Sodium in PDB 7nox: Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide

Protein crystallography data

The structure of Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide, PDB code: 7nox was solved by V.C.Correia, F.Trovao, B.A.Pinheiro, A.S.Palma, A.L.Carvalho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.86 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.842, 88.437, 156.148, 90, 90, 90
R / Rfree (%) 16.2 / 19

Other elements in 7nox:

The structure of Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide (pdb code 7nox). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide, PDB code: 7nox:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7nox

Go back to Sodium Binding Sites List in 7nox
Sodium binding site 1 out of 3 in the Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na608

b:23.6
occ:1.00
OE1 A:GLN276 2.4 23.9 1.0
O A:HOH962 2.4 26.0 1.0
OG A:SER273 2.5 17.1 1.0
O A:HOH897 2.5 17.4 1.0
O A:HOH1044 2.7 22.3 1.0
O A:HOH1066 3.5 28.4 1.0
O A:HOH1114 3.6 33.6 1.0
CD A:GLN276 3.6 19.8 1.0
CB A:SER273 3.7 14.6 1.0
CA A:SER273 3.9 12.1 1.0
O A:GLY271 4.1 15.2 1.0
N A:SER273 4.2 12.8 1.0
O A:ASP268 4.3 18.2 1.0
CB A:GLN276 4.3 15.7 1.0
CD1 A:ILE257 4.4 32.1 1.0
C A:GLY271 4.4 15.6 1.0
NE2 A:GLN276 4.5 19.4 1.0
O A:ASN272 4.5 16.4 1.0
O A:GLY54 4.5 16.8 1.0
C A:ASN272 4.6 15.8 1.0
CG A:GLN276 4.6 15.0 1.0
CA A:GLY271 4.7 15.4 1.0
CD1 A:LEU56 4.9 19.8 1.0
N A:GLY271 4.9 17.0 1.0

Sodium binding site 2 out of 3 in 7nox

Go back to Sodium Binding Sites List in 7nox
Sodium binding site 2 out of 3 in the Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na609

b:28.3
occ:1.00
O A:HOH714 2.6 29.8 1.0
O A:HOH941 2.6 21.5 1.0
O A:HOH786 2.8 16.2 1.0
O A:HOH798 3.0 30.0 1.0
CB A:ALA246 3.6 20.8 1.0
N1 A:AZI612 3.7 41.8 1.0
CA A:ALA432 3.9 14.6 1.0
CB A:ALA432 4.0 15.1 1.0
O A:HOH1019 4.1 37.7 1.0
CB A:ASP435 4.2 17.6 1.0
O A:HOH739 4.3 19.5 1.0
O A:HOH1180 4.4 39.8 1.0
OD2 A:ASP435 4.4 23.4 1.0
N2 A:AZI612 4.5 33.1 1.0
O A:ALA432 4.5 15.2 1.0
O A:HOH1010 4.6 24.2 1.0
N A:ALA246 4.7 20.2 1.0
OD2 A:ASP439 4.7 21.8 1.0
C A:ALA432 4.8 13.9 1.0
CA A:ALA246 4.8 19.5 1.0
O A:HOH832 4.8 17.1 1.0
CG A:ASP435 4.8 23.0 1.0
OG A:SER400 4.9 18.1 1.0
N A:ALA432 5.0 14.5 1.0

Sodium binding site 3 out of 3 in 7nox

Go back to Sodium Binding Sites List in 7nox
Sodium binding site 3 out of 3 in the Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Sgbp BO2743 From Bacteroides Ovatus in Complex with Mixed-Linked Gluco-Nonasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na610

b:25.3
occ:1.00
O B:HOH964 2.3 26.6 1.0
O B:HOH990 2.4 23.9 1.0
OE1 B:GLN276 2.4 23.4 1.0
OG B:SER273 2.4 18.7 1.0
O B:HOH743 2.6 21.9 1.0
O B:HOH1050 3.5 28.2 1.0
O B:HOH1017 3.5 27.1 1.0
CB B:SER273 3.6 18.0 1.0
CD B:GLN276 3.6 20.2 1.0
O B:HOH1040 3.7 26.3 1.0
CA B:SER273 3.7 16.2 1.0
O B:GLY271 4.0 21.0 1.0
N B:SER273 4.1 15.9 1.0
O B:ASP268 4.2 22.3 1.0
CB B:GLN276 4.4 18.3 1.0
O B:GLY54 4.4 19.7 1.0
C B:GLY271 4.4 22.4 1.0
C B:ASN272 4.5 17.1 1.0
O B:ASN272 4.5 17.7 1.0
NE2 B:GLN276 4.5 23.3 1.0
CG B:GLN276 4.6 18.0 1.0
CD1 B:LEU56 4.7 20.7 1.0
CA B:GLY271 4.8 16.1 1.0
CB B:LEU56 4.9 23.2 1.0
O B:HOH907 5.0 20.4 1.0
O B:ALA265 5.0 26.4 1.0

Reference:

V.C.Correia, F.Trovao, B.A.Pinheiro, A.S.Palma, A.L.Carvalho. Mapping Molecular Recognition of Beta 1,3/1,4 Glucans By A Surface Glycan Binding Protein From the Human Gut Symbiont Bacteroides Ovatus To Be Published.
Page generated: Thu Nov 25 10:32:17 2021

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