Magnesium in PDB 2rdx: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism, PDB code: 2rdx was solved by Y.Patskovsky, J.Bonanno, J.M.Sauder, S.Ozyurt, M.Gilmore, C.Lau, M.Maletic, T.Gheyi, S.R.Wasserman, J.Koss, J.A.Gerlt, S.K.Burley, S.C.Almo, New Yorksgx 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)	20.00 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.415, 169.219, 223.476, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 25.6

The binding sites of Magnesium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism (pdb code 2rdx). 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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism, PDB code: 2rdx:
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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg378 b:23.5 occ:1.00 O A:HOH506 1.9 21.1 1.0 OD2 A:ASP241 2.1 39.5 1.0 OE2 A:GLU218 2.2 34.5 1.0 O A:HOH388 2.2 23.3 1.0 O A:HOH492 2.3 23.6 1.0 OD2 A:ASP193 2.3 30.4 1.0 CG A:ASP241 3.2 22.1 1.0 CD A:GLU218 3.2 35.9 1.0 CG A:ASP193 3.4 34.6 1.0 OD1 A:ASP193 3.7 33.6 1.0 ND2 A:ASN195 3.7 12.3 0.5 CB A:ASP241 3.8 20.8 1.0 OE1 A:GLU242 4.0 39.5 1.0 OE1 A:GLU218 4.0 26.5 1.0 CG A:GLU218 4.0 25.7 1.0 NZ A:LYS265 4.2 18.2 1.0 OH A:TYR57 4.2 86.7 1.0 OD1 A:ASP241 4.2 28.8 1.0 NE2 A:GLN163 4.5 36.0 1.0 CB A:ASP193 4.6 17.8 1.0 NZ A:LYS239 4.7 24.8 1.0 SG A:CYS263 4.8 34.4 1.0 CG A:ASN195 4.9 28.7 0.5 OD1 A:ASN195 4.9 44.2 0.5 CD A:GLU242 4.9 44.9 1.0 O A:HOH508 5.0 26.1 1.0 CE A:LYS239 5.0 35.0 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg378 b:22.3 occ:1.00 OD2 B:ASP241 2.1 20.1 1.0 O B:HOH471 2.2 33.0 1.0 OE2 B:GLU218 2.2 28.9 1.0 O B:HOH380 2.3 14.1 1.0 OD2 B:ASP193 2.3 28.2 1.0 O B:HOH492 2.5 28.1 1.0 CG B:ASP241 3.1 33.2 1.0 CD B:GLU218 3.3 46.3 1.0 CG B:ASP193 3.3 32.9 1.0 CB B:ASP241 3.6 26.7 1.0 OD1 B:ASP193 3.7 20.7 1.0 OH B:TYR57 3.8 72.3 1.0 OD1 B:ASN195 3.9 51.5 1.0 CG B:GLU218 3.9 22.2 1.0 NE2 B:GLN163 3.9 23.5 1.0 OD1 B:ASP241 4.2 20.5 1.0 OE1 B:GLU218 4.2 15.9 1.0 OE1 B:GLU242 4.3 24.2 1.0 NZ B:LYS265 4.5 25.1 1.0 O B:HOH444 4.5 35.1 1.0 CB B:ASP193 4.6 11.0 1.0 NZ B:LYS239 4.7 44.4 1.0 CD B:GLN163 4.7 34.7 1.0 OE1 B:GLN163 4.8 27.2 1.0 CD B:GLU242 4.8 33.1 1.0 CG B:ASN195 4.9 38.5 1.0 CE B:LYS265 4.9 24.9 1.0 OE2 B:GLU242 5.0 48.9 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg378 b:13.2 occ:1.00 O C:HOH504 1.9 16.1 1.0 O C:HOH520 1.9 20.3 1.0 OE2 C:GLU218 2.0 23.5 1.0 OD2 C:ASP241 2.1 16.4 1.0 OD2 C:ASP193 2.2 20.4 1.0 O C:HOH411 2.2 16.0 1.0 CD C:GLU218 3.1 25.3 1.0 CG C:ASP193 3.2 34.9 1.0 CG C:ASP241 3.3 38.2 1.0 OD1 C:ASP193 3.6 27.7 1.0 CB C:ASP241 3.8 25.3 1.0 ND2 C:ASN195 3.9 35.1 1.0 CG C:GLU218 3.9 27.3 1.0 OE1 C:GLU218 4.0 32.4 1.0 NE2 C:GLN163 4.0 66.6 1.0 OH C:TYR57 4.1 69.0 1.0 OE1 C:GLU242 4.2 35.0 1.0 OD1 C:ASP241 4.3 16.1 1.0 CB C:ASP193 4.3 12.6 1.0 NZ C:LYS265 4.7 38.3 1.0 NZ C:LYS239 4.7 37.8 1.0 CG C:ASN195 4.8 45.5 1.0 CD C:GLU242 5.0 46.0 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg378 b:20.9 occ:1.00 O D:HOH506 1.9 18.3 1.0 O D:HOH489 2.0 13.5 1.0 OD2 D:ASP241 2.1 23.4 1.0 O D:HOH383 2.2 19.9 1.0 OE2 D:GLU218 2.2 32.0 1.0 OD2 D:ASP193 2.3 24.2 1.0 CG D:ASP193 3.2 25.8 1.0 CG D:ASP241 3.2 34.0 1.0 CD D:GLU218 3.2 47.4 1.0 OD1 D:ASP193 3.5 26.1 1.0 CB D:ASP241 3.6 17.1 1.0 ND2 D:ASN195 3.9 72.8 1.0 CG D:GLU218 3.9 26.6 1.0 OE1 D:GLU242 3.9 37.5 1.0 OE1 D:GLU218 4.2 19.1 1.0 OD1 D:ASP241 4.2 28.8 1.0 OH D:TYR57 4.3 84.9 1.0 NZ D:LYS265 4.3 16.8 1.0 O D:HOH482 4.4 35.6 1.0 NE2 D:GLN163 4.4 48.4 1.0 CB D:ASP193 4.5 9.8 1.0 CD D:GLU242 4.8 47.0 1.0 NZ D:LYS239 4.9 40.8 1.0 OE1 D:GLU292 4.9 32.4 1.0 CG D:ASN195 4.9 55.6 1.0 SG D:CYS263 5.0 40.2 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg378 b:24.6 occ:1.00 O E:HOH476 1.8 37.8 1.0 O E:HOH462 2.1 25.2 1.0 OD2 E:ASP241 2.1 22.9 1.0 OD2 E:ASP193 2.3 22.1 1.0 OE2 E:GLU218 2.4 26.9 1.0 O E:HOH383 2.4 19.6 1.0 CG E:ASP241 3.2 37.7 1.0 CG E:ASP193 3.3 30.6 1.0 CD E:GLU218 3.3 44.8 1.0 OH E:TYR57 3.6 83.8 1.0 OD1 E:ASP193 3.7 19.3 1.0 CB E:ASP241 3.7 21.9 1.0 ND2 E:ASN195 4.0 44.1 1.0 OE1 E:GLU218 4.1 28.7 1.0 NE2 E:GLN163 4.1 20.3 1.0 CG E:GLU218 4.1 34.0 1.0 OE1 E:GLU242 4.3 24.2 1.0 OD1 E:ASP241 4.3 23.0 1.0 NZ E:LYS265 4.4 29.7 1.0 CB E:ASP193 4.5 20.8 1.0 OE1 E:GLN163 4.7 50.5 1.0 CD E:GLN163 4.7 43.9 1.0 CE E:LYS265 4.9 18.8 1.0 CZ E:TYR57 5.0 78.3 1.0 CD E:GLU242 5.0 45.2 1.0 NZ E:LYS239 5.0 33.8 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg378 b:30.0 occ:1.00 O F:HOH467 2.0 37.6 1.0 OE2 F:GLU218 2.2 28.3 1.0 OD2 F:ASP241 2.3 20.8 1.0 OD2 F:ASP193 2.3 34.4 1.0 O F:HOH468 2.4 49.9 1.0 O F:HOH382 2.4 24.9 1.0 CD F:GLU218 3.3 19.5 1.0 CG F:ASP193 3.4 22.6 1.0 CG F:ASP241 3.4 27.5 1.0 OD1 F:ASP193 3.9 28.6 1.0 CB F:ASP241 3.9 13.7 1.0 CG F:GLU218 4.1 9.9 1.0 OE1 F:GLU218 4.1 18.3 1.0 NZ F:LYS265 4.2 27.7 1.0 OE1 F:GLU242 4.2 31.4 1.0 OH F:TYR57 4.4 93.0 1.0 NZ F:LYS239 4.4 37.3 1.0 OD1 F:ASP241 4.5 21.9 1.0 CB F:ASP193 4.5 26.0 1.0 NE2 F:GLN163 4.7 42.5 1.0 SG F:CYS263 4.9 34.7 1.0 CE F:LYS239 4.9 34.6 1.0 ND2 F:ASN195 5.0 36.0 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg378 b:19.2 occ:1.00 OD2 G:ASP241 1.9 31.1 1.0 O G:HOH492 2.0 16.9 1.0 O G:HOH517 2.2 21.9 1.0 OE2 G:GLU218 2.2 33.3 1.0 OD2 G:ASP193 2.2 22.6 1.0 O G:HOH420 2.3 13.9 1.0 CG G:ASP241 3.1 26.0 1.0 CD G:GLU218 3.3 33.8 1.0 CG G:ASP193 3.3 27.9 1.0 OD1 G:ASP193 3.7 30.8 1.0 CB G:ASP241 3.7 22.4 1.0 CG G:GLU218 4.0 28.9 1.0 ND2 G:ASN195 4.0 45.9 1.0 OD1 G:ASP241 4.1 29.3 1.0 OE1 G:GLU218 4.1 30.9 1.0 NZ G:LYS265 4.2 21.4 1.0 OE1 G:GLU242 4.3 31.6 1.0 OH G:TYR57 4.4 0.5 1.0 OE2 G:GLU242 4.5 55.0 1.0 CB G:ASP193 4.5 14.6 1.0 CD G:GLU242 4.7 24.6 1.0 NE2 G:GLN163 4.7 29.7 1.0 OE1 G:GLU292 4.8 38.9 1.0 NZ G:LYS239 4.8 29.4 1.0 SG G:CYS263 4.9 33.6 1.0 O G:HOH432 5.0 28.7 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg378 b:22.9 occ:1.00 O H:HOH494 1.9 18.6 1.0 OD2 H:ASP241 2.1 17.6 1.0 OE2 H:GLU218 2.2 22.3 1.0 OD2 H:ASP193 2.3 22.3 1.0 O H:HOH384 2.4 12.2 1.0 O H:HOH411 2.5 29.7 1.0 CD H:GLU218 3.3 32.6 1.0 CG H:ASP241 3.3 34.7 1.0 CG H:ASP193 3.4 28.2 1.0 CB H:ASP241 3.8 20.3 1.0 OH H:TYR57 3.9 84.5 1.0 OD1 H:ASP193 4.0 23.1 1.0 NZ H:LYS265 4.0 40.8 1.0 OE1 H:GLU218 4.0 20.2 1.0 NE2 H:GLN163 4.1 33.7 1.0 CG H:GLU218 4.1 12.0 1.0 ND2 H:ASN195 4.1 31.3 1.0 OD1 H:ASP241 4.3 27.4 1.0 OE1 H:GLU242 4.4 35.9 1.0 NZ H:LYS239 4.4 28.0 1.0 CB H:ASP193 4.6 23.9 1.0 CE H:LYS265 4.8 23.3 1.0 CD H:GLN163 4.9 43.5 1.0 OE1 H:GLN163 4.9 37.5 1.0 SG H:CYS263 5.0 32.8 1.0 CD H:GLU242 5.0 17.7 1.0

Y.Patskovsky, J.B.Bonanno, J.M.Sauder, M.Gilmore, S.Ozyurt, C.Lau, M.Maletic, T.Gheyi, S.R.Wasserman, J.Koss, J.A.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Nubinhibens Ism. To Be Published.