Magnesium in PDB 2qjm: Crystal Structure of the K271E Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate

The structure of Crystal Structure of the K271E Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate, PDB code: 2qjm was solved by A.A.Fedorov, E.V.Fedorov, J.F.Rakus, J.E.Vick, 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)	25.00 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	116.254, 165.312, 166.853, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.6

The binding sites of Magnesium atom in the Crystal Structure of the K271E Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate (pdb code 2qjm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the K271E Mutant of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and D-Mannonate, PDB code: 2qjm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the K271E 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 K271E 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:Mg1001 b:27.9 occ:1.00 OD2 A:ASP210 2.2 20.2 1.0 OE1 A:GLU236 2.2 22.6 1.0 OE1 A:GLU262 2.2 21.9 1.0 O A:HOH2150 2.3 16.9 1.0 O1B A:CS22001 2.4 24.1 1.0 O2 A:CS22001 2.4 26.2 1.0 CG A:ASP210 3.0 22.3 1.0 CD A:GLU236 3.1 23.9 1.0 CD A:GLU262 3.1 23.2 1.0 C1 A:CS22001 3.2 25.5 1.0 C2 A:CS22001 3.3 26.8 1.0 OD1 A:ASP210 3.3 21.3 1.0 OE2 A:GLU262 3.3 21.2 1.0 OE2 A:GLU236 3.7 18.7 1.0 NH2 A:ARG283 3.8 17.1 1.0 CG A:GLU236 3.9 19.5 1.0 O A:HOH2057 4.0 14.9 1.0 OD2 A:ASP237 4.1 22.3 1.0 O A:HOH2007 4.1 17.1 1.0 CD2 A:HIS212 4.2 29.9 1.0 CB A:ASP210 4.3 20.2 1.0 O1A A:CS22001 4.4 27.2 1.0 NE2 A:HIS212 4.4 28.8 1.0 CG A:GLU262 4.4 21.8 1.0 NH1 A:ARG147 4.5 30.4 1.0 C3 A:CS22001 4.6 26.6 1.0 CG A:ASP237 4.6 22.6 1.0 OH B:TYR75 4.6 26.2 1.0 CZ A:ARG283 4.8 20.3 1.0 NE A:ARG283 4.9 20.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the K271E 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 K271E 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:Mg1002 b:26.8 occ:1.00 OE1 B:GLU262 2.2 21.8 1.0 O B:HOH2162 2.2 22.6 1.0 OD2 B:ASP210 2.3 22.1 1.0 OE1 B:GLU236 2.3 19.7 1.0 O2 B:CS22002 2.4 24.8 1.0 O1B B:CS22002 2.5 28.0 1.0 CD B:GLU262 3.0 23.2 1.0 CG B:ASP210 3.1 23.3 1.0 CD B:GLU236 3.2 17.9 1.0 OE2 B:GLU262 3.3 21.8 1.0 C1 B:CS22002 3.3 27.4 1.0 OD1 B:ASP210 3.3 22.6 1.0 C2 B:CS22002 3.4 27.8 1.0 NH2 B:ARG283 3.9 16.9 1.0 OD2 B:ASP237 3.9 22.0 1.0 CG B:GLU236 4.0 17.8 1.0 OE2 B:GLU236 4.0 20.6 1.0 CD2 B:HIS212 4.0 28.0 1.0 O B:HOH2026 4.0 22.1 1.0 O B:HOH2028 4.1 18.9 1.0 CG B:GLU262 4.4 21.1 1.0 NE2 B:HIS212 4.4 29.2 1.0 CB B:ASP210 4.5 21.2 1.0 O1A B:CS22002 4.5 30.2 1.0 OH A:TYR75 4.6 27.7 1.0 CG B:ASP237 4.6 21.2 1.0 C3 B:CS22002 4.6 28.3 1.0 NH1 B:ARG147 4.8 27.4 1.0 CZ B:ARG283 4.9 18.6 1.0 NE B:ARG283 4.9 19.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the K271E 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 K271E 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:Mg1003 b:31.5 occ:1.00 OD2 C:ASP210 2.2 25.8 1.0 OE1 C:GLU236 2.2 23.6 1.0 OE1 C:GLU262 2.3 25.0 1.0 O C:HOH2146 2.3 27.9 1.0 O2 C:CS22003 2.5 36.5 1.0 O1B C:CS22003 2.5 33.3 1.0 CD C:GLU236 3.0 24.3 1.0 CG C:ASP210 3.0 23.8 1.0 CD C:GLU262 3.1 26.2 1.0 OD1 C:ASP210 3.2 22.7 1.0 C1 C:CS22003 3.3 36.3 1.0 OE2 C:GLU262 3.3 26.8 1.0 C2 C:CS22003 3.4 36.3 1.0 OD2 C:ASP237 3.7 22.6 1.0 OE2 C:GLU236 3.8 25.1 1.0 CG C:GLU236 3.8 23.7 1.0 NH2 C:ARG283 3.9 21.2 1.0 O C:HOH2004 3.9 18.7 1.0 CD2 C:HIS212 4.1 31.5 1.0 O C:HOH2006 4.2 21.4 1.0 CG C:ASP237 4.4 21.3 1.0 CG C:GLU262 4.4 25.1 1.0 CB C:ASP210 4.4 21.9 1.0 NE2 C:HIS212 4.5 34.1 1.0 O1A C:CS22003 4.5 36.4 1.0 OH D:TYR75 4.6 30.3 1.0 NH1 C:ARG147 4.6 33.4 1.0 C3 C:CS22003 4.6 36.2 1.0 CZ C:ARG283 4.9 25.2 1.0 NE C:ARG283 4.9 25.2 1.0 CB C:ASP237 4.9 18.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the K271E 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 K271E 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:Mg1004 b:33.6 occ:1.00 OD2 D:ASP210 2.2 25.9 1.0 O D:HOH2133 2.2 23.5 1.0 OE1 D:GLU262 2.3 27.1 1.0 OE1 D:GLU236 2.3 21.1 1.0 O2 D:CS22004 2.5 34.1 1.0 O1B D:CS22004 2.5 28.1 1.0 CG D:ASP210 3.0 25.8 1.0 CD D:GLU262 3.1 26.9 1.0 CD D:GLU236 3.1 22.9 1.0 OD1 D:ASP210 3.2 22.7 1.0 C1 D:CS22004 3.3 30.2 1.0 C2 D:CS22004 3.4 31.8 1.0 OE2 D:GLU262 3.4 26.7 1.0 OE2 D:GLU236 3.8 22.5 1.0 CG D:GLU236 3.9 22.1 1.0 NH2 D:ARG283 3.9 22.3 1.0 O D:HOH2007 3.9 24.8 1.0 OD2 D:ASP237 4.0 31.5 1.0 CD2 D:HIS212 4.1 34.4 1.0 O D:HOH2011 4.2 20.1 1.0 CG D:GLU262 4.4 25.3 1.0 CB D:ASP210 4.4 23.5 1.0 OH C:TYR75 4.4 33.4 1.0 CG D:ASP237 4.4 27.4 1.0 NE2 D:HIS212 4.5 35.5 1.0 O1A D:CS22004 4.5 30.1 1.0 C3 D:CS22004 4.6 32.5 1.0 NH1 D:ARG147 4.7 36.7 1.0 CZ D:ARG283 4.9 23.1 1.0 NE D:ARG283 4.9 22.1 1.0 CB D:ASP237 4.9 22.9 1.0 OD1 D:ASP237 4.9 28.7 1.0

J.F.Rakus, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, J.E.Vick, P.C.Babbitt, S.C.Almo, J.A.Gerlt. Evolution of Enzymatic Activities in the Enolase Superfamily: D-Mannonate Dehydratase From Novosphingobium Aromaticivorans. Biochemistry V. 46 12896 2007.
ISSN: ISSN 0006-2960
PubMed: 17944491
DOI: 10.1021/BI701703W