Magnesium in PDB 2hmc: The Crystal Structure of Dihydrodipicolinate Synthase Dapa From Agrobacterium Tumefaciens

The structure of The Crystal Structure of Dihydrodipicolinate Synthase Dapa From Agrobacterium Tumefaciens, PDB code: 2hmc was solved by Y.Kim, R.Zhang, X.Xu, H.Zheng, A.Savchenko, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.92 / 1.90
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.102, 101.102, 120.914, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 24.7

The binding sites of Magnesium atom in the The Crystal Structure of Dihydrodipicolinate Synthase Dapa From Agrobacterium Tumefaciens (pdb code 2hmc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of Dihydrodipicolinate Synthase Dapa From Agrobacterium Tumefaciens, PDB code: 2hmc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Crystal Structure of Dihydrodipicolinate Synthase Dapa From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Dihydrodipicolinate Synthase Dapa From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:38.3 occ:1.00 O A:HOH869 2.2 39.9 1.0 OD1 A:ASP184 2.4 39.1 1.0 O A:THR180 2.4 26.7 1.0 O A:HOH536 2.5 29.5 1.0 O A:VAL186 2.5 30.1 1.0 O A:ARG182 2.6 35.4 1.0 C A:THR180 3.2 27.5 1.0 CG A:ASP184 3.5 38.0 1.0 C A:VAL186 3.6 30.1 1.0 C A:ARG182 3.7 34.1 1.0 N A:ARG182 3.7 30.8 1.0 N A:VAL186 3.9 32.0 1.0 N A:SER181 3.9 27.9 1.0 N A:ASP184 4.0 37.8 1.0 CA A:VAL186 4.0 30.1 1.0 C A:SER181 4.0 29.3 1.0 OD2 A:ASP184 4.0 40.0 1.0 O A:HOH643 4.0 33.7 1.0 CA A:THR180 4.0 27.7 1.0 CB A:VAL186 4.0 29.5 1.0 O A:ASP184 4.1 37.0 1.0 CA A:SER181 4.1 27.9 1.0 O A:HOH883 4.2 66.2 1.0 CA A:ARG182 4.2 32.5 1.0 C A:ASP184 4.3 36.7 1.0 CA A:ASP184 4.5 37.2 1.0 O A:HOH881 4.5 78.3 1.0 CB A:ARG182 4.6 32.1 1.0 CB A:ASP184 4.6 37.5 1.0 N A:THR187 4.7 29.2 1.0 CB A:THR180 4.8 27.6 1.0 N A:ASP183 4.8 36.7 1.0 O A:SER181 4.8 28.8 1.0 CG1 A:VAL186 4.8 27.4 1.0 O A:ILE179 4.9 29.2 1.0 C A:GLU185 5.0 33.5 1.0

Magnesium binding site 2 out of 2 in the The Crystal Structure of Dihydrodipicolinate Synthase Dapa From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Dihydrodipicolinate Synthase Dapa From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:49.0 occ:1.00 O A:HOH873 2.1 42.5 1.0 O A:HOH603 2.2 36.6 1.0 O A:PRO105 2.8 27.5 1.0 O A:HOH568 3.0 29.2 1.0 N A:ALA80 3.3 29.0 1.0 O A:ALA80 3.4 31.9 1.0 C A:PRO105 3.6 28.1 1.0 CE1 A:HIS120 3.7 26.1 1.0 O A:ILE104 3.7 26.6 1.0 NE2 A:HIS120 3.8 30.6 1.0 CA A:GLY79 3.9 28.1 1.0 CA A:ARG106 4.0 28.2 1.0 C A:GLY79 4.1 28.9 1.0 CG2 A:ILE104 4.1 26.4 1.0 N A:ARG106 4.1 28.4 1.0 O A:THR78 4.1 28.5 1.0 C A:ALA80 4.1 31.0 1.0 CA A:ALA80 4.1 30.2 1.0 N A:VAL107 4.1 29.8 1.0 C A:ILE104 4.3 26.2 1.0 CG2 A:VAL107 4.3 30.7 1.0 CB A:ILE104 4.3 25.8 1.0 C A:ARG106 4.4 28.1 1.0 CB A:ALA80 4.5 30.6 1.0 O A:HOH879 4.7 55.7 1.0 CA A:PRO105 4.8 27.3 1.0 N A:PRO105 4.8 26.9 1.0 N A:GLY79 4.8 27.7 1.0 ND1 A:HIS120 4.8 28.8 1.0 C A:THR78 4.9 27.9 1.0 CG1 A:VAL107 4.9 31.0 1.0 CB A:ALA86 4.9 27.4 1.0 CA A:ILE104 5.0 26.1 1.0 CB A:VAL107 5.0 29.4 1.0

Y.Kim, R.Zhang, X.Xu, H.Zheng, A.Edwards, A.Savchenko, A.Joachimiak. The Crystal Structure of Dihydrodipicolinate Synthase Dapa From Agrobacterium Tumefaciens To Be Published 2006.