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

The structure of Crystal Structure of D-Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg, PDB code: 3vcc was solved by A.A.Fedorov, E.V.Fedorov, F.Groninger-Poe, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.52 / 1.64
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	154.347, 65.985, 75.636, 90.00, 93.56, 90.00
R / Rfree (%)	17.9 / 21.6

The binding sites of Magnesium atom in the Crystal Structure of D-Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg (pdb code 3vcc). 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 D-Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg, PDB code: 3vcc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of D-Galacturonate Dehydratase From Geobacillus Sp. 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 D-Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:21.2 occ:1.00 OE2 A:GLU238 2.1 14.8 1.0 OE2 A:GLU234 2.2 19.0 1.0 OD1 A:ASP261 2.2 17.1 1.0 O A:HOH501 2.2 15.2 1.0 O A:HOH714 2.2 19.1 1.0 O A:HOH511 2.2 16.3 1.0 CG A:ASP261 3.1 17.6 1.0 CD A:GLU238 3.1 16.5 1.0 CD A:GLU234 3.2 20.0 1.0 OD2 A:ASP261 3.4 18.8 1.0 OE1 A:GLU238 3.5 16.8 1.0 CG A:GLU234 3.6 16.3 1.0 O A:HOH685 3.8 24.4 1.0 N A:GLY262 4.2 16.7 1.0 OD1 A:ASN210 4.2 17.4 1.0 ND2 A:ASN210 4.2 20.8 1.0 ND1 A:HIS237 4.2 19.3 1.0 N A:GLU238 4.3 15.6 1.0 OE1 A:GLU234 4.3 21.2 1.0 O A:GLU263 4.4 18.3 1.0 CG A:GLU238 4.5 16.3 1.0 CB A:ASP261 4.5 18.9 1.0 CB A:GLU234 4.6 17.6 1.0 CG A:ASN210 4.7 21.2 1.0 CB A:GLU238 4.7 16.1 1.0 CA A:HIS237 4.7 22.6 1.0 CE1 A:HIS237 4.8 21.7 1.0 CA A:GLY262 4.9 16.4 1.0 N A:GLU263 4.9 20.3 1.0 CA A:ASP261 4.9 14.4 1.0 O A:PHE236 4.9 17.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Galacturonate Dehydratase From Geobacillus Sp. 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 D-Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:21.7 occ:1.00 OE2 A:GLU233 2.1 19.9 1.0 OE2 A:GLU263 2.1 17.9 1.0 O A:HOH522 2.2 18.6 1.0 O A:HOH534 2.2 21.7 1.0 OD2 A:ASP207 2.2 19.0 1.0 O A:HOH587 2.3 20.9 1.0 CD A:GLU263 3.0 20.8 1.0 CD A:GLU233 3.1 18.8 1.0 CG A:ASP207 3.1 20.2 1.0 OE1 A:GLU263 3.4 24.3 1.0 OD1 A:ASP207 3.4 18.5 1.0 CG A:GLU233 3.8 18.8 1.0 NZ A:LYS170 3.9 28.3 1.0 OE1 A:GLU233 4.1 18.3 1.0 NZ A:LYS168 4.1 20.6 1.0 O A:HOH555 4.2 25.0 1.0 OE1 A:GLU234 4.2 21.2 1.0 ND2 A:ASN209 4.2 20.1 1.0 O A:HOH536 4.3 20.6 1.0 O A:HOH657 4.3 26.5 1.0 CG A:GLU263 4.3 20.6 1.0 CB A:ASP207 4.5 17.0 1.0 CD2 A:HIS311 4.6 19.1 1.0 CE A:LYS168 4.7 20.0 1.0 CG A:ASN209 4.8 20.2 1.0 CG A:GLU234 4.9 16.3 1.0 OD1 A:ASN209 4.9 19.8 1.0 CD A:GLU234 4.9 20.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Galacturonate Dehydratase From Geobacillus Sp. 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 D-Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:21.0 occ:1.00 OD1 B:ASP261 2.1 19.5 1.0 OE2 B:GLU238 2.2 18.9 1.0 OE2 B:GLU234 2.2 20.7 1.0 O B:HOH504 2.2 18.6 1.0 O B:HOH503 2.2 17.5 1.0 O B:HOH505 2.2 20.0 1.0 CG B:ASP261 3.0 21.0 1.0 CD B:GLU234 3.2 19.6 1.0 CD B:GLU238 3.2 20.9 1.0 OD2 B:ASP261 3.4 19.0 1.0 CG B:GLU234 3.5 18.9 1.0 OE1 B:GLU238 3.5 19.9 1.0 O B:HOH533 3.7 25.4 1.0 N B:GLY262 4.2 21.3 1.0 OD1 B:ASN210 4.2 19.4 1.0 ND2 B:ASN210 4.3 22.0 1.0 OE1 B:GLU234 4.3 19.6 1.0 ND1 B:HIS237 4.3 22.1 1.0 N B:GLU238 4.3 16.9 1.0 O B:GLU263 4.3 22.1 1.0 CB B:ASP261 4.4 18.4 1.0 CB B:GLU234 4.4 20.1 1.0 CG B:GLU238 4.5 18.9 1.0 CG B:ASN210 4.7 22.8 1.0 CB B:GLU238 4.7 18.2 1.0 CA B:HIS237 4.8 20.2 1.0 CE1 B:HIS237 4.8 22.8 1.0 CA B:ASP261 4.9 15.6 1.0 CA B:GLY262 4.9 20.4 1.0 CA B:GLU234 5.0 17.5 1.0 N B:GLU263 5.0 21.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Galacturonate Dehydratase From Geobacillus Sp. 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 D-Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:22.7 occ:1.00 O B:HOH515 2.2 20.9 1.0 O B:HOH566 2.2 22.2 1.0 OD2 B:ASP207 2.2 20.0 1.0 O B:HOH519 2.2 20.6 1.0 OE2 B:GLU263 2.3 25.8 1.0 OE2 B:GLU233 2.3 23.1 1.0 CD B:GLU263 3.1 26.1 1.0 CG B:ASP207 3.1 20.8 1.0 CD B:GLU233 3.2 24.0 1.0 OE1 B:GLU263 3.3 25.2 1.0 OD1 B:ASP207 3.5 18.2 1.0 CG B:GLU233 3.8 20.3 1.0 NZ B:LYS170 3.9 28.8 1.0 O B:HOH667 4.0 34.2 1.0 OE1 B:GLU233 4.1 18.3 1.0 ND2 B:ASN209 4.2 22.1 1.0 O B:HOH601 4.2 27.6 1.0 NZ B:LYS168 4.2 27.0 1.0 OE1 B:GLU234 4.3 19.6 1.0 O B:HOH525 4.3 22.4 1.0 CG B:GLU263 4.4 22.5 1.0 CB B:ASP207 4.4 19.7 1.0 CD2 B:HIS311 4.6 23.8 1.0 CE B:LYS168 4.8 21.4 1.0 CG B:ASN209 4.8 18.3 1.0 OD1 B:ASN209 4.8 19.2 1.0 CD B:GLU234 5.0 19.6 1.0

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