Magnesium in PDB 3twb: Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid

The structure of Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid, PDB code: 3twb was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.76
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	144.727, 144.727, 446.996, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.6

The structure of Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid (pdb code 3twb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid, PDB code: 3twb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid


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 Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg420 b:14.7 occ:1.00 OE2 A:GLU251 2.0 13.7 1.0 O A:HOH518 2.1 10.1 1.0 OE1 A:GLU277 2.1 12.7 1.0 OD2 A:ASP225 2.1 12.3 1.0 O11 A:GCO423 2.3 14.3 1.0 O2 A:GCO423 2.3 14.6 1.0 C2 A:GCO423 2.9 47.0 1.0 C1 A:GCO423 3.0 44.1 1.0 CD A:GLU277 3.0 16.3 1.0 CD A:GLU251 3.0 16.8 1.0 CG A:ASP225 3.1 18.0 1.0 OE2 A:GLU277 3.3 15.6 1.0 OD1 A:ASP225 3.4 14.2 1.0 OE1 A:GLU251 3.7 15.3 1.0 NH2 A:ARG298 3.9 12.9 1.0 CG A:GLU251 3.9 11.5 1.0 CD2 A:HIS227 4.0 24.2 1.0 O A:HOH427 4.1 15.1 1.0 O A:HOH425 4.1 14.1 1.0 O12 A:GCO423 4.2 20.4 1.0 OD2 A:ASP252 4.2 14.6 1.0 NH1 A:ARG154 4.3 22.7 1.0 CG A:GLU277 4.3 11.1 1.0 C3 A:GCO423 4.4 44.1 1.0 CB A:ASP225 4.4 12.3 1.0 NE2 A:HIS227 4.6 18.6 1.0 OH A:TYR160 4.7 38.5 1.0 NE2 A:HIS327 4.8 16.3 1.0 CG A:ASP252 4.8 19.3 1.0 O3 A:GCO423 4.9 42.5 1.0 CZ A:ARG298 5.0 9.9 1.0 CG A:HIS227 5.0 20.5 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid


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 Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg420 b:15.4 occ:1.00 OE2 B:GLU251 2.0 14.9 1.0 OE1 B:GLU277 2.0 13.0 1.0 OD2 B:ASP225 2.1 16.0 1.0 O B:HOH622 2.1 14.1 1.0 O11 B:GCO422 2.3 23.3 1.0 O2 B:GCO422 2.3 18.3 1.0 C2 B:GCO422 2.9 57.0 1.0 CD B:GLU277 3.0 12.4 1.0 C1 B:GCO422 3.0 53.0 1.0 CD B:GLU251 3.0 15.6 1.0 CG B:ASP225 3.1 18.9 1.0 OE2 B:GLU277 3.3 17.2 1.0 OD1 B:ASP225 3.4 16.4 1.0 OE1 B:GLU251 3.7 17.2 1.0 NH2 B:ARG298 3.8 11.6 1.0 CG B:GLU251 3.9 14.0 1.0 O B:HOH423 4.1 13.4 1.0 CD2 B:HIS227 4.2 26.2 1.0 O B:HOH424 4.2 16.9 1.0 O12 B:GCO422 4.2 16.9 1.0 CG B:GLU277 4.2 13.3 1.0 NH1 B:ARG154 4.3 26.0 1.0 OD2 B:ASP252 4.3 17.7 1.0 CB B:ASP225 4.4 16.6 1.0 C3 B:GCO422 4.4 45.2 1.0 NE2 B:HIS227 4.8 23.5 1.0 NE2 B:HIS327 4.8 19.0 1.0 CG B:ASP252 4.8 21.8 1.0 CZ B:ARG298 4.8 17.5 1.0 NE B:ARG298 4.9 13.0 1.0 CB B:GLU277 4.9 13.4 1.0 OH B:TYR160 4.9 35.7 1.0 O3 B:GCO422 5.0 37.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid


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 Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg420 b:12.2 occ:1.00 OE2 C:GLU251 2.0 11.5 1.0 OD2 C:ASP225 2.1 9.7 1.0 O C:HOH520 2.1 10.2 1.0 OE1 C:GLU277 2.2 12.3 1.0 O11 C:GCO424 2.2 12.9 1.0 O2 C:GCO424 2.3 11.9 1.0 C2 C:GCO424 2.9 48.9 1.0 C1 C:GCO424 2.9 32.0 1.0 CD C:GLU251 3.0 12.9 1.0 CD C:GLU277 3.0 15.0 1.0 CG C:ASP225 3.0 12.6 1.0 OE2 C:GLU277 3.3 14.1 1.0 OD1 C:ASP225 3.4 10.2 1.0 OE1 C:GLU251 3.7 16.0 1.0 NH2 C:ARG298 3.9 11.3 1.0 CG C:GLU251 3.9 10.6 1.0 CD2 C:HIS227 4.0 17.0 1.0 O C:HOH431 4.1 9.5 1.0 O C:HOH430 4.1 13.7 1.0 O12 C:GCO424 4.1 15.2 1.0 OD2 C:ASP252 4.2 14.6 1.0 NH1 C:ARG154 4.3 14.0 1.0 CG C:GLU277 4.3 10.4 1.0 CB C:ASP225 4.4 11.7 1.0 C3 C:GCO424 4.4 34.5 1.0 OH C:TYR160 4.6 20.3 1.0 NE2 C:HIS227 4.6 14.2 1.0 NE2 C:HIS327 4.7 12.0 1.0 CG C:ASP252 4.8 15.6 1.0 O3 C:GCO424 4.9 28.9 1.0 CZ C:ARG298 4.9 15.2 1.0 NE C:ARG298 5.0 15.7 1.0 CG C:HIS227 5.0 13.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid


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 Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg420 b:14.2 occ:1.00 OE2 D:GLU251 2.0 15.6 1.0 O D:HOH618 2.1 10.6 1.0 OD2 D:ASP225 2.1 13.4 1.0 OE1 D:GLU277 2.1 12.3 1.0 O2 D:GCO422 2.2 15.4 1.0 O11 D:GCO422 2.2 16.6 1.0 C2 D:GCO422 2.9 56.4 1.0 C1 D:GCO422 2.9 42.5 1.0 CD D:GLU277 3.0 14.1 1.0 CD D:GLU251 3.1 19.5 1.0 CG D:ASP225 3.1 12.9 1.0 OE2 D:GLU277 3.3 16.1 1.0 OD1 D:ASP225 3.4 12.3 1.0 OE1 D:GLU251 3.8 15.4 1.0 NH2 D:ARG298 3.9 10.4 1.0 CG D:GLU251 4.0 8.6 1.0 CD2 D:HIS227 4.0 15.8 1.0 O D:HOH519 4.1 12.2 1.0 O D:HOH627 4.1 14.1 1.0 O12 D:GCO422 4.2 22.7 1.0 NH1 D:ARG154 4.2 19.0 1.0 OD2 D:ASP252 4.3 18.5 1.0 CG D:GLU277 4.4 9.1 1.0 C3 D:GCO422 4.4 49.0 1.0 CB D:ASP225 4.4 11.1 1.0 OH D:TYR160 4.6 26.7 1.0 NE2 D:HIS227 4.7 21.5 1.0 NE2 D:HIS327 4.8 16.5 1.0 CG D:ASP252 4.8 18.7 1.0 CZ D:ARG298 4.9 10.6 1.0 NE D:ARG298 4.9 17.4 1.0 O3 D:GCO422 5.0 41.1 1.0 CD2 D:HIS327 5.0 7.9 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid


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 Gluconate Dehydratase (Target Efi-501679) From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Str. P125109 Complexed with Magnesium and Gluconic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg420 b:24.2 occ:1.00 OE2 E:GLU251 2.0 25.8 1.0 O E:HOH761 2.1 21.2 1.0 OD2 E:ASP225 2.2 21.4 1.0 O11 E:GCO422 2.2 25.2 1.0 OE1 E:GLU277 2.2 23.4 1.0 O2 E:GCO422 2.3 31.8 1.0 C1 E:GCO422 2.8 56.1 1.0 C2 E:GCO422 2.9 69.6 1.0 CD E:GLU277 3.0 35.5 1.0 CD E:GLU251 3.1 38.6 1.0 CG E:ASP225 3.1 38.2 1.0 OE2 E:GLU277 3.2 19.5 1.0 OD1 E:ASP225 3.4 21.8 1.0 NH2 E:ARG298 3.8 19.9 1.0 OE1 E:GLU251 3.9 22.9 1.0 CG E:GLU251 4.0 23.3 1.0 CD2 E:HIS227 4.0 28.1 1.0 O12 E:GCO422 4.0 36.0 1.0 O E:HOH423 4.1 21.8 1.0 O E:HOH754 4.2 21.0 1.0 OD2 E:ASP252 4.2 28.8 1.0 NH1 E:ARG154 4.3 29.3 1.0 CG E:GLU277 4.3 24.3 1.0 C3 E:GCO422 4.4 56.8 1.0 CB E:ASP225 4.4 24.6 1.0 NE2 E:HIS227 4.6 37.5 1.0 NE2 E:HIS327 4.7 30.3 1.0 CG E:ASP252 4.8 27.3 1.0 OH E:TYR160 4.8 39.8 1.0 CZ E:ARG298 4.8 17.8 1.0 O3 E:GCO422 4.9 58.1 1.0 NE E:ARG298 4.9 26.9 1.0 CD2 E:HIS327 5.0 17.4 1.0

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo. Crystal Structure of Gluconate Dehydratase From Salmonella Enterica P125109 To Be Published.