Magnesium in PDB 2qjn: Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate

The structure of Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate, PDB code: 2qjn 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)	24.89 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	116.269, 165.241, 167.039, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.1

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

Magnesium binding site 1 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate


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 D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:28.9 occ:1.00 OD2 A:ASP210 2.2 19.5 1.0 OE1 A:GLU236 2.2 18.8 1.0 OE1 A:GLU262 2.3 23.5 1.0 O A:HOH2154 2.3 18.6 1.0 O5 A:KDG2001 2.5 33.3 1.0 O6A A:KDG2001 2.5 28.8 1.0 CD A:GLU262 3.1 21.3 1.0 CG A:ASP210 3.1 21.2 1.0 CD A:GLU236 3.2 22.0 1.0 C5 A:KDG2001 3.2 33.5 1.0 C6 A:KDG2001 3.2 32.4 1.0 OE2 A:GLU262 3.3 21.3 1.0 OD1 A:ASP210 3.4 17.9 1.0 NH2 A:ARG283 3.8 16.5 1.0 OE2 A:GLU236 3.9 16.7 1.0 O A:HOH2054 4.0 18.2 1.0 OD2 A:ASP237 4.0 20.1 1.0 CD2 A:HIS212 4.0 27.4 1.0 CG A:GLU236 4.0 20.3 1.0 O A:HOH2007 4.2 15.5 1.0 NE2 A:HIS212 4.3 28.2 1.0 CG A:GLU262 4.4 21.0 1.0 O6B A:KDG2001 4.4 31.9 1.0 CB A:ASP210 4.4 18.6 1.0 OH B:TYR75 4.5 20.5 1.0 NH1 A:ARG147 4.5 34.2 1.0 C4 A:KDG2001 4.6 33.8 1.0 CG A:ASP237 4.7 20.9 1.0 CZ A:ARG283 4.9 19.4 1.0 NE A:ARG283 5.0 18.5 1.0 CG A:HIS212 5.0 27.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate


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 D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:26.6 occ:1.00 O B:HOH2173 2.2 19.4 1.0 OE1 B:GLU262 2.2 21.8 1.0 OD2 B:ASP210 2.2 20.5 1.0 OE1 B:GLU236 2.3 21.0 1.0 O5 B:KDG2002 2.5 27.5 1.0 O6A B:KDG2002 2.5 26.8 1.0 CD B:GLU262 3.1 22.1 1.0 CG B:ASP210 3.1 21.3 1.0 C5 B:KDG2002 3.2 30.2 1.0 CD B:GLU236 3.2 22.2 1.0 C6 B:KDG2002 3.3 30.1 1.0 OE2 B:GLU262 3.3 22.7 1.0 OD1 B:ASP210 3.4 19.0 1.0 NH2 B:ARG283 3.9 17.0 1.0 OE2 B:GLU236 3.9 21.5 1.0 OD2 B:ASP237 4.0 24.3 1.0 CD2 B:HIS212 4.0 30.1 1.0 O B:HOH2028 4.0 19.1 1.0 CG B:GLU236 4.1 20.4 1.0 O B:HOH2026 4.1 18.0 1.0 NE2 B:HIS212 4.1 31.4 1.0 CG B:GLU262 4.4 19.9 1.0 O6B B:KDG2002 4.5 31.1 1.0 CB B:ASP210 4.5 20.0 1.0 OH A:TYR75 4.5 23.1 1.0 C4 B:KDG2002 4.6 30.5 1.0 CG B:ASP237 4.6 22.2 1.0 NH1 B:ARG147 4.8 34.0 1.0 CZ B:ARG283 4.9 17.9 1.0 NE B:ARG283 4.9 18.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate


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 D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1003 b:28.2 occ:1.00 OD2 C:ASP210 2.2 20.8 1.0 OE1 C:GLU236 2.3 21.6 1.0 OE1 C:GLU262 2.3 21.1 1.0 O C:HOH2157 2.3 23.0 1.0 O6A C:KDG2003 2.5 29.1 1.0 O5 C:KDG2003 2.5 31.7 1.0 CG C:ASP210 3.1 22.6 1.0 CD C:GLU262 3.1 22.9 1.0 C5 C:KDG2003 3.2 32.8 1.0 CD C:GLU236 3.2 22.8 1.0 C6 C:KDG2003 3.2 32.0 1.0 OE2 C:GLU262 3.3 22.2 1.0 OD1 C:ASP210 3.4 20.2 1.0 NH2 C:ARG283 3.9 18.2 1.0 OE2 C:GLU236 3.9 22.5 1.0 CG C:GLU236 4.0 21.6 1.0 OD2 C:ASP237 4.0 23.2 1.0 O C:HOH2007 4.1 20.2 1.0 CD2 C:HIS212 4.1 31.2 1.0 O C:HOH2005 4.2 19.6 1.0 NE2 C:HIS212 4.3 32.8 1.0 O6B C:KDG2003 4.4 33.7 1.0 CB C:ASP210 4.4 19.8 1.0 CG C:GLU262 4.4 20.1 1.0 OH D:TYR75 4.5 22.2 1.0 CG C:ASP237 4.6 22.5 1.0 NH1 C:ARG147 4.6 34.3 1.0 C4 C:KDG2003 4.6 33.0 1.0 CZ C:ARG283 4.9 20.4 1.0 NE C:ARG283 4.9 20.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate


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 D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1004 b:28.4 occ:1.00 OD2 D:ASP210 2.2 22.7 1.0 O D:HOH2139 2.2 18.8 1.0 OE1 D:GLU262 2.3 22.7 1.0 OE1 D:GLU236 2.3 20.9 1.0 O6A D:KDG2004 2.5 29.6 1.0 O5 D:KDG2004 2.5 32.6 1.0 CD D:GLU262 3.1 23.1 1.0 CG D:ASP210 3.1 23.3 1.0 CD D:GLU236 3.2 21.4 1.0 C5 D:KDG2004 3.2 33.9 1.0 C6 D:KDG2004 3.2 32.1 1.0 OE2 D:GLU262 3.3 22.2 1.0 OD1 D:ASP210 3.4 20.7 1.0 NH2 D:ARG283 3.8 19.9 1.0 OE2 D:GLU236 3.9 18.9 1.0 CG D:GLU236 4.0 20.3 1.0 O D:HOH2013 4.0 19.4 1.0 OD2 D:ASP237 4.1 25.6 1.0 O D:HOH2008 4.2 20.1 1.0 CD2 D:HIS212 4.3 32.7 1.0 NE2 D:HIS212 4.4 35.4 1.0 CG D:GLU262 4.4 20.4 1.0 CB D:ASP210 4.4 21.8 1.0 O6B D:KDG2004 4.4 32.0 1.0 OH C:TYR75 4.6 23.7 1.0 NH1 D:ARG147 4.6 33.2 1.0 C4 D:KDG2004 4.6 33.7 1.0 CG D:ASP237 4.7 24.1 1.0 CZ D:ARG283 4.8 21.5 1.0 NE D:ARG283 4.9 19.9 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