Magnesium in PDB 3ops: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate, PDB code: 3ops was solved by V.N.Malashkevich, Y.Patskovsky, U.Ramagopal, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	159.989, 66.375, 154.854, 90.00, 96.59, 90.00
R / Rfree (%)	22.8 / 31.1

The binding sites of Magnesium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate (pdb code 3ops). 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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate, PDB code: 3ops:
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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate


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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:21.8 occ:1.00 O A:HOH606 2.0 39.6 1.0 OD1 A:ASP261 2.1 30.0 1.0 OE2 A:GLU238 2.1 29.2 1.0 OE2 A:GLU234 2.2 28.6 1.0 O A:HOH602 2.4 17.2 1.0 O41 A:TAR503 2.5 39.8 1.0 CG A:ASP261 3.0 33.6 1.0 CD A:GLU234 3.1 29.4 1.0 OD2 A:ASP261 3.2 29.8 1.0 CD A:GLU238 3.2 28.7 1.0 C4 A:TAR503 3.5 56.6 1.0 CG A:GLU234 3.5 28.6 1.0 OE1 A:GLU238 3.7 29.5 1.0 O4 A:TAR503 3.9 39.4 1.0 OD1 A:ASN210 4.1 19.2 1.0 OE1 A:GLU234 4.2 28.8 1.0 N A:GLY262 4.2 30.5 1.0 N A:GLU238 4.3 28.5 1.0 CB A:GLU234 4.3 29.4 1.0 ND2 A:ASN210 4.3 18.9 1.0 CB A:ASP261 4.4 30.2 1.0 CD2 A:HIS237 4.5 28.7 1.0 O A:GLU263 4.5 26.9 1.0 CG A:GLU238 4.5 29.6 1.0 CA A:HIS237 4.6 28.4 1.0 CB A:GLU238 4.6 28.7 1.0 CG A:ASN210 4.7 20.0 1.0 C3 A:TAR503 4.7 40.4 1.0 CG A:HIS237 4.7 29.6 1.0 O A:PHE236 4.8 28.5 1.0 NE2 A:HIS237 4.8 30.0 1.0 CA A:ASP261 4.9 30.1 1.0 C A:HIS237 5.0 28.4 1.0 CA A:GLU234 5.0 30.1 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate


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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:23.1 occ:1.00 OE2 A:GLU263 1.9 30.0 1.0 O A:HOH612 2.0 22.1 1.0 OE2 A:GLU233 2.1 29.5 1.0 OD2 A:ASP207 2.5 24.7 1.0 O2 A:TAR504 2.5 38.3 1.0 O11 A:TAR504 2.6 40.0 1.0 CD A:GLU263 2.9 28.9 1.0 CD A:GLU233 3.0 31.7 1.0 C2 A:TAR504 3.1 40.5 1.0 C1 A:TAR504 3.2 38.8 1.0 CG A:ASP207 3.3 15.6 1.0 OE1 A:GLU263 3.4 29.9 1.0 OD1 A:ASP207 3.5 24.9 1.0 CG A:GLU233 3.7 29.6 1.0 OE1 A:GLU233 4.0 29.9 1.0 OE1 A:GLU234 4.0 28.8 1.0 ND2 A:ASN209 4.0 22.6 1.0 CG A:GLU263 4.1 29.8 1.0 NZ A:LYS168 4.1 20.3 1.0 O A:HOH731 4.2 23.8 1.0 NZ A:LYS170 4.2 23.7 1.0 O1 A:TAR504 4.4 40.1 1.0 OD1 A:ASN209 4.5 22.1 1.0 CB A:ASP207 4.5 25.6 1.0 CG A:ASN209 4.5 32.6 1.0 CD2 A:HIS311 4.6 32.1 1.0 C3 A:TAR504 4.6 38.4 1.0 CD A:GLU234 4.7 29.4 1.0 CE A:LYS168 4.7 20.8 1.0 CG A:GLU234 4.9 28.6 1.0 O A:HOH730 4.9 23.8 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate


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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:30.6 occ:1.00 OE2 B:GLU238 2.0 24.3 1.0 O B:HOH600 2.0 36.9 1.0 O B:HOH601 2.0 21.5 1.0 O B:HOH602 2.1 17.3 1.0 OD1 B:ASP261 2.2 27.1 1.0 OE2 B:GLU234 2.4 40.5 1.0 CG B:ASP261 3.1 29.9 1.0 CD B:GLU238 3.1 29.7 1.0 CD B:GLU234 3.3 29.1 1.0 OD2 B:ASP261 3.3 27.1 1.0 CG B:GLU234 3.5 40.6 1.0 OE1 B:GLU238 3.7 23.7 1.0 OD1 B:ASN210 3.9 28.7 1.0 N B:GLU238 4.0 29.2 1.0 ND1 B:HIS237 4.1 26.3 1.0 ND2 B:ASN210 4.3 28.8 1.0 CB B:GLU234 4.3 27.4 1.0 CG B:GLU238 4.3 24.2 1.0 CA B:HIS237 4.4 27.4 1.0 OE1 B:GLU234 4.4 40.5 1.0 CB B:GLU238 4.5 29.9 1.0 CG B:ASN210 4.5 38.3 1.0 O B:PHE236 4.5 25.9 1.0 CB B:ASP261 4.5 26.7 1.0 N B:GLY262 4.6 27.1 1.0 O B:HOH1139 4.7 43.7 1.0 C B:HIS237 4.7 28.4 1.0 CE1 B:HIS237 4.7 27.0 1.0 O B:GLU263 4.8 29.1 1.0 CA B:GLU238 4.8 30.0 1.0 CA B:GLU234 4.9 26.8 1.0 CG B:HIS237 4.9 27.5 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate


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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:26.6 occ:1.00 O B:HOH1610 2.0 29.6 1.0 O41 B:TAR503 2.1 29.1 1.0 OD2 B:ASP207 2.1 33.6 1.0 OE2 B:GLU263 2.2 26.9 1.0 OE2 B:GLU233 2.3 23.4 1.0 O2 B:TAR503 2.7 31.4 1.0 CG B:ASP207 3.0 30.3 1.0 CD B:GLU263 3.1 29.5 1.0 C4 B:TAR503 3.2 36.9 1.0 OD1 B:ASP207 3.3 34.3 1.0 CD B:GLU233 3.3 24.7 1.0 OE1 B:GLU263 3.4 27.3 1.0 C2 B:TAR503 3.5 37.2 1.0 CG B:GLU233 3.7 24.5 1.0 OE1 B:GLU234 3.8 40.5 1.0 C3 B:TAR503 3.9 30.3 1.0 NZ B:LYS170 3.9 32.8 1.0 NZ B:LYS168 4.0 33.8 1.0 ND2 B:ASN209 4.1 25.6 1.0 O4 B:TAR503 4.3 29.8 1.0 O B:HOH681 4.3 24.1 1.0 CB B:ASP207 4.3 34.0 1.0 O B:HOH1302 4.4 23.8 1.0 CG B:GLU263 4.4 27.3 1.0 OE1 B:GLU233 4.4 24.1 1.0 CE B:LYS168 4.5 26.9 1.0 CD B:GLU234 4.6 29.1 1.0 O B:HOH639 4.6 34.3 1.0 CG B:GLU234 4.7 40.6 1.0 CB B:GLU233 4.7 25.8 1.0 CD2 B:HIS311 4.8 28.2 1.0 CG B:ASN209 4.9 21.6 1.0 C1 B:TAR503 4.9 31.6 1.0 O3 B:TAR503 5.0 37.6 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate


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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg500 b:21.9 occ:1.00 O C:HOH600 1.8 19.7 1.0 OE2 C:GLU238 1.9 23.4 1.0 OD1 C:ASP261 1.9 21.2 1.0 O C:HOH603 2.0 12.7 1.0 OE2 C:GLU234 2.2 18.1 1.0 O C:HOH601 2.4 12.2 1.0 CG C:ASP261 2.9 13.3 1.0 CD C:GLU238 2.9 21.4 1.0 OD2 C:ASP261 3.1 21.2 1.0 CD C:GLU234 3.2 18.7 1.0 OE1 C:GLU238 3.2 22.7 1.0 CG C:GLU234 3.6 16.6 1.0 O C:HOH920 3.9 28.9 1.0 N C:GLY262 4.1 19.0 1.0 CG C:GLU238 4.2 23.2 1.0 N C:GLU238 4.2 21.5 1.0 CB C:ASP261 4.2 20.7 1.0 OE1 C:GLU234 4.3 17.4 1.0 OD1 C:ASN210 4.3 21.7 1.0 O C:GLU263 4.3 22.5 1.0 ND1 C:HIS237 4.3 20.5 1.0 CB C:GLU238 4.4 21.1 1.0 CB C:GLU234 4.6 19.5 1.0 ND2 C:ASN210 4.7 21.5 1.0 CA C:ASP261 4.7 20.1 1.0 CE1 C:HIS237 4.7 22.6 1.0 CA C:GLU238 4.9 21.2 1.0 CA C:HIS237 4.9 20.5 1.0 O C:PHE236 4.9 20.9 1.0 CG C:ASN210 5.0 22.7 1.0 C C:ASP261 5.0 19.4 1.0 N C:GLU263 5.0 21.1 1.0 CA C:GLY262 5.0 19.9 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate


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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:39.0 occ:1.00 OE2 C:GLU233 1.8 14.4 1.0 OE2 C:GLU263 1.9 27.8 1.0 O C:HOH605 2.0 29.8 1.0 O2 C:TAR503 2.3 18.9 1.0 O1 C:TAR503 2.3 34.5 1.0 OD2 C:ASP207 2.3 21.8 1.0 C2 C:TAR503 2.9 34.8 1.0 C1 C:TAR503 3.0 19.6 1.0 CD C:GLU233 3.1 22.9 1.0 CD C:GLU263 3.1 21.5 1.0 CG C:ASP207 3.3 20.6 1.0 OD1 C:ASP207 3.5 22.2 1.0 OE1 C:GLU263 3.6 27.4 1.0 OE1 C:GLU233 3.9 13.7 1.0 CG C:GLU233 4.0 14.0 1.0 ND2 C:ASN209 4.1 18.8 1.0 O C:HOH742 4.1 14.4 1.0 O11 C:TAR503 4.2 34.5 1.0 OE1 C:GLU234 4.2 17.4 1.0 CG C:GLU263 4.3 27.9 1.0 NZ C:LYS168 4.4 25.3 1.0 O C:HOH771 4.4 16.4 1.0 C3 C:TAR503 4.4 19.8 1.0 NZ C:LYS170 4.5 20.7 1.0 CB C:ASP207 4.6 21.5 1.0 CD2 C:HIS311 4.6 14.7 1.0 CG C:GLU234 4.8 16.6 1.0 CG C:ASN209 4.9 25.3 1.0 CD C:GLU234 4.9 18.7 1.0 CB C:GLU263 5.0 21.2 1.0 NE2 C:HIS311 5.0 13.4 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate


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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg500 b:31.6 occ:1.00 O D:HOH601 1.7 21.0 1.0 OE2 D:GLU234 2.1 27.9 1.0 OE2 D:GLU238 2.1 37.4 1.0 O D:HOH602 2.1 32.5 1.0 O D:HOH600 2.1 33.6 1.0 OD1 D:ASP261 2.3 46.3 1.0 CD D:GLU238 3.1 41.8 1.0 CD D:GLU234 3.2 36.4 1.0 CG D:ASP261 3.2 39.2 1.0 OE1 D:GLU238 3.3 38.0 1.0 OD2 D:ASP261 3.5 47.4 1.0 O D:HOH604 3.6 41.9 1.0 CG D:GLU234 3.7 28.7 1.0 O D:GLU263 4.1 41.7 1.0 ND2 D:ASN210 4.1 31.2 1.0 OD1 D:ASN210 4.1 31.8 1.0 OE1 D:GLU234 4.3 28.8 1.0 N D:GLY262 4.5 45.9 1.0 CG D:GLU238 4.5 38.2 1.0 N D:GLU238 4.5 42.2 1.0 CB D:GLU234 4.5 37.2 1.0 CB D:ASP261 4.5 47.2 1.0 CG D:ASN210 4.6 39.9 1.0 ND1 D:HIS237 4.6 41.1 1.0 CA D:HIS237 4.9 41.7 1.0 CB D:GLU238 5.0 42.6 1.0 N D:GLU263 5.0 43.7 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate


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 Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:59.6 occ:1.00 OE2 D:GLU263 2.0 41.4 1.0 OD2 D:ASP207 2.0 34.4 1.0 O4 D:TAR503 2.2 48.0 1.0 OE2 D:GLU233 2.4 35.8 1.0 CD D:GLU263 2.8 44.2 1.0 CG D:ASP207 3.0 43.6 1.0 OE1 D:GLU263 3.2 41.2 1.0 OD1 D:ASP207 3.2 34.7 1.0 O D:HOH1175 3.3 37.5 1.0 CD D:GLU233 3.3 39.5 1.0 C4 D:TAR503 3.3 55.9 1.0 OE1 D:GLU234 3.5 28.8 1.0 CG D:GLU233 3.8 36.3 1.0 ND2 D:ASN209 3.9 31.9 1.0 C3 D:TAR503 4.0 48.0 1.0 CG D:GLU263 4.1 40.9 1.0 O41 D:TAR503 4.2 47.9 1.0 CD D:GLU234 4.2 36.4 1.0 CG D:GLU234 4.2 28.7 1.0 OE1 D:GLU233 4.2 36.3 1.0 NZ D:LYS168 4.3 44.5 1.0 CB D:ASP207 4.4 34.7 1.0 CG D:ASN209 4.6 21.6 1.0 NZ D:LYS170 4.7 30.4 1.0 O3 D:TAR503 4.7 55.2 1.0 OD1 D:ASN209 4.8 31.8 1.0 CB D:GLU234 4.8 37.2 1.0 O D:HOH1020 4.9 38.5 1.0 CB D:GLU263 5.0 43.7 1.0

V.N.Malashkevich, Y.Patskovsky, U.Ramagopal, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure Ofmandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 Complexed with Magnesium/Tartrate To Be Published.