Magnesium in PDB 4k1w: Crystal Structure of the A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate

The structure of Crystal Structure of the A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate, PDB code: 4k1w 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)	46.21 / 1.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	116.223, 165.363, 167.197, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 18.4

The binding sites of Magnesium atom in the Crystal Structure of the A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate (pdb code 4k1w). 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 A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate, PDB code: 4k1w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate


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 A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:19.2 occ:1.00 O A:HOH848 2.0 19.3 1.0 O2 A:CS2502 2.0 25.4 1.0 OE1 A:GLU236 2.1 19.3 1.0 OD2 A:ASP210 2.1 16.4 1.0 OE1 A:GLU262 2.1 19.9 1.0 O1B A:CS2502 2.2 21.8 1.0 C1 A:CS2502 2.9 32.8 1.0 C2 A:CS2502 3.0 31.4 1.0 CD A:GLU262 3.0 21.4 1.0 CG A:ASP210 3.1 19.6 1.0 CD A:GLU236 3.2 17.7 1.0 OE2 A:GLU262 3.2 19.6 1.0 OD1 A:ASP210 3.5 16.1 1.0 NH2 A:ARG283 3.9 16.3 1.0 OE2 A:GLU236 3.9 15.8 1.0 CD2 A:HIS212 4.0 27.1 1.0 OD2 A:ASP237 4.0 19.5 1.0 O A:HOH634 4.1 19.1 1.0 CG A:GLU236 4.1 19.3 1.0 O1A A:CS2502 4.2 29.6 1.0 NE2 A:HIS212 4.2 34.8 1.0 C3 A:CS2502 4.2 34.2 1.0 O A:HOH617 4.3 16.4 1.0 CB A:ASP210 4.4 17.8 1.0 CG A:GLU262 4.4 15.1 1.0 OH B:TYR75 4.5 24.9 1.0 NH1 A:ARG147 4.5 29.2 1.0 CG A:ASP237 4.6 19.4 1.0 CD2 A:HIS312 4.8 21.0 1.0 CZ A:ARG283 4.9 16.4 1.0 C4 A:CS2502 5.0 35.8 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate


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 A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:18.0 occ:1.00 O B:HOH856 1.8 16.4 1.0 OE1 B:GLU236 2.0 16.6 1.0 OD2 B:ASP210 2.1 17.6 1.0 O1B B:CS2502 2.1 21.9 1.0 O2 B:CS2502 2.1 20.9 1.0 OE1 B:GLU262 2.1 19.5 1.0 C1 B:CS2502 2.9 29.5 1.0 C2 B:CS2502 3.0 24.5 1.0 CD B:GLU262 3.1 18.6 1.0 CG B:ASP210 3.1 17.1 1.0 CD B:GLU236 3.1 17.7 1.0 OE2 B:GLU262 3.3 19.8 1.0 OD1 B:ASP210 3.5 17.0 1.0 NH2 B:ARG283 3.8 16.9 1.0 OE2 B:GLU236 3.9 16.5 1.0 O B:HOH625 3.9 18.6 1.0 OD2 B:ASP237 4.0 18.5 1.0 CG B:GLU236 4.1 14.2 1.0 CD2 B:HIS212 4.1 30.5 1.0 O1A B:CS2502 4.1 28.3 1.0 O B:HOH629 4.2 17.1 1.0 C3 B:CS2502 4.2 28.0 1.0 NE2 B:HIS212 4.4 33.7 1.0 CB B:ASP210 4.4 19.0 1.0 CG B:GLU262 4.4 17.2 1.0 OH A:TYR75 4.5 26.3 1.0 NH1 B:ARG147 4.6 33.1 1.0 CG B:ASP237 4.7 19.5 1.0 CD2 B:HIS312 4.8 17.7 1.0 CZ B:ARG283 4.8 18.5 1.0 C4 B:CS2502 4.9 29.2 1.0 NE B:ARG283 4.9 16.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate


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 A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:16.9 occ:0.56 O B:HOH883 2.0 47.5 1.0 O B:HOH874 2.0 43.6 1.0 O B:HOH882 2.1 47.3 1.0 O D:HOH812 2.1 40.5 1.0 O B:GLN252 4.3 16.8 1.0 O D:GLN252 4.4 19.7 1.0 O B:HOH858 4.5 26.4 1.0 O D:HOH803 4.5 30.1 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate


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 A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:21.1 occ:1.00 O C:HOH812 2.0 19.9 1.0 OE1 C:GLU236 2.1 20.8 1.0 OD2 C:ASP210 2.1 23.3 1.0 O2 C:CS2502 2.1 27.3 1.0 OE1 C:GLU262 2.1 23.5 1.0 O1B C:CS2502 2.2 25.9 1.0 C1 C:CS2502 3.0 35.5 1.0 C2 C:CS2502 3.0 34.8 1.0 CD C:GLU262 3.0 24.8 1.0 CG C:ASP210 3.1 23.3 1.0 CD C:GLU236 3.1 23.4 1.0 OE2 C:GLU262 3.3 25.3 1.0 OD1 C:ASP210 3.4 22.3 1.0 NH2 C:ARG283 3.9 19.5 1.0 OE2 C:GLU236 3.9 23.0 1.0 CD2 C:HIS212 4.0 28.1 1.0 OD2 C:ASP237 4.0 24.0 1.0 O C:HOH613 4.0 20.7 1.0 CG C:GLU236 4.0 17.3 1.0 O1A C:CS2502 4.2 31.5 1.0 NE2 C:HIS212 4.2 35.5 1.0 C3 C:CS2502 4.2 38.2 1.0 O C:HOH604 4.3 21.4 1.0 CG C:GLU262 4.4 22.4 1.0 CB C:ASP210 4.4 19.6 1.0 OH D:TYR75 4.5 31.3 1.0 CG C:ASP237 4.6 21.7 1.0 NH1 C:ARG147 4.7 33.9 1.0 CZ C:ARG283 4.9 22.4 1.0 CD2 C:HIS312 4.9 27.7 1.0 NE C:ARG283 4.9 24.4 1.0 C4 C:CS2502 5.0 37.4 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate


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 A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:22.8 occ:1.00 O D:HOH801 2.0 21.8 1.0 OE1 D:GLU236 2.1 24.2 1.0 OD2 D:ASP210 2.1 23.4 1.0 O2 D:CS2502 2.1 25.8 1.0 OE1 D:GLU262 2.2 23.0 1.0 O1B D:CS2502 2.2 23.3 1.0 C1 D:CS2502 3.0 34.3 1.0 C2 D:CS2502 3.0 34.1 1.0 CG D:ASP210 3.0 23.6 1.0 CD D:GLU262 3.1 24.6 1.0 CD D:GLU236 3.2 22.3 1.0 OE2 D:GLU262 3.3 22.6 1.0 OD1 D:ASP210 3.4 21.7 1.0 NH2 D:ARG283 3.8 23.9 1.0 OE2 D:GLU236 3.9 22.6 1.0 O D:HOH621 4.0 19.1 1.0 CD2 D:HIS212 4.1 35.0 1.0 OD2 D:ASP237 4.1 23.6 1.0 CG D:GLU236 4.1 18.5 1.0 O1A D:CS2502 4.2 31.2 1.0 C3 D:CS2502 4.2 34.7 1.0 O D:HOH639 4.3 18.9 1.0 CB D:ASP210 4.3 20.4 1.0 NE2 D:HIS212 4.3 39.8 1.0 CG D:GLU262 4.5 20.2 1.0 OH C:TYR75 4.5 31.6 1.0 CG D:ASP237 4.7 27.4 1.0 NH1 D:ARG147 4.7 42.7 1.0 CZ D:ARG283 4.8 23.9 1.0 NE D:ARG283 4.9 22.1 1.0 CD2 D:HIS312 4.9 25.4 1.0 C4 D:CS2502 4.9 33.2 1.0

A.A.Fedorov, E.V.Fedorov, D.Wichelecki, J.A.Gerlt, S.C.Almo. Crystal Structure of the A314P Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate To Be Published.