.7 1.0 CD2 H:HIS324 4.0 22.1 1.0 O H:HOH579 4.1 13.3 1.0 OE1 H:GLU247 4.2 16.7 1.0 CG H:GLU274 4.4 18.5 1.0 OE2 H:GLU248 4.6 22.1 1.0 CE H:LYS184 4.6 15.9 1.0 CB H:ASP221 4.6 13.9 1.0 NE2 H:HIS324 4.6 20.7 1.0 CB H:GLU247 5.0 12.1 1.0 OE2 H:GLU344 5.0 15.9 1.0

A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo. Crystal Structure of Rhamnonate Dehydratase From Gibberella Zeae Complexed with Mg To Be Published.