Magnesium in PDB 3cxo: Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and 3-Deoxy-L- Rhamnonate

The structure of Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and 3-Deoxy-L- Rhamnonate, PDB code: 3cxo was solved by A.A.Fedorov, E.V.Fedorov, J.F.Rakus, B.K.Hubbard, 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)	24.91 / 2.00
Space group	F 4 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	272.833, 272.833, 272.833, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 23.4

The binding sites of Magnesium atom in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and 3-Deoxy-L- Rhamnonate (pdb code 3cxo). 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-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and 3-Deoxy-L- Rhamnonate, PDB code: 3cxo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and 3-Deoxy-L- Rhamnonate


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-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and 3-Deoxy-L- Rhamnonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:17.6 occ:1.00 OE2 A:GLU252 2.0 16.0 1.0 OE1 A:GLU280 2.0 17.4 1.0 OD2 A:ASP226 2.1 16.7 1.0 O A:HOH767 2.1 18.5 1.0 O1B A:3LR501 2.2 16.8 1.0 O2 A:3LR501 2.2 18.9 1.0 CD A:GLU280 3.0 21.3 1.0 C1 A:3LR501 3.0 21.2 1.0 CD A:GLU252 3.0 16.8 1.0 CG A:ASP226 3.1 15.1 1.0 C2 A:3LR501 3.1 21.2 1.0 OE2 A:GLU280 3.3 18.8 1.0 OD1 A:ASP226 3.4 15.7 1.0 CG A:GLU252 3.7 15.1 1.0 NZ A:LYS189 3.9 15.0 1.0 OE1 A:GLU252 4.0 13.7 1.0 O A:HOH581 4.0 19.4 1.0 O A:HOH504 4.1 15.6 1.0 OE1 A:GLU253 4.2 16.5 1.0 C3 A:3LR501 4.2 25.0 1.0 O1A A:3LR501 4.2 19.6 1.0 CG A:GLU280 4.3 18.3 1.0 CD2 A:HIS329 4.4 28.9 1.0 CB A:ASP226 4.4 15.5 1.0 CE A:LYS189 4.6 15.4 1.0 C4 A:3LR501 4.8 26.2 1.0 CB A:GLU252 4.9 13.5 1.0 CB A:GLU253 4.9 16.3 1.0 CB A:GLU280 5.0 17.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and 3-Deoxy-L- Rhamnonate


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-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed with Mg and 3-Deoxy-L- Rhamnonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:32.8 occ:1.00 OE2 B:GLU252 2.0 27.0 1.0 OE1 B:GLU280 2.0 27.5 1.0 OD2 B:ASP226 2.0 25.0 1.0 O B:HOH672 2.1 25.0 1.0 O2 B:1N5502 2.1 27.7 1.0 O1A B:1N5502 2.2 30.7 1.0 CD B:GLU280 3.0 28.9 1.0 C1 B:1N5502 3.0 31.2 1.0 CG B:ASP226 3.0 25.4 1.0 C2 B:1N5502 3.1 30.1 1.0 CD B:GLU252 3.1 26.9 1.0 OE2 B:GLU280 3.3 29.0 1.0 OD1 B:ASP226 3.3 25.5 1.0 CG B:GLU252 3.8 27.1 1.0 NZ B:LYS189 3.9 30.6 1.0 OE1 B:GLU252 4.0 26.9 1.0 O B:HOH583 4.0 30.5 1.0 O B:HOH517 4.1 32.3 1.0 C3 B:1N5502 4.1 30.9 1.0 OE1 B:GLU253 4.2 28.0 1.0 O1B B:1N5502 4.2 31.6 1.0 CG B:GLU280 4.3 27.1 1.0 CB B:ASP226 4.4 28.6 1.0 CD2 B:HIS329 4.4 31.2 1.0 CE B:LYS189 4.6 31.4 1.0 C4 B:1N5502 4.9 29.5 1.0 CB B:GLU252 4.9 28.5 1.0 CB B:GLU253 5.0 27.3 1.0 CD1 B:TRP228 5.0 22.3 1.0 CB B:GLU280 5.0 25.7 1.0

J.F.Rakus, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, B.K.Hubbard, J.D.Delli, P.C.Babbitt, S.C.Almo, J.A.Gerlt. Evolution of Enzymatic Activities in the Enolase Superfamily: L-Rhamnonate Dehydratase. Biochemistry V. 47 9944 2008.
ISSN: ISSN 0006-2960
PubMed: 18754693
DOI: 10.1021/BI800914R