Magnesium in PDB 2qjj: Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans

The structure of Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans, PDB code: 2qjj 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)	23.16 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	117.465, 167.711, 166.441, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.2

The binding sites of Magnesium atom in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans (pdb code 2qjj). 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, PDB code: 2qjj:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:19.8 occ:1.00 OD2 A:ASP210 2.2 5.9 1.0 O A:HOH1219 2.3 8.9 1.0 OE1 A:GLU262 2.3 7.0 1.0 O A:HOH1220 2.3 13.4 1.0 OE1 A:GLU236 2.3 7.1 1.0 O A:HOH1221 2.4 19.3 1.0 CD A:GLU262 3.0 7.5 1.0 CG A:ASP210 3.2 8.2 1.0 OE2 A:GLU262 3.2 8.4 1.0 CD A:GLU236 3.3 9.3 1.0 OD1 A:ASP210 3.5 6.9 1.0 CD2 A:HIS212 3.9 18.4 1.0 NH2 A:ARG283 3.9 8.6 1.0 O A:HOH1020 3.9 6.9 1.0 OE2 A:GLU236 4.0 6.5 1.0 NE2 A:HIS212 4.1 19.5 1.0 OD2 A:ASP237 4.1 7.6 1.0 CG A:GLU236 4.2 7.2 1.0 O A:HOH1083 4.2 11.9 1.0 OH A:TYR159 4.3 23.6 1.0 O A:HOH1018 4.3 6.1 1.0 CG A:GLU262 4.4 6.8 1.0 CB A:ASP210 4.5 6.7 1.0 OH B:TYR75 4.5 8.3 1.0 NH1 A:ARG147 4.5 14.8 1.0 CG A:ASP237 4.8 7.1 1.0 CZ A:TYR159 4.8 22.5 1.0 CZ A:ARG283 4.9 10.3 1.0 CG A:HIS212 5.0 17.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:17.0 occ:1.00 OD2 B:ASP210 2.2 8.0 1.0 OE1 B:GLU262 2.2 6.6 1.0 O B:HOH1218 2.3 11.6 1.0 OE1 B:GLU236 2.3 9.8 1.0 O B:HOH1217 2.3 14.2 1.0 O B:HOH1219 2.4 14.7 1.0 CD B:GLU262 3.0 8.4 1.0 CG B:ASP210 3.2 9.3 1.0 OE2 B:GLU262 3.2 9.6 1.0 CD B:GLU236 3.2 10.0 1.0 OD1 B:ASP210 3.5 7.5 1.0 NH2 B:ARG283 3.9 8.5 1.0 CD2 B:HIS212 3.9 19.4 1.0 OE2 B:GLU236 3.9 8.7 1.0 O B:HOH1018 4.0 7.3 1.0 NE2 B:HIS212 4.1 19.6 1.0 OD2 B:ASP237 4.1 6.6 1.0 CG B:GLU236 4.2 7.2 1.0 OH B:TYR159 4.2 24.5 1.0 O B:HOH1015 4.2 6.3 1.0 O B:HOH1073 4.3 12.3 1.0 CG B:GLU262 4.4 7.2 1.0 CB B:ASP210 4.5 9.1 1.0 OH A:TYR75 4.6 10.4 1.0 NH1 B:ARG147 4.6 16.1 1.0 CZ B:TYR159 4.7 21.9 1.0 CG B:ASP237 4.7 6.4 1.0 CZ B:ARG283 4.9 7.7 1.0 CE2 B:TYR159 4.9 20.6 1.0 NE B:ARG283 5.0 9.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1003 b:16.6 occ:1.00 O C:HOH1213 2.2 10.5 1.0 OD2 C:ASP210 2.2 6.0 1.0 OE1 C:GLU262 2.2 6.6 1.0 OE1 C:GLU236 2.3 8.1 1.0 O C:HOH1214 2.3 11.2 1.0 O C:HOH1212 2.3 10.4 1.0 CD C:GLU262 3.0 8.1 1.0 CG C:ASP210 3.1 9.7 1.0 OE2 C:GLU262 3.2 10.1 1.0 CD C:GLU236 3.3 9.6 1.0 OD1 C:ASP210 3.4 8.2 1.0 OE2 C:GLU236 3.9 7.2 1.0 NH2 C:ARG283 4.0 8.3 1.0 O C:HOH1013 4.1 7.0 1.0 OD2 C:ASP237 4.1 6.2 1.0 NE2 C:HIS212 4.1 22.5 1.0 CG C:GLU236 4.1 8.2 1.0 CD2 C:HIS212 4.2 20.3 1.0 O C:HOH1017 4.3 5.8 1.0 CG C:GLU262 4.4 6.9 1.0 O C:HOH1044 4.4 8.8 1.0 NH1 C:ARG147 4.5 16.8 1.0 CB C:ASP210 4.5 7.8 1.0 OH D:TYR75 4.5 8.9 1.0 CG C:ASP237 4.7 8.3 1.0 CE1 C:HIS212 4.8 22.3 1.0 O C:HOH1206 4.9 23.6 1.0 CZ C:ARG283 5.0 9.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1004 b:20.7 occ:1.00 OD2 D:ASP210 2.2 5.7 1.0 OE1 D:GLU262 2.2 8.9 1.0 O D:HOH1212 2.2 8.3 1.0 O D:HOH1211 2.3 9.1 1.0 OE1 D:GLU236 2.3 6.0 1.0 O D:HOH1213 2.4 14.2 1.0 CD D:GLU262 3.0 10.4 1.0 CG D:ASP210 3.1 7.8 1.0 OE2 D:GLU262 3.2 10.9 1.0 CD D:GLU236 3.3 6.6 1.0 OD1 D:ASP210 3.4 7.5 1.0 NH2 D:ARG283 4.0 8.9 1.0 OE2 D:GLU236 4.0 5.3 1.0 O D:HOH1005 4.1 5.5 1.0 OD2 D:ASP237 4.1 6.2 1.0 O D:HOH1025 4.2 7.3 1.0 CG D:GLU236 4.2 6.1 1.0 CD2 D:HIS212 4.3 18.6 1.0 NE2 D:HIS212 4.3 22.8 1.0 O D:HOH1161 4.4 15.0 1.0 CG D:GLU262 4.4 7.0 1.0 OH C:TYR75 4.5 9.1 1.0 NH1 D:ARG147 4.5 15.2 1.0 CB D:ASP210 4.5 7.2 1.0 CG D:ASP237 4.7 6.4 1.0 CZ D:ARG283 5.0 10.4 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