Magnesium in PDB 6epz: Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58

The structure of Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58, PDB code: 6epz was solved by A.Vigouroux, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	351.610, 73.730, 107.580, 90.00, 105.38, 90.00
R / Rfree (%)	17.7 / 19.5

The structure of Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	28 atoms

The binding sites of Magnesium atom in the Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58 (pdb code 6epz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58, PDB code: 6epz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:28.7 occ:1.00 O A:HOH821 2.1 24.1 1.0 O A:HOH807 2.1 20.4 1.0 O A:HOH870 2.2 23.9 1.0 O A:HOH840 2.2 26.7 1.0 O A:HOH964 2.2 20.2 1.0 O A:ALA169 3.9 20.0 1.0 OG A:SER240 4.1 26.9 1.0 OD1 A:ASP174 4.2 24.6 1.0 OD2 A:ASP174 4.3 22.2 1.0 OD1 A:ASN171 4.3 23.7 1.0 OE2 A:GLU168 4.4 34.1 1.0 CB A:ASP173 4.5 26.9 1.0 CG A:GLU168 4.5 40.4 1.0 ND1 A:HIS241 4.5 24.2 1.0 CG A:ASP174 4.5 24.9 1.0 CB A:HIS241 4.6 22.0 1.0 OD2 A:ASP173 4.7 46.1 1.0 ND2 A:ASN171 4.7 24.8 1.0 CG A:ASN171 4.8 33.6 1.0 N A:HIS241 4.8 23.2 1.0 CG A:HIS241 4.9 23.3 1.0

Magnesium binding site 2 out of 5 in the Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:41.3 occ:1.00 O D:HOH957 1.9 33.0 1.0 O D:HOH1037 2.0 28.2 1.0 OE1 D:GLU168 2.0 47.0 1.0 O D:HOH891 2.1 25.3 1.0 O D:HOH830 2.2 25.9 1.0 O D:ALA169 2.3 26.1 1.0 CD D:GLU168 3.1 60.7 1.0 C D:ALA169 3.5 26.3 1.0 OE2 D:GLU168 3.6 52.0 1.0 OD2 D:ASP174 4.0 25.8 1.0 N D:ALA169 4.1 25.2 1.0 CA D:ALA169 4.2 24.3 1.0 ND1 D:HIS241 4.2 31.3 1.0 OD1 D:ASP174 4.3 24.5 1.0 CB D:ALA169 4.4 26.0 1.0 CG D:GLU168 4.4 41.1 1.0 NE1 D:TRP164 4.6 24.7 1.0 N D:PHE170 4.6 22.2 1.0 OD1 D:ASN171 4.6 25.8 1.0 CG D:ASP174 4.6 25.2 1.0 CD1 D:TRP164 4.6 24.9 1.0 C D:GLU168 4.6 29.7 1.0 ND2 D:ASN171 4.6 28.0 1.0 CB D:GLU168 4.7 27.7 1.0 CG D:ASN171 4.8 37.5 1.0 CG D:HIS241 4.8 30.0 1.0 CB D:HIS241 4.8 28.0 1.0 CA D:PHE170 4.8 20.4 1.0 CE1 D:HIS241 5.0 30.1 1.0 OG D:SER240 5.0 30.8 1.0

Magnesium binding site 3 out of 5 in the Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:30.0 occ:1.00 O C:ALA182 2.3 30.0 1.0 O C:VAL188 2.4 30.8 1.0 O C:HOH941 2.4 26.7 1.0 O C:ASP185 2.5 29.8 1.0 O C:VAL183 2.5 30.4 1.0 O C:HOH1125 3.1 38.8 1.0 C C:VAL183 3.2 29.9 1.0 C C:ALA182 3.4 29.9 1.0 C C:VAL188 3.5 30.2 1.0 C C:ASP185 3.5 30.7 1.0 CA C:VAL183 3.6 24.7 1.0 N C:VAL183 3.9 25.2 1.0 O C:HOH1003 4.2 36.0 1.0 N C:ASP185 4.2 28.6 1.0 N C:VAL188 4.3 26.6 1.0 CA C:VAL188 4.3 25.5 1.0 N C:VAL184 4.3 26.7 1.0 CA C:PRO186 4.3 27.2 1.0 N C:PRO186 4.4 28.5 1.0 C C:VAL184 4.4 31.1 1.0 CB C:VAL188 4.4 27.4 1.0 CA C:ASP185 4.4 28.6 1.0 O C:HOH1012 4.5 32.5 1.0 N C:SER189 4.5 24.4 1.0 CD C:PRO190 4.6 26.6 1.0 C C:PRO186 4.6 29.5 1.0 O C:ALA195 4.6 25.7 1.0 CA C:ALA182 4.6 25.4 1.0 O C:VAL184 4.6 29.8 1.0 CA C:SER189 4.7 24.6 1.0 CA C:VAL184 4.9 25.7 1.0 CB C:ASP185 4.9 29.1 1.0 O C:PRO186 4.9 28.0 1.0

Magnesium binding site 4 out of 5 in the Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:36.4 occ:1.00 O C:HOH984 1.9 34.8 1.0 O C:HOH1166 2.0 35.3 1.0 O C:HOH1075 2.1 36.3 1.0 O C:HOH982 2.1 34.9 1.0 O C:HOH928 2.3 30.4 1.0 O C:HOH901 2.3 30.2 1.0 O C:ALA169 4.2 27.2 1.0 OG C:SER240 4.2 30.1 1.0 CB C:HIS241 4.3 30.2 1.0 OD1 C:ASP174 4.4 29.7 1.0 ND1 C:HIS241 4.5 34.7 1.0 OD1 C:ASN171 4.5 29.4 1.0 OD2 C:ASP174 4.6 25.3 1.0 CB C:ASP173 4.7 29.4 1.0 N C:HIS241 4.7 27.7 1.0 ND2 C:ASN171 4.7 31.1 1.0 OD2 C:ASP173 4.7 48.2 1.0 CG C:HIS241 4.8 33.1 1.0 CG C:ASP174 4.8 27.9 1.0 CA C:HIS241 5.0 28.9 1.0 CG C:ASN171 5.0 39.0 1.0

Magnesium binding site 5 out of 5 in the Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:39.7 occ:1.00 O B:HOH1082 2.0 30.7 1.0 O B:HOH817 2.0 36.5 1.0 O B:HOH906 2.2 40.3 1.0 O B:HOH885 2.2 31.4 1.0 O B:HOH993 2.3 39.4 1.0 O B:HOH822 2.4 30.8 1.0 O B:ALA169 4.0 31.7 1.0 OG B:SER240 4.2 39.2 1.0 OD1 B:ASP174 4.4 29.7 1.0 CB B:HIS241 4.4 33.4 1.0 OD1 B:ASN171 4.4 35.9 1.0 OD2 B:ASP174 4.5 31.1 1.0 ND1 B:HIS241 4.5 35.4 1.0 CB B:ASP173 4.6 36.5 1.0 ND2 B:ASN171 4.7 36.6 1.0 OD2 B:ASP173 4.7 60.2 1.0 N B:HIS241 4.8 32.7 1.0 CG B:ASP174 4.8 32.3 1.0 CG B:HIS241 4.9 35.2 1.0 CG B:ASN171 4.9 44.8 1.0

T.Meyer, A.Vigouroux, M.Aumont-Nicaise, G.Comte, L.Vial, C.Lavire, S.Morera. The Plant Defense Signal Galactinol Is Specifically Used As A Nutrient By the Bacterial Pathogenagrobacterium Fabrum. J. Biol. Chem. V. 293 7930 2018.
ISSN: ESSN 1083-351X
PubMed: 29602905
DOI: 10.1074/JBC.RA118.001856