Magnesium in PDB 4ibo: Crystal Structure of A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446)

The structure of Crystal Structure of A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446), PDB code: 4ibo was solved by M.W.Vetting, J.T.Bouvier, F.Groninger-Poe, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative(Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.29 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.783, 135.783, 126.165, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / 18.7

The structure of Crystal Structure of A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446) (pdb code 4ibo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446), PDB code: 4ibo:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446)


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 A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:23.5 occ:1.00 O A:HOH533 2.1 14.8 1.0 O A:HOH534 2.1 18.0 1.0 OD2 A:ASP88 2.1 22.1 1.0 CG A:ASP88 3.1 24.6 1.0 CB A:ASP88 3.5 15.8 1.0 O A:HOH418 3.9 27.4 1.0 OH A:TYR139 4.0 28.1 1.0 OD1 A:ASP90 4.1 20.4 1.0 OD2 A:ASP90 4.1 18.2 1.0 OD1 A:ASP88 4.3 21.7 1.0 O A:HOH417 4.3 25.5 1.0 CG A:ASP90 4.6 21.0 1.0 CA A:ASP88 4.9 16.5 1.0 CD A:ARG137 4.9 19.6 1.0 O A:GLY11 5.0 27.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446)


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 A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:56.0 occ:1.00 O C:HOH560 2.1 59.0 1.0 O C:HOH561 2.1 52.0 1.0 O C:HOH559 2.1 44.1 1.0 O C:HOH524 2.1 34.6 1.0 O C:HOH521 2.1 39.7 1.0 O C:HOH468 4.0 30.2 1.0 ND1 C:HIS60 4.1 23.4 1.0 O C:ALA32 4.1 19.4 1.0 O C:GLY59 4.1 24.3 1.0 O C:HOH562 4.3 39.3 1.0 CA C:HIS60 4.6 22.1 1.0 C C:GLY59 4.7 22.5 1.0 CE1 C:HIS60 4.7 21.1 1.0 CA C:GLY35 4.9 14.0 1.0 N C:HIS60 5.0 17.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446)


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 A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:47.7 occ:1.00 O D:GLY11 2.0 37.7 1.0 O D:HOH527 2.1 40.0 1.0 O D:HOH526 2.1 48.8 1.0 O D:HOH430 2.1 34.2 1.0 C D:GLY11 3.1 32.4 1.0 CA D:GLY11 3.7 30.5 1.0 O D:HOH453 4.0 45.4 1.0 N D:ARG12 4.2 29.9 1.0 OD2 D:ASP90 4.3 36.0 1.0 O D:HOH420 4.3 32.5 1.0 O D:HOH417 4.5 36.4 1.0 CA D:ARG12 4.5 24.6 1.0 O D:HOH402 4.6 19.5 1.0 OG1 D:THR13 4.9 31.2 1.0 C D:ARG12 5.0 30.3 1.0

M.W.Vetting, J.T.Bouvier, F.Groninger-Poe, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of A Putative Gluconate Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506446) To Be Published.