Magnesium in PDB 3sbf: Crystal Structure of the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate

The structure of Crystal Structure of the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate, PDB code: 3sbf was solved by A.A.Fedorov, E.V.Fedorov, D.Wichelecki, 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)	46.79 / 1.50
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	163.372, 163.372, 110.412, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.6

The binding sites of Magnesium atom in the Crystal Structure of the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate (pdb code 3sbf). 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 the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate, PDB code: 3sbf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate


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 the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:17.2 occ:1.00 OE2 A:GLU233 2.1 15.9 1.0 O A:HOH405 2.1 17.0 1.0 OE1 A:GLU259 2.1 17.3 1.0 OAJ A:D8T404 2.1 19.6 1.0 OD2 A:ASP207 2.2 17.4 1.0 OAK A:D8T404 2.2 18.7 1.0 CAD A:D8T404 3.0 21.3 1.0 CD A:GLU259 3.1 18.0 1.0 CD A:GLU233 3.1 18.1 1.0 CAE A:D8T404 3.1 20.4 1.0 CG A:ASP207 3.1 16.5 1.0 OE2 A:GLU259 3.4 19.9 1.0 OD1 A:ASP207 3.4 17.4 1.0 OE1 A:GLU233 3.8 18.6 1.0 CG A:GLU233 4.0 15.5 1.0 NH1 A:ARG280 4.0 17.1 1.0 O A:HOH1364 4.0 23.8 1.0 O A:HOH431 4.0 19.6 1.0 O A:HOH406 4.1 16.0 1.0 OAA A:D8T404 4.2 22.5 1.0 OAB A:D8T404 4.2 21.0 1.0 CAF A:D8T404 4.3 22.6 1.0 CG A:GLU259 4.3 16.9 1.0 CB A:ASP207 4.4 16.8 1.0 CD2 A:HIS209 4.4 23.3 1.0 OD2 A:ASP234 4.6 24.6 1.0 CD2 A:HIS309 4.6 20.0 1.0 O A:HOH534 4.7 27.2 1.0 NE2 A:HIS209 4.7 25.6 1.0 OH D:TYR81 4.8 23.4 1.0 CG A:ASP234 4.9 21.5 1.0 CAG A:D8T404 5.0 25.1 1.0 CZ A:ARG280 5.0 17.2 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate


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 the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:17.7 occ:1.00 OE2 B:GLU233 2.1 17.7 1.0 OD2 B:ASP207 2.1 16.9 1.0 OE1 B:GLU259 2.1 18.1 1.0 OAJ B:D8T404 2.1 19.1 1.0 O B:HOH405 2.1 17.6 1.0 OAK B:D8T404 2.2 22.3 1.0 CAD B:D8T404 2.9 26.3 1.0 CD B:GLU259 3.0 16.9 1.0 CAE B:D8T404 3.0 26.6 1.0 CD B:GLU233 3.1 18.7 1.0 CG B:ASP207 3.1 17.3 1.0 OE2 B:GLU259 3.3 19.4 1.0 OD1 B:ASP207 3.5 16.8 1.0 OE1 B:GLU233 3.8 18.7 1.0 NH1 B:ARG280 4.0 17.9 1.0 O B:HOH414 4.0 19.6 1.0 CG B:GLU233 4.0 18.0 1.0 O B:HOH423 4.1 18.3 1.0 OAA B:D8T404 4.1 28.9 1.0 OAB B:D8T404 4.2 26.1 1.0 CAF B:D8T404 4.2 26.9 1.0 CG B:GLU259 4.3 18.6 1.0 CD2 B:HIS209 4.4 27.0 1.0 OD2 B:ASP234 4.4 23.8 1.0 CB B:ASP207 4.4 18.9 1.0 CD2 B:HIS309 4.5 18.2 1.0 NH1 B:ARG153 4.6 33.1 1.0 NE2 B:HIS209 4.8 31.2 1.0 OH C:TYR81 4.8 27.4 1.0 NE2 B:HIS309 4.9 18.5 1.0 CG B:ASP234 4.9 19.8 1.0 CAG B:D8T404 4.9 30.1 1.0 CZ B:ARG280 5.0 17.7 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate


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 the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:24.9 occ:1.00 O B:HOH498 2.2 23.3 1.0 O B:HOH457 2.2 24.6 1.0 O B:HOH509 2.2 23.5 1.0 O B:HOH513 2.2 23.2 1.0 O B:HOH1426 2.2 24.4 1.0 O B:HOH1162 4.1 33.6 1.0 O B:HOH494 4.1 25.3 1.0 O B:HOH804 4.2 31.1 1.0 OD1 B:ASP139 4.2 28.1 1.0 OE2 B:GLU146 4.3 33.6 1.0 O B:HOH794 4.3 31.1 1.0 OE1 B:GLU146 4.5 28.6 1.0 O B:ASP139 4.5 21.4 1.0 CD B:GLU146 4.8 29.4 1.0 O B:HOH636 4.8 30.3 1.0 N B:GLY143 4.8 18.1 1.0 CA B:GLY143 4.9 19.9 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate


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 the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:17.7 occ:1.00 OE2 C:GLU233 2.1 17.4 1.0 OAJ C:D8T404 2.1 19.3 1.0 OE1 C:GLU259 2.2 16.7 1.0 OD2 C:ASP207 2.2 18.1 1.0 OAK C:D8T404 2.2 20.2 1.0 O C:HOH406 2.2 17.6 1.0 CAD C:D8T404 2.9 26.7 1.0 CAE C:D8T404 3.1 22.8 1.0 CD C:GLU233 3.1 16.8 1.0 CD C:GLU259 3.1 19.3 1.0 CG C:ASP207 3.2 17.6 1.0 OE2 C:GLU259 3.4 19.9 1.0 OD1 C:ASP207 3.5 16.5 1.0 OE1 C:GLU233 3.8 19.4 1.0 NH1 C:ARG280 3.9 17.6 1.0 O C:HOH438 4.0 19.1 1.0 CG C:GLU233 4.0 15.9 1.0 O C:HOH1407 4.1 30.6 1.0 OAA C:D8T404 4.1 25.3 1.0 OAB C:D8T404 4.1 22.0 1.0 O C:HOH415 4.1 17.9 1.0 CAF C:D8T404 4.2 24.1 1.0 OD2 C:ASP234 4.4 23.2 1.0 CD2 C:HIS209 4.4 21.3 1.0 CG C:GLU259 4.4 19.2 1.0 CB C:ASP207 4.4 18.2 1.0 CD2 C:HIS309 4.6 20.9 1.0 NE2 C:HIS209 4.7 25.7 1.0 OH B:TYR81 4.8 23.7 1.0 CG C:ASP234 4.9 22.3 1.0 CZ C:ARG280 5.0 17.5 1.0 NE2 C:HIS309 5.0 22.3 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate


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 the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:19.0 occ:1.00 OD2 D:ASP207 2.1 19.3 1.0 OE2 D:GLU233 2.1 19.3 1.0 OAJ D:D8T403 2.1 24.0 1.0 OAK D:D8T403 2.2 22.9 1.0 OE1 D:GLU259 2.2 20.9 1.0 O D:HOH404 2.2 18.3 1.0 CAD D:D8T403 2.9 32.4 1.0 CAE D:D8T403 3.0 28.6 1.0 CD D:GLU259 3.1 20.4 1.0 CD D:GLU233 3.1 20.1 1.0 CG D:ASP207 3.1 20.5 1.0 OE2 D:GLU259 3.3 22.0 1.0 OD1 D:ASP207 3.5 17.0 1.0 OE1 D:GLU233 3.8 20.2 1.0 CG D:GLU233 4.0 17.5 1.0 NH1 D:ARG280 4.1 16.6 1.0 OAA D:D8T403 4.2 36.1 1.0 O D:HOH427 4.2 20.9 1.0 CD2 D:HIS209 4.3 22.1 1.0 O D:HOH424 4.3 18.8 1.0 CAF D:D8T403 4.3 33.9 1.0 CB D:ASP207 4.4 17.3 1.0 CG D:GLU259 4.4 19.6 1.0 OAB D:D8T403 4.5 39.1 1.0 NH1 D:ARG153 4.5 36.8 1.0 CD2 D:HIS309 4.5 20.3 1.0 OD2 D:ASP234 4.5 25.0 1.0 NE2 D:HIS209 4.7 26.4 1.0 NE2 D:HIS309 4.8 22.1 1.0 OH A:TYR81 4.9 23.2 1.0 CAG D:D8T403 5.0 33.2 1.0 CG D:ASP234 5.0 20.2 1.0

A.A.Fedorov, E.V.Fedorov, D.Wichelecki, J.A.Gerlt, S.C.Almo. Crystal Structure of the Mutant P311A of Enolase Superfamily Member From Vibrionales Bacterium Complexed with Mg and D-Arabinonate To Be Published.