Magnesium in PDB 3p3b: Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Tartrate

The structure of Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Tartrate, PDB code: 3p3b was solved by A.A.Fedorov, E.V.Fedorov, F.Groninger-Poe, J.A.Gerlt, S.K.Burley, S.C.Almo, New York 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)	41.20 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	158.859, 66.051, 75.664, 90.00, 95.48, 90.00
R / Rfree (%)	21.6 / 25.2

The binding sites of Magnesium atom in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Tartrate (pdb code 3p3b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Tartrate, PDB code: 3p3b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg393 b:21.8 occ:1.00 OE2 A:GLU233 2.1 20.2 1.0 O11 A:TAR395 2.1 19.1 1.0 OD2 A:ASP207 2.2 19.4 1.0 O A:HOH606 2.2 19.9 1.0 OE2 A:GLU263 2.2 19.1 1.0 O2 A:TAR395 2.4 19.3 1.0 C1 A:TAR395 2.9 24.0 1.0 CD A:GLU233 3.0 18.8 1.0 C2 A:TAR395 3.1 23.0 1.0 CD A:GLU263 3.1 19.1 1.0 CG A:ASP207 3.1 20.0 1.0 OE1 A:GLU263 3.4 24.6 1.0 OD1 A:ASP207 3.4 20.9 1.0 CG A:GLU233 3.7 21.6 1.0 NZ A:LYS168 3.8 19.4 1.0 OE1 A:GLU233 4.0 17.6 1.0 O1 A:TAR395 4.1 21.4 1.0 O A:HOH406 4.2 19.6 1.0 ND2 A:ASN209 4.2 19.5 1.0 O A:HOH403 4.2 19.2 1.0 OE1 A:GLU234 4.3 19.8 1.0 CE A:LYS168 4.4 19.4 1.0 CB A:ASP207 4.4 18.7 1.0 C3 A:TAR395 4.4 25.1 1.0 CG A:GLU263 4.4 19.2 1.0 NZ A:LYS170 4.6 26.3 1.0 CD2 A:HIS311 4.6 19.8 1.0 O3 A:TAR395 4.7 23.4 1.0 CG A:GLU234 4.9 17.2 1.0 CG A:ASN209 5.0 18.3 1.0 CD A:GLU234 5.0 18.2 1.0 CB A:GLU233 5.0 19.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg394 b:22.9 occ:1.00 OD1 A:ASP261 2.1 21.2 1.0 O A:HOH608 2.1 19.1 1.0 OE2 A:GLU234 2.1 18.0 1.0 OE2 A:GLU238 2.2 18.5 1.0 O A:HOH609 2.2 19.3 1.0 O A:HOH607 2.2 19.4 1.0 CG A:ASP261 3.1 22.3 1.0 CD A:GLU238 3.2 21.6 1.0 CD A:GLU234 3.2 18.2 1.0 OD2 A:ASP261 3.3 18.7 1.0 OE1 A:GLU238 3.5 21.0 1.0 CG A:GLU234 3.6 17.2 1.0 O A:HOH497 4.0 27.0 1.0 ND2 A:ASN210 4.2 23.5 1.0 N A:GLY262 4.2 18.1 1.0 ND1 A:HIS237 4.2 26.0 1.0 OD1 A:ASN210 4.3 22.0 1.0 N A:GLU238 4.3 20.2 1.0 OE1 A:GLU234 4.3 19.8 1.0 O A:GLU263 4.4 21.6 1.0 CB A:ASP261 4.4 18.4 1.0 CG A:GLU238 4.5 20.3 1.0 CB A:GLU234 4.5 19.7 1.0 O A:HOH577 4.5 34.8 1.0 CB A:GLU238 4.7 21.0 1.0 CG A:ASN210 4.7 21.5 1.0 CA A:HIS237 4.7 22.6 1.0 CE1 A:HIS237 4.8 23.9 1.0 CA A:ASP261 4.9 18.1 1.0 O A:PHE236 4.9 20.1 1.0 CA A:GLY262 4.9 18.6 1.0 N A:GLU263 5.0 19.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg393 b:28.5 occ:1.00 O B:HOH478 2.1 24.4 1.0 OE2 B:GLU263 2.1 27.8 1.0 OE2 B:GLU233 2.2 28.9 1.0 OD2 B:ASP207 2.2 24.9 1.0 O11 B:TAR395 2.3 30.7 1.0 O2 B:TAR395 2.3 26.8 1.0 CD B:GLU263 3.0 28.4 1.0 CG B:ASP207 3.1 25.4 1.0 CD B:GLU233 3.1 29.8 1.0 C1 B:TAR395 3.1 28.7 1.0 C2 B:TAR395 3.2 30.7 1.0 OE1 B:GLU263 3.4 28.5 1.0 OD1 B:ASP207 3.4 25.6 1.0 CG B:GLU233 3.6 26.7 1.0 NZ B:LYS168 3.9 28.8 1.0 OE1 B:GLU233 4.1 31.1 1.0 OE1 B:GLU234 4.1 27.8 1.0 O B:HOH412 4.2 30.4 1.0 O B:HOH415 4.2 29.2 1.0 ND2 B:ASN209 4.2 30.1 1.0 O1 B:TAR395 4.3 29.9 1.0 CG B:GLU263 4.3 29.3 1.0 CB B:ASP207 4.3 23.1 1.0 NZ B:LYS170 4.5 34.1 1.0 C3 B:TAR395 4.5 30.8 1.0 CD2 B:HIS311 4.6 29.9 1.0 CE B:LYS168 4.7 27.5 1.0 O3 B:TAR395 4.8 36.9 1.0 CD B:GLU234 4.9 28.4 1.0 CG B:ASN209 4.9 26.6 1.0 CG B:GLU234 4.9 25.0 1.0 OD1 B:ASN209 5.0 25.7 1.0 CB B:GLU233 5.0 26.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Tartrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg394 b:27.4 occ:1.00 OD1 B:ASP261 2.1 22.3 1.0 OE2 B:GLU238 2.1 27.6 1.0 OE2 B:GLU234 2.1 26.1 1.0 O B:HOH481 2.2 28.4 1.0 O B:HOH479 2.2 23.0 1.0 O B:HOH480 2.2 26.5 1.0 CG B:ASP261 3.1 23.3 1.0 CD B:GLU234 3.1 28.4 1.0 CD B:GLU238 3.2 26.1 1.0 OD2 B:ASP261 3.4 24.9 1.0 CG B:GLU234 3.4 25.0 1.0 OE1 B:GLU238 3.6 29.1 1.0 O B:HOH420 3.9 33.1 1.0 N B:GLY262 4.2 27.0 1.0 OD1 B:ASN210 4.2 25.4 1.0 OE1 B:GLU234 4.2 27.8 1.0 N B:GLU238 4.2 23.7 1.0 ND2 B:ASN210 4.3 26.5 1.0 O B:GLU263 4.3 29.4 1.0 ND1 B:HIS237 4.3 25.5 1.0 CB B:ASP261 4.4 25.9 1.0 CG B:GLU238 4.4 24.9 1.0 CB B:GLU234 4.5 24.0 1.0 CB B:GLU238 4.6 24.0 1.0 CG B:ASN210 4.7 25.2 1.0 CA B:HIS237 4.8 25.9 1.0 CE1 B:HIS237 4.8 28.9 1.0 CA B:GLY262 4.9 28.2 1.0 CA B:ASP261 4.9 25.2 1.0 N B:GLU263 4.9 31.5 1.0

A.A.Fedorov, E.V.Fedorov, F.Groninger-Poe, J.A.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Tartrate. To Be Published.