Magnesium in PDB 4ip5: Crystal Structure of L-Fuconate Dehydratase From Silicibacter Sp. TM1040 Liganded with Mg and D-Erythronohydroxamate

The structure of Crystal Structure of L-Fuconate Dehydratase From Silicibacter Sp. TM1040 Liganded with Mg and D-Erythronohydroxamate, PDB code: 4ip5 was solved by A.A.Fedorov, E.V.Fedorov, T.Lukk, 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)	38.80 / 2.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.993, 141.362, 59.807, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 18.4

The binding sites of Magnesium atom in the Crystal Structure of L-Fuconate Dehydratase From Silicibacter Sp. TM1040 Liganded with Mg and D-Erythronohydroxamate (pdb code 4ip5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of L-Fuconate Dehydratase From Silicibacter Sp. TM1040 Liganded with Mg and D-Erythronohydroxamate, PDB code: 4ip5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of L-Fuconate Dehydratase From Silicibacter Sp. TM1040 Liganded with Mg and D-Erythronohydroxamate


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 L-Fuconate Dehydratase From Silicibacter Sp. TM1040 Liganded with Mg and D-Erythronohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:13.2 occ:1.00 ON A:EHM501 2.0 18.9 1.0 O A:HOH869 2.1 11.7 1.0 OD2 A:ASP246 2.1 10.9 1.0 OE2 A:GLU272 2.1 14.0 1.0 O1 A:EHM501 2.1 14.6 1.0 OE1 A:GLU299 2.1 12.3 1.0 N A:EHM501 2.7 16.0 1.0 C1 A:EHM501 2.7 17.5 1.0 CD A:GLU272 3.0 19.3 1.0 CG A:ASP246 3.1 20.1 1.0 CD A:GLU299 3.2 17.3 1.0 OD1 A:ASP246 3.5 14.2 1.0 NZ A:LYS218 3.5 20.7 1.0 OE2 A:GLU299 3.7 15.9 1.0 CG A:GLU272 3.8 12.8 1.0 OE1 A:GLU272 3.8 15.1 1.0 NZ A:LYS216 3.9 12.8 1.0 O A:HOH618 4.1 15.8 1.0 ND2 A:ASN248 4.1 10.2 1.0 O A:HOH647 4.1 15.4 1.0 C2 A:EHM501 4.2 19.7 1.0 OE1 A:GLU273 4.3 15.2 1.0 CD2 A:HIS349 4.4 17.6 1.0 CG A:GLU299 4.4 10.2 1.0 CB A:ASP246 4.4 15.4 1.0 OD1 A:ASN248 4.6 15.8 1.0 O2 A:EHM501 4.6 16.9 1.0 CG A:ASN248 4.7 11.8 1.0 CE A:LYS216 4.8 17.2 1.0 NE2 A:HIS349 4.8 16.2 1.0 C3 A:EHM501 4.9 16.9 1.0 O3 A:EHM501 5.0 14.2 1.0 CB A:GLU272 5.0 13.7 1.0 CE A:LYS218 5.0 14.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of L-Fuconate Dehydratase From Silicibacter Sp. TM1040 Liganded with Mg and D-Erythronohydroxamate


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 L-Fuconate Dehydratase From Silicibacter Sp. TM1040 Liganded with Mg and D-Erythronohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:14.0 occ:1.00 OE2 B:GLU272 2.0 12.4 1.0 O B:HOH603 2.0 12.3 1.0 ON B:EHM501 2.1 17.2 1.0 OE1 B:GLU299 2.1 10.6 1.0 O1 B:EHM501 2.1 15.9 1.0 OD2 B:ASP246 2.1 12.7 1.0 N B:EHM501 2.7 16.9 1.0 C1 B:EHM501 2.7 20.0 1.0 CD B:GLU272 3.0 18.7 1.0 CD B:GLU299 3.1 17.3 1.0 CG B:ASP246 3.2 16.2 1.0 OE2 B:GLU299 3.5 16.7 1.0 OD1 B:ASP246 3.6 12.1 1.0 NZ B:LYS218 3.6 14.5 1.0 OE1 B:GLU272 3.8 13.7 1.0 CG B:GLU272 3.9 12.4 1.0 NZ B:LYS216 3.9 14.0 1.0 O B:HOH736 4.1 12.3 1.0 C2 B:EHM501 4.2 19.1 1.0 O B:HOH639 4.2 12.8 1.0 ND2 B:ASN248 4.2 12.3 1.0 OE1 B:GLU273 4.3 13.2 1.0 CG B:GLU299 4.3 11.7 1.0 CD2 B:HIS349 4.4 14.8 1.0 CB B:ASP246 4.5 13.5 1.0 OD1 B:ASN248 4.6 15.1 1.0 O2 B:EHM501 4.6 16.3 1.0 CE B:LYS216 4.7 13.1 1.0 CG B:ASN248 4.7 22.0 1.0 O3 B:EHM501 4.8 17.7 1.0 NE2 B:HIS349 4.8 18.6 1.0 C3 B:EHM501 4.9 18.4 1.0 CB B:GLU299 5.0 9.0 1.0 CB B:GLU272 5.0 13.0 1.0 CG B:GLU273 5.0 12.3 1.0

A.A.Fedorov, E.V.Fedorov, T.Lukk, J.A.Gerlt, S.C.Almo. Crystal Structure of L-Fuconate Dehydratase From Silicibacter Sp. TM1040 Liganded with Mg and D-Erythronohydroxamate To Be Published.