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Sodium in PDB 6rgw: Photorhabdus Asymbiotica Lectin Phl in Complex with O-Methylated Pgl- 1-Derived Disaccharide

Protein crystallography data

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with O-Methylated Pgl- 1-Derived Disaccharide, PDB code: 6rgw was solved by J.Houser, E.Fujdiarova, G.Jancarikova, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.48 / 1.75
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.893, 80.893, 113.642, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21

Other elements in 6rgw:

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with O-Methylated Pgl- 1-Derived Disaccharide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin Phl in Complex with O-Methylated Pgl- 1-Derived Disaccharide (pdb code 6rgw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Photorhabdus Asymbiotica Lectin Phl in Complex with O-Methylated Pgl- 1-Derived Disaccharide, PDB code: 6rgw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6rgw

Go back to Sodium Binding Sites List in 6rgw
Sodium binding site 1 out of 2 in the Photorhabdus Asymbiotica Lectin Phl in Complex with O-Methylated Pgl- 1-Derived Disaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Photorhabdus Asymbiotica Lectin Phl in Complex with O-Methylated Pgl- 1-Derived Disaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:41.1
occ:1.00
O A:HOH734 2.5 45.5 1.0
OE2 A:GLU284 2.7 28.7 1.0
NE2 A:GLN347 3.1 29.5 1.0
O A:HOH605 3.1 32.4 1.0
NE1 A:TRP352 3.1 32.1 1.0
OE1 A:GLU284 3.2 30.1 1.0
CD A:GLU284 3.3 29.0 1.0
CE1 A:HIS296 3.6 33.1 1.0
CE2 A:TRP352 3.8 32.1 1.0
CZ2 A:TRP352 3.8 32.0 1.0
O A:HOH727 3.9 45.6 1.0
ND1 A:HIS296 3.9 31.4 1.0
O A:HOH603 4.0 46.8 1.0
CD A:GLN347 4.1 29.3 1.0
CG A:GLN347 4.2 29.2 1.0
CD1 A:TRP352 4.3 32.6 1.0
NE2 A:HIS296 4.8 31.9 1.0
CG A:GLU284 4.8 28.3 1.0
CE3 A:TRP298 4.9 33.4 1.0
CD2 A:TRP298 4.9 33.0 1.0

Sodium binding site 2 out of 2 in 6rgw

Go back to Sodium Binding Sites List in 6rgw
Sodium binding site 2 out of 2 in the Photorhabdus Asymbiotica Lectin Phl in Complex with O-Methylated Pgl- 1-Derived Disaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Photorhabdus Asymbiotica Lectin Phl in Complex with O-Methylated Pgl- 1-Derived Disaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:32.6
occ:1.00
O A:HOH713 2.3 36.9 1.0
OD1 A:ASN37 2.4 31.8 1.0
O A:THR38 2.5 25.9 1.0
O A:HOH732 2.5 38.4 1.0
CG A:ASN37 3.4 31.3 1.0
O A:ASN37 3.5 30.9 1.0
C A:THR38 3.6 26.3 1.0
C A:ASN37 3.8 30.0 1.0
CA A:GLY41 4.1 24.3 1.0
ND2 A:ASN37 4.1 31.7 1.0
N A:GLY41 4.2 23.9 1.0
N A:THR38 4.2 28.1 1.0
CB A:ASN37 4.2 29.8 1.0
N A:SER39 4.4 27.0 1.0
CA A:SER39 4.4 26.9 1.0
CA A:THR38 4.5 27.7 1.0
CA A:ASN37 4.6 29.6 1.0
O A:HOH766 4.6 46.9 1.0
C A:SER39 4.6 26.3 1.0
O A:HOH751 4.7 29.1 1.0
O A:HOH525 4.7 30.2 1.0
O A:SER39 4.8 26.2 1.0

Reference:

E.Fujdiarova, J.Houser, P.Dobes, G.Paulikova, N.Kondakov, L.Kononov, P.Hyrsl, M.Wimmerova. Heptabladed Beta-Propeller Lectins PLL2 and Phl From Photorhabdus Spp. Recognize O-Methylated Sugars and Influence the Host Immune System. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32559333
DOI: 10.1111/FEBS.15457
Page generated: Tue Dec 15 12:53:58 2020

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