Magnesium in PDB 4kem: Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site

The structure of Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site, PDB code: 4kem was solved by M.W.Vetting, D.Wichelecki, L.L.Morisco, S.R.Wasserman, S.Sojitra, M.Stead, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzymefunction Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.40 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.167, 82.925, 103.266, 90.00, 100.86, 90.00
R / Rfree (%)	16.4 / 18.6

The structure of Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site (pdb code 4kem). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site, PDB code: 4kem:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site


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 Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:9.9 occ:1.00 O A:HOH532 2.0 10.0 1.0 OE1 A:GLU264 2.0 10.9 1.0 O A:AKR405 2.1 13.9 1.0 OE2 A:GLU238 2.1 8.8 1.0 CB A:AKR405 2.1 10.3 1.0 OD2 A:ASP212 2.2 8.8 1.0 C A:AKR405 2.9 9.7 1.0 CA A:AKR405 2.9 20.5 1.0 CD A:GLU264 3.0 11.3 1.0 CG A:ASP212 3.1 7.2 1.0 OE2 A:GLU264 3.3 8.9 1.0 CD A:GLU238 3.3 6.9 1.0 OD1 A:ASP212 3.4 6.3 1.0 HZ2 A:LYS181 3.4 8.6 1.0 HZ1 A:LYS181 3.6 8.6 1.0 HD22 A:ASN214 3.7 16.5 1.0 HG2 A:GLU238 3.7 7.7 1.0 HZ2 A:LYS183 3.7 15.8 1.0 HD2 A:HIS321 3.8 9.3 1.0 HZ3 A:LYS183 3.8 15.8 1.0 O A:HOH536 3.8 10.6 1.0 NZ A:LYS181 3.9 7.2 1.0 HZ1 A:LYS183 3.9 15.8 1.0 NZ A:LYS183 4.0 13.2 1.0 CG A:GLU238 4.1 6.4 1.0 ND2 A:ASN214 4.1 13.7 1.0 HE3 A:LYS181 4.1 9.8 1.0 OE1 A:GLU238 4.1 7.4 1.0 OXT A:AKR405 4.2 16.3 1.0 O A:HOH510 4.2 8.1 1.0 CG A:GLU264 4.3 7.4 1.0 HD21 A:ASN214 4.4 16.5 1.0 CB A:ASP212 4.4 6.0 1.0 HG2 A:GLU264 4.4 8.8 1.0 HB2 A:ASP212 4.5 7.3 1.0 HB3 A:GLU264 4.5 8.0 1.0 HG3 A:GLU238 4.5 7.7 1.0 HA A:ASN214 4.6 9.3 1.0 CE A:LYS181 4.6 8.2 1.0 OE1 A:GLU239 4.6 11.6 1.0 HZ3 A:LYS181 4.6 8.6 1.0 HB2 A:GLU239 4.6 7.2 1.0 CD2 A:HIS321 4.6 7.7 1.0 CG A:ASN214 4.7 7.5 1.0 OD1 A:ASN214 4.8 7.6 1.0 HB3 A:ASP212 4.8 7.3 1.0 CB A:GLU264 4.9 6.7 1.0 HG3 A:GLU264 5.0 8.8 1.0 HZ2 B:LYS100 5.0 10.8 1.0 H A:ASN214 5.0 8.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site


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 Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:9.3 occ:1.00 O B:HOH519 2.1 9.2 1.0 OE1 B:GLU264 2.1 9.3 1.0 O B:AKR405 2.1 14.0 1.0 OE2 B:GLU238 2.1 8.3 1.0 CB B:AKR405 2.1 10.7 1.0 OD2 B:ASP212 2.1 8.0 1.0 C B:AKR405 2.9 16.2 1.0 CA B:AKR405 3.0 20.3 1.0 CD B:GLU264 3.0 9.1 1.0 CG B:ASP212 3.1 6.8 1.0 CD B:GLU238 3.2 6.5 1.0 OE2 B:GLU264 3.3 9.2 1.0 OD1 B:ASP212 3.4 6.2 1.0 HZ2 B:LYS181 3.4 8.3 1.0 HZ1 B:LYS181 3.6 8.3 1.0 HD22 B:ASN214 3.7 16.2 1.0 HG2 B:GLU238 3.7 8.8 1.0 HZ1 B:LYS183 3.7 13.9 1.0 HD2 B:HIS321 3.7 8.5 1.0 HZ3 B:LYS183 3.8 13.9 1.0 O B:HOH561 3.9 11.3 1.0 NZ B:LYS181 3.9 7.0 1.0 NZ B:LYS183 4.0 11.6 1.0 HE3 B:LYS181 4.1 9.3 1.0 CG B:GLU238 4.1 7.3 1.0 ND2 B:ASN214 4.1 13.5 1.0 OE1 B:GLU238 4.1 6.4 1.0 OXT B:AKR405 4.1 17.5 1.0 O B:HOH514 4.2 8.0 1.0 CG B:GLU264 4.3 7.9 1.0 HD21 B:ASN214 4.4 16.2 1.0 CB B:ASP212 4.4 5.1 1.0 HB2 B:ASP212 4.4 6.1 1.0 HG2 B:GLU264 4.5 9.4 1.0 HB3 B:GLU264 4.5 7.4 1.0 HG3 B:GLU238 4.5 8.8 1.0 CE B:LYS181 4.6 7.8 1.0 OE1 B:GLU239 4.6 10.3 1.0 CD2 B:HIS321 4.6 7.1 1.0 HA B:ASN214 4.6 7.8 1.0 HZ3 B:LYS181 4.6 8.3 1.0 HB2 B:GLU239 4.6 6.1 1.0 CG B:ASN214 4.7 6.6 1.0 OD1 B:ASN214 4.8 8.0 1.0 HB3 B:ASP212 4.8 6.1 1.0 HZ1 A:LYS100 5.0 10.6 1.0 CB B:GLU264 5.0 6.2 1.0 HG3 B:GLU264 5.0 9.4 1.0

M.W.Vetting, D.Wichelecki, L.L.Morisco, S.R.Wasserman, S.Sojitra, M.Stead, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site To Be Published.