Magnesium in PDB 7v09: Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein

The structure of Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein, PDB code: 7v09 was solved by P.J.Stogios, T.Skarina, N.Mesa, R.Di Leo, A.Savchenko, A.Joachimiak, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.956, 67.618, 86.656, 90, 104.22, 90
R / Rfree (%)	25 / 29.6

The binding sites of Magnesium atom in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein (pdb code 7v09). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein, PDB code: 7v09:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein


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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:21.6 occ:1.00 O A:PHE284 2.1 28.6 1.0 O A:HOH791 2.3 28.0 1.0 OE2 A:GLU367 2.3 28.7 1.0 OE2 A:GLU164 2.4 36.0 1.0 OE1 A:GLU164 2.8 33.7 1.0 CD A:GLU164 2.9 30.3 1.0 C A:PHE284 3.3 26.8 1.0 CD A:GLU367 3.4 33.5 1.0 OE1 A:GLU367 3.9 33.0 1.0 N A:PHE284 4.0 26.9 1.0 CA A:PHE284 4.1 29.2 1.0 N A:VAL285 4.4 28.3 1.0 CG A:GLU164 4.4 31.2 1.0 CB A:PHE284 4.4 31.8 1.0 CA A:VAL285 4.6 26.2 1.0 CG A:GLU367 4.7 32.9 1.0 O A:HOH725 4.7 29.8 1.0 OH A:TYR152 4.8 29.1 1.0 CE1 A:TYR152 5.0 30.3 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein


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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:19.5 occ:1.00 O A:SER245 2.2 29.4 1.0 OE2 A:GLU250 2.3 34.5 1.0 OE1 B:GLU68 2.4 36.5 1.0 O B:HOH643 2.4 23.3 0.5 OE2 B:GLU68 2.4 35.2 1.0 O A:HOH726 2.5 30.2 1.0 CD B:GLU68 2.7 34.3 1.0 OE1 A:GLU250 2.7 27.1 1.0 CD A:GLU250 2.9 29.5 1.0 C A:SER245 3.3 27.9 1.0 O B:HOH643 3.6 26.1 0.5 N A:SER245 4.0 26.0 1.0 CA A:SER245 4.1 27.4 1.0 CG B:GLU68 4.2 34.2 1.0 N A:ASN246 4.3 28.1 1.0 OD2 A:ASP247 4.3 27.7 1.0 CG A:GLU250 4.4 26.9 1.0 CB A:SER245 4.4 26.0 1.0 CA A:ASN246 4.5 27.2 1.0 OD1 A:ASN246 4.7 28.8 1.0 O A:HOH849 4.9 33.8 1.0 OD2 B:ASP70 4.9 33.4 1.0 CB B:GLU68 4.9 30.6 1.0 N A:ASP247 4.9 27.0 1.0 C A:GLY244 5.0 29.3 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein


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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:30.5 occ:1.00 OE1 A:GLN307 2.3 31.9 1.0 OE2 A:GLU87 2.4 33.6 1.0 O A:HOH731 2.6 27.0 0.5 O A:HOH658 2.9 39.7 1.0 OE1 A:GLU311 2.9 34.7 1.0 OE2 A:GLU311 2.9 37.4 1.0 CD A:GLU311 3.1 35.7 1.0 O A:HOH664 3.1 36.2 1.0 CD A:GLN307 3.5 31.8 1.0 CD A:GLU87 3.6 31.1 1.0 O A:HOH731 3.9 27.6 0.5 NE2 A:GLN307 4.2 30.0 1.0 CG A:GLU311 4.4 33.2 1.0 CG A:GLU87 4.5 31.5 1.0 OE1 A:GLU87 4.5 27.9 1.0 O A:LEU85 4.6 28.3 1.0 CG A:GLN307 4.6 31.4 1.0 O A:HOH842 4.7 37.5 1.0 CB A:GLN307 4.7 33.1 1.0 CA A:GLN307 4.8 33.8 1.0 CB A:GLU311 4.9 34.6 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein


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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:28.2 occ:1.00 O B:HOH696 2.1 30.6 1.0 OE2 B:GLU250 2.4 39.3 1.0 OE1 A:GLU68 2.4 39.6 1.0 O A:HOH690 2.4 33.0 1.0 O B:SER245 2.5 33.3 1.0 OE1 B:GLU250 2.7 31.3 1.0 OE2 A:GLU68 2.8 40.3 1.0 CD B:GLU250 2.9 38.1 1.0 CD A:GLU68 2.9 32.7 1.0 C B:SER245 3.5 32.1 1.0 N B:SER245 4.2 33.4 1.0 N B:ASN246 4.4 32.2 1.0 CG B:GLU250 4.4 34.5 1.0 CA B:SER245 4.4 31.3 1.0 CA B:ASN246 4.4 33.7 1.0 O A:HOH728 4.4 36.7 1.0 CG A:GLU68 4.4 33.4 1.0 OD1 B:ASN246 4.5 35.0 1.0 O A:HOH806 4.6 32.4 1.0 OD2 B:ASP247 4.6 34.9 1.0 OD2 A:ASP70 4.8 35.5 1.0 CB B:SER245 4.9 30.9 1.0 C B:GLY244 5.0 32.8 1.0 N B:ASP247 5.0 32.1 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein


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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:37.2 occ:1.00 OE2 B:GLU164 2.0 52.2 1.0 O B:PHE284 2.0 49.1 1.0 O B:HOH632 2.1 43.5 1.0 OE2 B:GLU367 2.1 45.4 1.0 CD B:GLU164 2.8 52.7 1.0 OE1 B:GLU164 3.1 57.4 1.0 C B:PHE284 3.2 44.4 1.0 CD B:GLU367 3.3 40.6 1.0 OE1 B:GLU367 3.8 41.1 1.0 O B:HOH802 4.1 40.3 1.0 N B:VAL285 4.1 39.9 1.0 CA B:VAL285 4.1 42.8 1.0 CG B:GLU164 4.2 55.4 1.0 CA B:PHE284 4.2 44.7 1.0 N B:PHE284 4.3 46.3 1.0 O B:HOH688 4.3 37.7 1.0 CG B:GLU367 4.5 42.8 1.0 CB B:PHE284 4.6 40.1 1.0 CD2 B:PHE284 4.8 42.1 1.0 CB B:VAL285 4.9 48.7 1.0

P.J.Stogios, P.J.Stogios, T.Skarina, N.Mesa, R.Di Leo, A.Savchenko, A.Joachimiak, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). N/A N/A.