Sodium 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:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 28 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 28 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 Sodium with other atoms in the Na 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:Na707 b:27.4 occ:1.00 OH A:TYR280 2.9 31.7 1.0 N A:ASP283 3.2 32.3 1.0 CD A:ARG96 3.6 29.3 1.0 CA A:PRO282 3.8 30.8 1.0 CZ A:TYR280 3.8 33.4 1.0 CE1 A:TYR280 3.8 29.5 1.0 CD1 A:LEU314 3.8 26.1 1.0 C A:PRO282 3.9 33.9 1.0 OD1 A:ASP283 4.0 46.6 1.0 CD A:PRO97 4.0 31.1 1.0 CA A:ASP283 4.0 32.4 1.0 CB A:ARG96 4.1 26.7 1.0 CB A:PRO282 4.3 33.5 1.0 CG A:ARG96 4.3 26.1 1.0 CG A:ASP283 4.3 49.2 1.0 NE A:ARG96 4.5 32.3 1.0 CG A:PRO97 4.6 34.9 1.0 OD2 A:ASP283 4.7 57.2 1.0 CB A:ASP283 4.8 35.4 1.0 N A:PRO97 4.8 29.4 1.0 CA A:ARG96 4.8 26.8 1.0 N A:PRO282 5.0 30.8 1.0

Sodium binding site 2 out of 28 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 Sodium with other atoms in the Na 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 A:Na708 b:55.1 occ:1.00 O A:ASP173 2.9 24.9 1.0 O A:HOH929 3.1 39.4 1.0 N A:PHE177 3.6 25.2 1.0 C A:ASP173 3.8 26.2 1.0 CB A:PHE177 3.8 25.7 1.0 CA A:PHE177 3.9 24.2 1.0 CA A:ASP173 3.9 24.1 1.0 CB A:MET176 4.0 25.7 1.0 CB A:ASP173 4.1 26.9 1.0 C A:MET176 4.2 27.2 1.0 NZ A:LYS244 4.4 64.4 1.0 OD1 A:ASP173 4.6 42.8 1.0 CA A:MET176 4.6 22.5 1.0 CG A:ASP173 4.7 40.5 1.0 OE1 A:GLU180 4.8 46.0 1.0 O A:MET176 4.9 25.8 1.0 CG A:PHE177 4.9 27.0 1.0 CD1 A:PHE177 4.9 29.2 1.0 CD A:LYS244 5.0 43.8 1.0

Sodium binding site 3 out of 28 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 Sodium with other atoms in the Na 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 A:Na709 b:51.3 occ:1.00 N A:TYR255 3.1 32.8 1.0 O A:HOH1057 3.3 34.3 1.0 CB A:THR254 3.6 41.3 1.0 CA A:THR254 3.7 35.0 1.0 CD2 A:TYR255 3.7 33.8 1.0 C A:THR254 3.9 36.3 1.0 CB A:TYR255 4.0 32.0 1.0 CA A:TYR255 4.1 31.0 1.0 CG2 A:THR254 4.3 39.7 1.0 CG A:TYR255 4.3 32.8 1.0 O A:HOH1101 4.5 51.6 1.0 CE2 A:TYR255 4.6 34.6 1.0 OG1 A:THR254 4.7 39.7 1.0 O A:HOH1134 4.9 60.7 1.0 N A:ASN256 5.0 31.3 1.0

Sodium binding site 4 out of 28 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 Sodium with other atoms in the Na 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 A:Na710 b:34.7 occ:1.00 O A:HOH1108 3.0 39.4 1.0 OG1 A:THR229 3.0 29.3 1.0 N A:ASN544 3.0 20.5 1.0 O A:GLN225 3.1 26.5 1.0 N A:THR545 3.2 24.5 1.0 O A:VAL542 3.2 24.6 1.0 CB A:TYR228 3.4 23.2 1.0 CA A:ASN544 3.4 20.6 1.0 OG1 A:THR545 3.5 27.0 1.0 N A:THR229 3.7 24.1 1.0 C A:ASN544 3.8 25.7 1.0 C A:GLN543 4.0 24.3 1.0 CB A:THR545 4.0 27.7 1.0 C A:TYR228 4.1 24.9 1.0 C A:GLN225 4.1 26.9 1.0 CG A:GLN225 4.1 24.8 1.0 OE1 A:GLU546 4.2 32.1 1.0 CB A:THR229 4.2 29.2 1.0 CA A:THR545 4.2 23.6 1.0 CA A:TYR228 4.2 21.9 1.0 C A:VAL542 4.2 24.8 1.0 CA A:THR229 4.3 23.7 1.0 CA A:GLN543 4.3 23.0 1.0 CG A:TYR228 4.5 22.6 1.0 N A:TYR228 4.6 23.1 1.0 N A:GLN543 4.7 23.0 1.0 CB A:GLN225 4.7 24.2 1.0 CB A:ASN544 4.8 23.2 1.0 O A:TYR228 4.8 23.6 1.0 CA A:GLN225 4.9 24.0 1.0 NE2 A:GLN225 4.9 28.8 1.0 N A:TYR226 4.9 24.1 1.0 N A:GLU546 5.0 25.7 1.0 CA A:TYR226 5.0 22.4 1.0 O A:GLN543 5.0 22.5 1.0

Sodium binding site 5 out of 28 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 Sodium with other atoms in the Na 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 A:Na711 b:33.1 occ:1.00 NZ B:LYS457 3.1 0.5 1.0 NE1 A:TRP179 3.2 28.7 1.0 NZ B:LYS469 3.4 0.1 1.0 N A:LEU206 3.5 28.1 1.0 CA A:THR205 3.5 29.5 1.0 CB A:THR205 3.6 38.7 1.0 CE B:LYS457 3.6 0.3 1.0 O A:LEU206 3.8 32.6 1.0 CG2 A:THR205 4.0 41.0 1.0 C A:THR205 4.0 32.1 1.0 CD1 A:TRP179 4.0 29.1 1.0 CE2 A:TRP179 4.2 29.8 1.0 O A:THR204 4.5 31.8 1.0 CZ2 A:TRP179 4.5 30.1 1.0 CA A:LEU206 4.5 27.7 1.0 C A:LEU206 4.5 32.7 1.0 CE B:LYS469 4.8 0.5 1.0 N A:THR205 4.8 29.4 1.0 CG2 A:VAL184 4.8 30.8 1.0 OG1 A:THR205 4.8 40.0 1.0

Sodium binding site 6 out of 28 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 Sodium with other atoms in the Na binding site number 6 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:Na712 b:63.4 occ:1.00 N A:ASP150 3.1 41.0 1.0 O A:HOH1064 3.2 45.6 1.0 N A:GLU149 3.4 42.5 1.0 CG A:ASP150 3.4 49.0 1.0 OD1 A:ASP150 3.6 45.9 1.0 OD2 A:ASP150 3.7 54.7 1.0 CB A:GLU149 3.7 46.6 1.0 CB A:SER148 3.7 40.2 1.0 CB A:ASP150 3.8 42.2 1.0 CA A:GLU149 3.8 43.2 1.0 C A:GLU149 3.9 44.9 1.0 CA A:ASP150 4.0 40.1 1.0 OG A:SER148 4.1 37.6 1.0 C A:SER148 4.1 42.8 1.0 NZ D:LYS414 4.2 0.4 1.0 CA A:SER148 4.4 37.8 1.0 CE D:LYS414 4.4 93.8 1.0 CD D:LYS414 4.7 78.0 1.0

Sodium binding site 7 out of 28 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 Sodium with other atoms in the Na binding site number 7 of Structure of the Periplasmic Binding Protein Melb (ATU4661) in Complex with Melibiose From Agrobacterium Fabrum C58 within 5.0Å range:

Sodium binding site 8 out of 28 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 Sodium with other atoms in the Na binding site number 8 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:Na706 b:30.0 occ:1.00 O1 D:PEG710 2.7 40.0 1.0 NE1 D:TRP48 3.2 26.6 1.0 O D:HOH1095 3.2 39.7 1.0 OD1 D:ASN308 3.3 32.4 1.0 CD1 D:TRP48 3.7 28.1 1.0 C1 D:PEG710 3.8 42.6 1.0 CB D:TYR85 3.9 25.3 1.0 CB D:PRO46 3.9 25.4 1.0 ND2 D:ASN308 4.1 24.2 1.0 CG D:ASN308 4.1 36.6 1.0 N D:GLY86 4.3 23.8 1.0 C D:TYR85 4.4 27.3 1.0 CE2 D:TRP48 4.4 27.0 1.0 CG D:PRO46 4.5 29.1 1.0 CA D:GLY86 4.5 24.2 1.0 O D:TYR85 4.7 26.6 1.0 O D:HOH850 4.7 37.6 1.0 O D:HOH873 4.7 26.5 1.0 CA D:PRO46 4.8 24.3 1.0 CA D:TYR85 4.8 24.3 1.0 O D:HOH1093 4.8 47.2 1.0 CG D:TYR85 4.9 25.2 1.0 C2 D:PEG710 4.9 43.6 1.0

Sodium binding site 9 out of 28 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 Sodium with other atoms in the Na binding site number 9 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:Na707 b:49.5 occ:1.00 O D:HOH1126 2.5 43.6 1.0 O D:HOH1106 2.8 46.1 1.0 OG D:SER343 3.0 29.9 1.0 N D:SER343 3.8 31.4 1.0 CG2 D:VAL325 3.8 32.1 1.0 CA D:SER343 3.8 30.6 1.0 CA D:VAL322 3.9 25.6 1.0 CB D:SER343 3.9 31.6 1.0 N D:VAL322 4.0 25.9 1.0 C D:ASP321 4.0 28.7 1.0 O D:ASP321 4.1 27.5 1.0 CG2 D:VAL322 4.1 29.7 1.0 C D:ALA342 4.2 37.6 1.0 CB D:ASP321 4.2 29.8 1.0 CB D:ALA342 4.3 35.7 1.0 O D:ASN339 4.4 29.5 1.0 O D:ALA342 4.5 37.0 1.0 CB D:VAL322 4.6 29.6 1.0 O D:HOH894 4.6 33.1 1.0 CA D:ASP321 4.8 27.4 1.0 CG1 D:VAL325 4.8 31.9 1.0 CA D:ALA342 4.9 34.6 1.0 CB D:VAL325 5.0 32.1 1.0

Sodium binding site 10 out of 28 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 Sodium with other atoms in the Na binding site number 10 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:Na708 b:35.8 occ:1.00 OD1 D:ASP87 2.7 25.4 1.0 OG1 D:THR88 3.0 31.7 1.0 N D:TYR659 3.0 20.5 1.0 O D:GLY657 3.1 25.5 1.0 O D:HOH895 3.2 32.3 1.0 N D:THR88 3.2 23.3 1.0 CA D:ASP87 3.3 22.4 1.0 C D:ASP87 3.5 25.6 1.0 CB D:THR88 3.5 28.3 1.0 C D:GLY657 3.6 26.9 1.0 CG D:ASP87 3.6 25.7 1.0 CA D:TYR659 3.6 19.9 1.0 CB D:TYR659 3.6 22.3 1.0 N D:GLU660 3.7 20.5 1.0 C D:TYR659 3.9 23.3 1.0 CD2 D:TYR659 4.0 24.4 1.0 CB D:ASP87 4.0 22.8 1.0 C D:LYS658 4.0 24.9 1.0 CA D:THR88 4.0 23.1 1.0 N D:LYS658 4.0 24.1 1.0 CA D:LYS658 4.1 23.1 1.0 CG D:TYR659 4.1 24.3 1.0 CG D:GLU660 4.2 28.0 1.0 N D:ASP87 4.3 22.6 1.0 CA D:GLY657 4.4 24.7 1.0 O D:ASP87 4.4 25.6 1.0 OD2 D:ASP87 4.6 27.6 1.0 CA D:GLU660 4.7 21.1 1.0 N D:GLY657 4.7 24.3 1.0 OE1 D:GLU660 4.8 37.0 1.0 CD D:GLU660 4.9 41.1 1.0 CB D:GLU660 4.9 22.4 1.0 O D:TYR659 4.9 21.5 1.0 O D:THR88 4.9 23.4 1.0 CG2 D:THR88 4.9 24.8 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