Magnesium in PDB 3qke: Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate, PDB code: 3qke 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)	41.22 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	195.536, 85.782, 195.143, 90.00, 110.33, 90.00
R / Rfree (%)	17.9 / 21.1

The binding sites of Magnesium atom in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate (pdb code 3qke). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate, PDB code: 3qke:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:21.7 occ:1.00 OD2 A:ASP213 2.1 19.2 1.0 O A:HOH2510 2.1 20.9 1.0 OE1 A:GLU265 2.1 17.8 1.0 OE1 A:GLU239 2.2 18.3 1.0 O11 A:GCO406 2.2 22.3 1.0 O2 A:GCO406 2.3 23.6 1.0 C1 A:GCO406 2.9 30.5 1.0 C2 A:GCO406 2.9 29.0 1.0 CD A:GLU265 3.0 21.0 1.0 CG A:ASP213 3.1 21.6 1.0 CD A:GLU239 3.2 20.9 1.0 OE2 A:GLU265 3.3 22.7 1.0 OD1 A:ASP213 3.5 18.4 1.0 NH2 A:ARG286 3.9 19.2 1.0 OE2 A:GLU239 3.9 21.1 1.0 CD2 A:HIS215 4.0 24.1 1.0 O A:HOH415 4.0 19.5 1.0 CG A:GLU239 4.0 18.1 1.0 O A:HOH412 4.2 18.8 1.0 OD2 A:ASP240 4.2 20.5 1.0 O12 A:GCO406 4.2 23.6 1.0 CG A:GLU265 4.3 19.4 1.0 CB A:ASP213 4.4 19.1 1.0 OH A:TYR161 4.4 27.4 1.0 NH1 A:ARG149 4.4 25.6 1.0 C3 A:GCO406 4.4 35.5 1.0 NE2 A:HIS215 4.4 22.1 1.0 OH B:TYR77 4.7 20.0 1.0 CG A:ASP240 4.7 17.2 1.0 CZ A:ARG286 4.9 22.3 1.0 O3 A:GCO406 4.9 40.5 1.0 NE A:ARG286 4.9 25.0 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg407 b:21.1 occ:1.00 OD2 B:ASP213 2.1 19.4 1.0 OE1 B:GLU239 2.1 17.8 1.0 O B:HOH2505 2.2 19.5 1.0 OE1 B:GLU265 2.2 19.0 1.0 O11 B:GCO406 2.2 23.0 1.0 O2 B:GCO406 2.2 22.7 1.0 C1 B:GCO406 2.9 29.4 1.0 C2 B:GCO406 2.9 30.3 1.0 CD B:GLU265 3.1 21.7 1.0 CG B:ASP213 3.1 18.0 1.0 CD B:GLU239 3.2 19.4 1.0 OE2 B:GLU265 3.3 23.9 1.0 OD1 B:ASP213 3.5 17.1 1.0 NH2 B:ARG286 3.8 18.8 1.0 OE2 B:GLU239 3.9 19.3 1.0 CD2 B:HIS215 3.9 21.1 1.0 O B:HOH409 3.9 21.4 1.0 CG B:GLU239 4.1 21.6 1.0 OD2 B:ASP240 4.2 18.9 1.0 O12 B:GCO406 4.2 22.8 1.0 OH B:TYR161 4.3 31.1 1.0 O B:HOH431 4.3 18.7 1.0 NE2 B:HIS215 4.3 26.4 1.0 CB B:ASP213 4.4 20.8 1.0 C3 B:GCO406 4.4 35.2 1.0 NH1 B:ARG149 4.4 26.6 1.0 CG B:GLU265 4.4 19.6 1.0 OH A:TYR77 4.7 21.6 1.0 O3 B:GCO406 4.8 38.4 1.0 CG B:ASP240 4.8 19.9 1.0 CZ B:ARG286 4.9 22.6 1.0 CZ B:TYR161 4.9 30.6 1.0 NE B:ARG286 5.0 22.5 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg407 b:23.3 occ:1.00 OE1 C:GLU239 2.1 22.7 1.0 OD2 C:ASP213 2.1 25.3 1.0 OE1 C:GLU265 2.2 21.1 1.0 O C:HOH2509 2.2 21.3 1.0 O11 C:GCO406 2.3 26.1 1.0 O2 C:GCO406 2.4 29.4 1.0 C1 C:GCO406 3.0 34.5 1.0 C2 C:GCO406 3.0 33.7 1.0 CD C:GLU265 3.0 21.8 1.0 CG C:ASP213 3.1 23.1 1.0 CD C:GLU239 3.2 23.1 1.0 OE2 C:GLU265 3.3 24.1 1.0 OD1 C:ASP213 3.6 23.9 1.0 NH2 C:ARG286 3.8 23.9 1.0 CD2 C:HIS215 3.9 21.5 1.0 OE2 C:GLU239 4.0 22.8 1.0 O C:HOH413 4.0 23.5 1.0 CG C:GLU239 4.1 20.0 1.0 OD2 C:ASP240 4.2 22.9 1.0 O C:HOH426 4.2 21.4 1.0 O12 C:GCO406 4.3 31.5 1.0 OH C:TYR161 4.3 35.1 1.0 NE2 C:HIS215 4.3 27.6 1.0 CB C:ASP213 4.4 23.5 1.0 CG C:GLU265 4.4 23.1 1.0 C3 C:GCO406 4.5 39.5 1.0 NH1 C:ARG149 4.5 30.8 1.0 CG C:ASP240 4.7 23.6 1.0 OH E:TYR77 4.7 23.7 1.0 CZ C:ARG286 4.8 26.6 1.0 NE C:ARG286 4.9 26.9 1.0 O3 C:GCO406 4.9 43.7 1.0 CB C:GLU265 5.0 23.4 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg407 b:24.6 occ:1.00 OD2 D:ASP213 2.2 20.9 1.0 O2 D:GCO406 2.2 25.9 1.0 OE1 D:GLU265 2.2 22.4 1.0 OE1 D:GLU239 2.2 24.8 1.0 O D:HOH2507 2.2 21.1 1.0 O11 D:GCO406 2.3 23.8 1.0 C2 D:GCO406 2.9 31.6 1.0 C1 D:GCO406 2.9 32.3 1.0 CD D:GLU265 3.0 21.5 1.0 CG D:ASP213 3.2 21.6 1.0 CD D:GLU239 3.2 27.2 1.0 OE2 D:GLU265 3.3 23.2 1.0 OD1 D:ASP213 3.6 20.5 1.0 NH2 D:ARG286 3.7 21.3 1.0 O D:HOH431 3.9 22.0 1.0 OE2 D:GLU239 3.9 24.1 1.0 CD2 D:HIS215 4.0 25.2 1.0 CG D:GLU239 4.1 21.7 1.0 OD2 D:ASP240 4.2 23.3 1.0 O12 D:GCO406 4.2 31.8 1.0 NE2 D:HIS215 4.3 25.8 1.0 C3 D:GCO406 4.3 36.1 1.0 O D:HOH409 4.3 19.9 1.0 CG D:GLU265 4.4 22.0 1.0 NH1 D:ARG149 4.4 29.2 1.0 CB D:ASP213 4.4 21.6 1.0 OH D:TYR161 4.4 31.9 1.0 OH H:TYR77 4.7 21.7 1.0 CZ D:ARG286 4.8 22.4 1.0 CG D:ASP240 4.8 23.5 1.0 O3 D:GCO406 4.8 42.1 1.0 NE D:ARG286 4.9 22.3 1.0 C4 D:GCO406 5.0 33.6 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate


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 D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg407 b:22.9 occ:1.00 OD2 E:ASP213 2.1 17.8 1.0 OE1 E:GLU239 2.1 20.4 1.0 OE1 E:GLU265 2.2 21.3 1.0 O E:HOH2511 2.2 20.1 1.0 O2 E:GCO406 2.3 23.0 1.0 O11 E:GCO406 2.3 24.7 1.0 C1 E:GCO406 3.0 33.8 1.0 C2 E:GCO406 3.0 32.1 1.0 CD E:GLU265 3.1 21.8 1.0 CG E:ASP213 3.1 20.8 1.0 CD E:GLU239 3.1 20.5 1.0 OE2 E:GLU265 3.3 23.9 1.0 OD1 E:ASP213 3.5 19.1 1.0 NH2 E:ARG286 3.8 21.6 1.0 OE2 E:GLU239 3.9 18.9 1.0 O E:HOH424 3.9 20.5 1.0 CD2 E:HIS215 4.0 23.1 1.0 CG E:GLU239 4.1 18.7 1.0 OD2 E:ASP240 4.2 21.9 1.0 O E:HOH408 4.2 19.9 1.0 O12 E:GCO406 4.3 27.2 1.0 CB E:ASP213 4.4 20.8 1.0 NE2 E:HIS215 4.4 22.7 1.0 CG E:GLU265 4.4 19.1 1.0 OH E:TYR161 4.4 31.6 1.0 C3 E:GCO406 4.4 35.8 1.0 NH1 E:ARG149 4.4 25.7 1.0 OH C:TYR77 4.7 23.0 1.0 CG E:ASP240 4.8 21.2 1.0 CZ E:ARG286 4.8 23.0 1.0 O3 E:GCO406 4.9 39.6 1.0 NE E:ARG286 4.9 23.7 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg407 b:21.6 occ:1.00 OD2 F:ASP213 2.0 18.6 1.0 OE1 F:GLU239 2.1 19.9 1.0 O F:HOH2506 2.2 19.9 1.0 OE1 F:GLU265 2.2 19.2 1.0 O2 F:GCO406 2.2 21.4 1.0 O11 F:GCO406 2.3 24.4 1.0 C2 F:GCO406 2.9 33.7 1.0 C1 F:GCO406 3.0 28.6 1.0 CG F:ASP213 3.0 20.9 1.0 CD F:GLU265 3.1 18.1 1.0 CD F:GLU239 3.1 19.1 1.0 OE2 F:GLU265 3.3 19.5 1.0 OD1 F:ASP213 3.5 18.8 1.0 NH2 F:ARG286 3.8 21.4 1.0 OE2 F:GLU239 3.8 19.3 1.0 O F:HOH418 3.9 19.9 1.0 CD2 F:HIS215 3.9 20.6 1.0 CG F:GLU239 4.0 21.0 1.0 OD2 F:ASP240 4.2 21.2 1.0 O F:HOH419 4.3 18.8 1.0 CB F:ASP213 4.3 19.2 1.0 O12 F:GCO406 4.3 27.1 1.0 CG F:GLU265 4.4 18.7 1.0 C3 F:GCO406 4.4 35.2 1.0 NE2 F:HIS215 4.4 22.6 1.0 NH1 F:ARG149 4.4 22.1 1.0 OH F:TYR161 4.4 29.9 1.0 CG F:ASP240 4.7 19.8 1.0 OH G:TYR77 4.8 18.7 1.0 CZ F:ARG286 4.8 22.0 1.0 O3 F:GCO406 4.9 40.0 1.0 NE F:ARG286 5.0 21.1 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg407 b:21.9 occ:1.00 OD2 G:ASP213 2.1 18.6 1.0 O G:HOH2508 2.1 21.0 1.0 OE1 G:GLU239 2.2 19.2 1.0 O11 G:GCO406 2.2 22.1 1.0 OE1 G:GLU265 2.2 18.9 1.0 O2 G:GCO406 2.3 23.5 1.0 C1 G:GCO406 2.9 29.6 1.0 C2 G:GCO406 2.9 30.0 1.0 CG G:ASP213 3.0 19.3 1.0 CD G:GLU265 3.1 22.8 1.0 CD G:GLU239 3.1 16.6 1.0 OE2 G:GLU265 3.4 22.6 1.0 OD1 G:ASP213 3.4 17.7 1.0 NH2 G:ARG286 3.8 19.3 1.0 OE2 G:GLU239 3.8 18.8 1.0 CD2 G:HIS215 3.9 23.1 1.0 O G:HOH419 4.0 19.3 1.0 CG G:GLU239 4.0 17.7 1.0 OD2 G:ASP240 4.1 20.4 1.0 O G:HOH435 4.2 19.4 1.0 O12 G:GCO406 4.2 23.2 1.0 OH G:TYR161 4.3 31.2 1.0 CB G:ASP213 4.3 19.8 1.0 NH1 G:ARG149 4.3 25.3 1.0 C3 G:GCO406 4.4 34.5 1.0 NE2 G:HIS215 4.4 24.7 1.0 CG G:GLU265 4.4 17.5 1.0 CG G:ASP240 4.7 18.4 1.0 OH F:TYR77 4.7 20.5 1.0 CZ G:ARG286 4.8 20.6 1.0 O3 G:GCO406 4.8 35.8 1.0 NE G:ARG286 4.9 22.7 1.0 CZ G:TYR161 5.0 29.8 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg407 b:19.7 occ:1.00 O H:HOH2512 2.1 19.5 1.0 OE1 H:GLU239 2.1 17.8 1.0 OD2 H:ASP213 2.1 19.0 1.0 OE1 H:GLU265 2.2 19.5 1.0 O11 H:GCO406 2.2 22.1 1.0 O2 H:GCO406 2.3 25.5 1.0 C1 H:GCO406 2.9 32.2 1.0 C2 H:GCO406 3.0 33.1 1.0 CD H:GLU265 3.1 22.5 1.0 CG H:ASP213 3.1 18.5 1.0 CD H:GLU239 3.1 19.1 1.0 OE2 H:GLU265 3.3 19.2 1.0 OD1 H:ASP213 3.4 18.1 1.0 OE2 H:GLU239 3.8 17.3 1.0 NH2 H:ARG286 3.8 20.6 1.0 O H:HOH463 3.9 20.2 1.0 CG H:GLU239 4.0 16.8 1.0 CD2 H:HIS215 4.0 20.5 1.0 OD2 H:ASP240 4.1 19.5 1.0 O12 H:GCO406 4.3 22.3 1.0 O H:HOH413 4.3 19.2 1.0 CB H:ASP213 4.4 18.9 1.0 NH1 H:ARG149 4.4 22.2 1.0 CG H:GLU265 4.4 19.2 1.0 C3 H:GCO406 4.5 36.0 1.0 OH H:TYR161 4.5 25.6 1.0 NE2 H:HIS215 4.5 22.9 1.0 CG H:ASP240 4.7 19.8 1.0 OH D:TYR77 4.7 20.1 1.0 CZ H:ARG286 4.9 20.4 1.0 NE H:ARG286 5.0 23.6 1.0 O3 H:GCO406 5.0 38.6 1.0

A.A.Fedorov, E.V.Fedorov, D.Wichelecki, J.A.Gerlt, S.C.Almo. Cystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate To Be Published.